COVID-19: A Collection of Articles

Collection

1. 1. Ecology
   2. Microbiology and Infectious Disease

   Variation in the ACE2 receptor has limited utility for SARS-CoV-2 host prediction

   Nardus Mollentze, Deborah Keen ... Daniel G Streicker

   The success of angiotensin-converting enzyme 2 (ACE2)-based predictions of severe acute respiratory syndrome-associated virus 2 (SARS-CoV-2) host range stems from phylogenetic correlation, allowing development of scalable models which predict susceptibility to SARS-CoV-2 and other sarbecoviruses without requiring additional ACE2 sequencing.
2. 1. Medicine

   Exploratory data on the clinical efficacy of monoclonal antibodies against SARS-CoV-2 Omicron variant of concern

   Fulvia Mazzaferri, Massimo Mirandola ... Evelina Tacconelli

   Compared with casirivimab/imdevimab and bamlanivimab/etesevimab, early treatment with sotrovimab seems to reduce the time to sustained recovery among adult outpatients with mild-to-moderate SARS-CoV-2 infection due to Omicron BA.1 and BA.1.1.
3. 1. Structural Biology and Molecular Biophysics

   Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simulations and crystallography

   Alberto Borsatto, Obaeda Akkad ... Francesco Luigi Gervasio

   A combination of simulations and experiments was used to discover druggable cryptic pockets in non-structural protein 1, a promising but difficult target for coronaviruses, indicating a viable drug discovery approach for otherwise undruggable targets.
4. 1. Immunology and Inflammation

   SARS-CoV-2-specific CD4⁺ and CD8⁺ T cell responses can originate from cross-reactive CMV-specific T cells

   Cilia R Pothast, Romy C Dijkland ... Mirjam HM Heemskerk
5. 1. Epidemiology and Global Health
   2. Immunology and Inflammation

   Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study

   James A Hay, Stephen M Kissler ... Yonatan H Grad

   Variation in SARS-CoV-2 viral kinetics are partly explained by an individual's immune state and the infecting variant, but substantial interpersonal variation limits the reliability of isolation policies tailored to an individual's vaccination status.
6. 1. Epidemiology and Global Health
   2. Evolutionary Biology

   Taxonium, a web-based tool for exploring large phylogenetic trees

   Theo Sanderson

   A new tool allows researchers to dive into phylogenetic trees containing millions of nodes using just their web browser.
7. 1. Microbiology and Infectious Disease

   Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats

   Kevin S Kuchinski, Kara D Loos ... Andrew DS Cameron

   Hybridization probe capture is useful for discovery and surveillance of novel coronaviruses, and its unique strengths complement existing methods like amplicon sequencing and deep metagenomic sequencing.
8. 1. Epidemiology and Global Health
   2. Immunology and Inflammation

   HIV skews the SARS-CoV-2 B cell response towards an extrafollicular maturation pathway

   Robert Krause, Jumari Snyman ... Alasdair Leslie

   A skewed B cell response in people living with HIV proceeds via an extrafollicular path and could result in reduced affinity B cell memory and antibody responses.
9. 1. Structural Biology and Molecular Biophysics

   Structure of SARS-CoV-2 M protein in lipid nanodiscs

   Kimberly A Dolan, Mandira Dutta ... Stephen G Brohawn

   A cryo-EM structure of the SARS-CoV-2 M protein, the most abundant protein in the viral envelope, provides insight into its essential role in virus assembly.
10. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study

    Oliver Stirrup, James Blackstone ... Judith Breuer

    Sequencing of viral genomes could be useful for infection prevention and control within hospitals, but did not lead to a reduction in the rate of hospital-acquired SARS-CoV-2 infections over winter 2020/2021 in a large multicentre UK study.
11. 1. Immunology and Inflammation
    2. Medicine

    Differences in the immune response elicited by two immunization schedules with an inactivated SARS-CoV-2 vaccine in a randomized phase 3 clinical trial

    Nicolás MS Gálvez, Gaspar A Pacheco ... Alexis M Kalergis

    The humoral and cellular immune responses were evaluated for two immunization schedules for the inactivated SARS-CoV-2 vaccine, CoronaVac, with two doses separated by 2 or 4 weeks, showing that these responses are mostly similar, with differences in neutralization capacities.
12. 1. Epidemiology and Global Health

    How should COVID-19 vaccines be distributed between the Global North and South: a discrete choice experiment in six European countries

    Janina I Steinert, Henrike Sternberg ... Tim Büthe

    In a large discrete choice experiment, respondents from six European countries reveal preferences for global vaccine solidarity, where female, younger, more educated respondents are most likely to prioritise candidates from the Global South in their allocation choices for COVID-19 vaccines.
13. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    COVID-19 cluster size and transmission rates in schools from crowdsourced case reports

    Paul Tupper, Shraddha Pai ... Caroline Colijn

    Fitting a simple model of COVID-19 transmission to crowdsourced case report data allowed the estimation of mean cluster size and transmission rates in Canadian schools, as well as determining which interventions are most likely to limit transmission.
14. 1. Epidemiology and Global Health

    Genetically predicted high IGF-1 levels showed protective effects on COVID-19 susceptibility and hospitalization: a Mendelian randomisation study with data from 60 studies across 25 countries

    Xinxuan Li, Yajing Zhou ... Xue Li

    Genetically predicted high insulin-like growth factor levels may decrease the risk of COVID-19 susceptibility and hospitalization.
15. 1. Immunology and Inflammation
    2. Medicine

    Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study

    Zicheng Hu, Kattria van der Ploeg ... Prasanna Jagannathan

    Immune markers measured at the early stage of COVID-19 infection are associated with various clinical outcomes and can be used to predict disease progression, T cell memory, viral shedding, and the antibody response of the COVID-19 patients.
16. 1. Computational and Systems Biology

    A model-based analysis of the health impacts of COVID-19 disruptions to primary cervical screening by time since last screen for current and future disruptions

    Emily A Burger, Inge MCM de Kok ... Megan A Smith

    Despite the overall impact of COVID-19-related cervical cancer screening disruptions on cervical cancer outcomes being small, disruptions disproportionately affect underscreened women, underpinning the importance of reaching such women as a critical area of focus, regardless of temporary disruptions.
17. 1. Epidemiology and Global Health

    SARS-CoV-2 antibody dynamics in blood donors and COVID-19 epidemiology in eight Brazilian state capitals: A serial cross-sectional study

    Carlos A Prete Jr, Lewis F Buss ... Ester C Sabino

    Blood donor serosurveillance in eight of Brazil’s most populous cities reveals extensive variation of SARS-CoV-2 attack rate across cities, age, and sex groups in December 2020 and increased intrinsic severity of the Gamma variant of concern.
18. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients

    Bronner P Gonçalves, Matthew Hall ... ISARIC Clinical Characterisation Group

    Combined analyses of publicly available population-level variant data and detailed individual-level clinical data can be used to quantify the clinical impact of new SARS-CoV-2 variants in different settings.
19. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Regional importation and asymmetric within-country spread of SARS-CoV-2 variants of concern in the Netherlands

    Alvin X Han, Eva Kozanli ... Chantal Reusken

    Flight restrictions targeted at countries where SARS-CoV-2 variant-of-concern first emerged have limited effectiveness in deterring their introduction into the Netherlands due to the strength of regional travel importation risks in Europe.
20. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2

    Jana S Huisman, Jérémie Scire ... Tanja Stadler

    A new and throughly validated method for timely estimation of the effective reproductive number of SARS-CoV-2 aided in the public health response to the COVID-19 pandemic.
21. 1. Computational and Systems Biology
    2. Epidemiology and Global Health

    The unmitigated profile of COVID-19 infectiousness

    Ron Sender, Yinon Bar-On ... Ron Milo

    In the absence of COVID-19 mitigation measures, SARS-CoV-2 remains infectious for longer than previously estimated.
22. 1. Epidemiology and Global Health

    Effects of side-effect risk framing strategies on COVID-19 vaccine intentions: a randomized controlled trial

    Nikkil Sudharsanan, Caterina Favaretti ... Alain Vandormael

    Small changes to the way COVID-19 vaccine side-effect rates are framed and communicated have meaningful impacts on individuals' vaccination intentions.
23. 1. Epidemiology and Global Health

    COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron)

    Wan Yang, Jeffrey L Shaman

    Model-inference reconstructed SARS-CoV-2 transmission dynamics in South Africa during March 2020 to February 2022, and quantified the immune erosion potential and transmissibility of three major variants (Beta, Delta, and Omicron), highlighting their common characteristics and the need for more proactive preparedness.
24. 1. Immunology and Inflammation

    Unsuppressed HIV infection impairs T cell responses to SARS-CoV-2 infection and abrogates T cell cross-recognition

    Thandeka Nkosi, Caroline Chasara ... Zaza M Ndhlovu

    Cross-reactive T cell immunity against the SARS-CoV-2 is severely compromised in HIV viremic individual.
25. 1. Epidemiology and Global Health
    2. Evolutionary Biology

    Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada

    Angela McLaughlin, Vincent Montoya ... Jeffrey B Joy

    Canadian COVID-19 travel restrictions imposed in March 2020 greatly reduced SARS-CoV-2 importations, but were insufficient to prevent new sublineages of similar transmissibility from being introduced and replacing early sublineages.
26. 1. Immunology and Inflammation
    2. Medicine

    Immune dynamics in SARS-CoV-2 experienced immunosuppressed rheumatoid arthritis or multiple sclerosis patients vaccinated with mRNA-1273

    Niels JM Verstegen, Ruth R Hagen ... Carolien E van de Sandt

    SARS-CoV-2 experienced ocrelizumab-treated MS patients benefit from SARS-CoV-2 mRNA vaccination by inducing broadprotective CD8+ T-cells, whereas methotrexate-treated RA patients induce delayed but strong antibody responses, which support vaccine strategies for these patient groups.
27. 1. Medicine
    2. Microbiology and Infectious Disease

    Reconstruction of transmission chains of SARS-CoV-2 amidst multiple outbreaks in a geriatric acute-care hospital: a combined retrospective epidemiological and genomic study

    Mohamed Abbas, Anne Cori ... Stephan Harbarth

    Nosocomial transmission of SARS-Cov-2 in geriatric settings is complex, with different patterns between patients and healthcare workers working in Covid/non-Covid wards that should be taken into account when designing infection control strategies.
28. 1. Microbiology and Infectious Disease

    Process- and product-related impurities in the ChAdOx1 nCov-19 vaccine

    Lea Krutzke, Reinhild Rösler ... Stefan Kochanek

    Analysis of protein content and protein composition of the ChAdOx1 nCov-19 vaccine, but not of the Ad26.COV2.S vaccine, indicated significantly higher than expected levels of host cell proteins (HCPs) and of free viral proteins.
29. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study

    Charles N Agoti, Lynette Isabella Ochola-Oyier ... George Githinji

    Genomic analysis of initial SARS-CoV-2 waves in Kenya revealed Mombasa City as a key gateway for variants entering Coastal Kenya with onward inter-county transmission highlighting significance of surveillance in major cities for early warning of lineages entering local populations.
30. 1. Immunology and Inflammation

    Modelling the response to vaccine in non-human primates to define SARS-CoV-2 mechanistic correlates of protection

    Marie Alexandre, Romain Marlin ... Rodolphe Thiébaut

    A model-based approach for modelling the immune control of viral dynamics is applied to quantify the effect of several SARS-CoV-2 vaccine platforms and to define mechanistic correlates of protection.
31. 1. Microbiology and Infectious Disease

    Host chitinase 3-like-1 is a universal therapeutic target for SARS-CoV-2 viral variants in COVID-19

    Suchitra Kamle, Bing Ma ... Jack A Elias

    Intervention of CHI3L1 using anti-CHI3L1 monoclonal antibody or chitinase inhibitor kasugamycin blocks epithelial infection of various SARS-CoV2 variants, suggesting that CHI3L1 is a universal and effective therapeutic target of COVID-19 infection, including recent omicron variants.
32. 1. Immunology and Inflammation

    Efferocytosis of SARS-CoV-2-infected dying cells impairs macrophage anti-inflammatory functions and clearance of apoptotic cells

    Ana CG Salina, Douglas dos-Santos ... Larissa D Cunha

    Internalization of apoptotic SARS-CoV-2 infected cells leads to proinflammatory macrophage activation and reduction in macrophage capacity to perform further efferocytosis.
33. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Controlling SARS-CoV-2 in schools using repetitive testing strategies

    Andrea Torneri, Lander Willem ... Pieter JK Libin

    In primary schools, where vaccination coverage can be low, a repetitive testing strategy reduces SARS-CoV-2 infections while keeping classes and schools open, as such limiting infection transmissions and absenteeism.
34. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    SARS-CoV-2 host-shutoff impacts innate NK cell functions, but antibody-dependent NK activity is strongly activated through non-spike antibodies

    Ceri Alan Fielding, Pragati Sabberwal ... Richard J Stanton

    SARS-CoV-2 host-shutoff inhibits innate NK surveillance by suppressing activating ligands, however ADCC provides a potent NK stimulus that is mediated by antibodies targeting Nucleocapsid, ORF3a, and Membrane, with those targeting Spike being significantly weaker.
35. 1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    Comprehensive fitness landscape of SARS-CoV-2 M^pro reveals insights into viral resistance mechanisms

    Julia M Flynn, Neha Samant ... Daniel NA Bolon

    Comprehensive mutational scanning of the SARS-CoV-2 protease, M^pro, provides functional and structural information to aid in the design of more effective inhibitors against the protease with reduced potential of evolving viral resistance.
36. 1. Epidemiology and Global Health

    Projected resurgence of COVID-19 in the United States in July—December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination

    Shaun Truelove, Claire P Smith ... Cecile Viboud

    Multi-model ensembling projected that the Delta variant would lead to a substantial COVID-19 resurgence in the US, with higher vaccination uptake being a critical factor for limiting transmission and impact between states.
37. 1. Epidemiology and Global Health

    Impact of the COVID-19 pandemic on breast cancer screening indicators in a Spanish population-based program: a cohort study

    Guillermo Bosch, Margarita Posso ... Francesc Macià

    The COVID-19 pandemic reduced participation in a Spanish population-based breast cancer screening program, especially among regular participants, while other outcomes like recall and cancer detection were not negatively affected by the interruption of screening.
38. 1. Epidemiology and Global Health
    2. Evolutionary Biology

    Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants

    François Blanquart, Nathanaël Hozé ... Simon Cauchemez

    Selection acting on SARS-CoV-2 variants altering the infectivity profile depends on levels of transmission in the community, and this dependence is used to infer Alpha and Delta variants infectivity profiles.
39. 1. Computational and Systems Biology
    2. Medicine

    Development and evaluation of a machine learning-based in-hospital COVID-19 disease outcome predictor (CODOP): A multicontinental retrospective study

    Riku Klén, Disha Purohit ... David Gómez-Varela

    The generalizability of CODOP in distinct world regions and its flexibility to reckon with the changing availability of hospital resources makes it a clinically useful tool potentially improving the outcome prediction and the management of COVID-19 hospitalized patients.
40. 1. Microbiology and Infectious Disease

    A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva

    Robert Warneford-Thomson, Parisha P Shah ... Roberto Bonasio

    COV-ID is a highly scalable technology that utilizes a two-step barcoding strategy to detect viral RNAs in saliva samples combining RT-LAMP, PCR, and next generation sequencing.
41. 1. Chromosomes and Gene Expression
    2. Microbiology and Infectious Disease

    SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome

    Michela Zaffagni, Jenna M Harris ... Sebastian Kadener

    In the context of SARS-CoV-2 infection, Nsp14 alters gene expression of the host cell through the interaction with the cellular enzyme IMPDH2.
42. 1. Immunology and Inflammation
    2. Medicine

    Innate lymphoid cells and COVID-19 severity in SARS-CoV-2 infection

    Noah J Silverstein, Yetao Wang ... Jeremy Luban

    Homeostatic innate lymphoid cell abundance, adjusted for age and sex, correlates inversely with COVID-19 severity in adults and children.
43. 1. Medicine

    Drug targeting Nsp1-ribosomal complex shows antiviral activity against SARS-CoV-2

    Mohammad Afsar, Rohan Narayan ... Tanweer Hussain

    Drug targeting Nsp1-ribosome interaction shows rescue of Nsp1-mediated translation inhibition and has antiviral activity against SARS-CoV-2.
44. 1. Chromosomes and Gene Expression
    2. Microbiology and Infectious Disease

    Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression

    Georgia M Cook, Katherine Brown ... Ian Brierley

    Combining ribosome profiling and RNA sequencing illuminates novel features of porcine reproductive and respiratory syndrome virus gene expression, including the regulation of polyprotein stoichiometry through temporal modulation of ribosomal frameshifting and the synthesis of non-canonical transcripts.
45. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    SARS-CoV2 variant-specific replicating RNA vaccines protect from disease following challenge with heterologous variants of concern

    David W Hawman, Kimberly Meade-White ... Jesse H Erasmus

    A replicating RNA vaccine platform generated significant immunity against SARS-CoV2 in mice and hamsters, and can be updated to target variants of concern.
46. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein

    Hisham M Dokainish, Suyong Re ... Yuji Sugita

    Computer simulations explore the experimentally unknown S-protein structures, revealing novel drug binding sites.
47. 1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics

    Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike

    Marco A Díaz-Salinas, Qi Li ... James B Munro

    The function of the SARS-CoV-2 spike is controlled by allosterically modulating the dynamics of the receptor-binding domain.
48. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Boosting of cross-reactive antibodies to endemic coronaviruses by SARS-CoV-2 infection but not vaccination with stabilized spike

    Andrew R Crowley, Harini Natarajan ... Margaret E Ackerman

    Non-neutralizing antibodies to the SARS-CoV-2 spike protein’s S2 domain that also recognize widely circulating endemic coronavirus strains are rapidly boosted by natural infection but not vaccination with stabilized spike-based vaccines.
49. 1. Epidemiology and Global Health
    2. Medicine

    Investigating phenotypes of pulmonary COVID-19 recovery: A longitudinal observational prospective multicenter trial

    Thomas Sonnweber, Piotr Tymoszuk ... Judith Löffler-Ragg

    Protracted systemic and microvascular inflammation, as well as high anti-SARS-CoV-2 antibody levels, is associated with a high risk of persistent structural and functional lung deficits 6 months after COVID-19.
50. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection

    Meghan E Garrett, Jared G Galloway ... Julie M Overbaugh

    Sera from vaccinated subjects bound additional linear epitopes compared to sera from individuals with mild infection, in addition the pathways of escape from antibodies from vaccination were more uniform than those from mildly infected individuals.
51. 1. Cell Biology
    2. Microbiology and Infectious Disease

    Vaccine-induced COVID-19 mimicry syndrome

    Eric Kowarz, Lea Krutzke ... Rolf Marschalek

    The Spike gene expressed by the vector-based vaccine Vaxzevria bears the risk of cryptic splicing, which in turn may lead to cellular production of soluble, instead of membrane-anchored, Spike protein variants.
52. 1. Microbiology and Infectious Disease

    Golden Syrian hamster as a model to study cardiovascular complications associated with SARS-CoV-2 infection

    Zaigham Abbas Rizvi, Rajdeep Dalal ... Amit Awasthi

    SARS-CoV-2 infection in hamsters causes cardiovascular pathologies.
53. 1. Epidemiology and Global Health
    2. Medicine

    Ten months of temporal variation in the clinical journey of hospitalised patients with COVID-19: An observational cohort

    ISARIC Clinical Characterisation Group, Matthew D Hall ... Piero L Olliaro

    Patient outcomes, and the time spent by patients during hospital admission, showed considerable variation over the first year of the COVID-19 pandemic.
54. 1. Immunology and Inflammation
    2. Medicine

    Effects of IFIH1 rs1990760 variants on systemic inflammation and outcome in critically ill COVID-19 patients in an observational translational study

    Laura Amado-Rodríguez, Estefania Salgado del Riego ... Guillermo M Albaiceta

    Patients with different rs1990760 variants have a differential inflammatory response to severe SARS-CoV-2 infections, so that those with a TT genotype have an attenuated systemic inflammation and may not benefit from steroid therapy.
55. 1. Cell Biology
    2. Microbiology and Infectious Disease

    Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences

    Jeffrey Y Lee, Peter AC Wing ... Ilan Davis

    Single-molecule analysis of SARS-CoV-2 RNA identifies significant heterogeneity in cellular viral RNA levels and highlights slower replication kinetics for the Alpha variant compared to the Victoria strain.
56. 1. Immunology and Inflammation

    ACE2 is the critical in vivo receptor for SARS-CoV-2 in a novel COVID-19 mouse model with TNF- and IFNγ-driven immunopathology

    Riem Gawish, Philipp Starkl ... Sylvia Knapp

    Only three Spike mutations enable murine SARS-CoV-2 infection, which is still strictly ACE2 dependent and causes a COVID-19-like disease in mice with immunopathology-driven lung damage.
57. 1. Computational and Systems Biology
    2. Medicine

    Data mining methodology for response to hypertension symptomology—application to COVID-19-related pharmacovigilance

    Xuan Xu, Jessica Kawakami ... Majid Jaberi-Douraki

    Quantitative models and data-driven approaches developed for the COVID-19 pandemic and predicting SARS-Cov-2 comorbidities for high-risk populations including hypertension show that the future of large-scale biomedical science will be significantly underscored by data-driven decision-making and AI knowledge-based development and validation.
58. 1. Epidemiology and Global Health

    3D virtual histopathology of cardiac tissue from Covid-19 patients based on phase-contrast X-ray tomography

    Marius Reichardt, Patrick Moller Jensen ... Tim Salditt

    X-ray phase-contrast tomography reveals pathology of capillaries in heart tissue from patients who succumbed to Covid-19, as well as alterations in the three-dimensional cardiac tissue structure.
59. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor

    Tümay Capraz, Nikolaus F Kienzl ... Johannes Stadlmann

    Molecular dynamics simulation assisted engineering of recombinant soluble human ACE2 N-glycosylation by site-directed mutagenesis or glycosidase treatment yields a superior SARS-CoV-2 decoy receptor.
60. 1. Epidemiology and Global Health
    2. Medicine

    Association of lipid-lowering drugs with COVID-19 outcomes from a Mendelian randomization study

    Wuqing Huang, Jun Xiao ... Liangwan Chen

    A two-sample Mendelian randomization study suggested a potential causal relationship between HMGCR inhibition and the reduced risk of COVID-19 hospitalization.
61. 1. Immunology and Inflammation

    SARS-CoV-2 spike protein induces inflammation via TLR2-dependent activation of the NF-κB pathway

    Shahanshah Khan, Mahnoush S Shafiei ... Hasan Zaki

    Recognition of SARS-CoV-2 spike protein by innate immune sensor TLR2 leads to the induction of inflammatory mediators and constitutes a mechanism for cytokine storm during COVID-19.
62. 1. Microbiology and Infectious Disease

    HIV status alters disease severity and immune cell responses in Beta variant SARS-CoV-2 infection wave

    Farina Karim, Inbal Gazy ... Alex Sigal

    HIV infection increases SARS-CoV-2 disease severity and alters immune cell dynamics in a beta variant dominated infection wave.
63. 1. Physics of Living Systems

    Stochastic social behavior coupled to COVID-19 dynamics leads to waves, plateaus, and an endemic state

    Alexei V Tkachenko, Sergei Maslov ... Nigel Goldenfeld

    Time-varying heterogeneous social activity explains transient suppression of epidemic waves followed by long plateaus and eventual transition towards the endemic state of an emergent pathogen, such as COVID-19.
64. 1. Microbiology and Infectious Disease

    Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape

    Fred D Mast, Peter C Fridy ... Michael P Rout

    A large repertoire of nanobodies that target discrete regions of SARS-CoV-2 spike shows effective neutralization against variants of concern with many pairwise combinations resistant to escape and demonstrating synergistic neutralization activities.
65. 1. Immunology and Inflammation
    2. Structural Biology and Molecular Biophysics

    Neutrophil-mediated oxidative stress and albumin structural damage predict COVID-19-associated mortality

    Mohamed A Badawy, Basma A Yasseen ... Sameh Saad Ali

    Electron paramagnetic resonance spectroscopy quantitatively correlates structural damages of serum albumin with COVID-19 severity and mortality thus suggesting albumin replacement therapy as a strategy to rescue patients at risk of mortality.
66. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Efficacy of FFP3 respirators for prevention of SARS-CoV-2 infection in healthcare workers

    Mark Ferris, Rebecca Ferris ... Michael P Weekes

    Healthcare workers working on COVID-19 wards experience a 31-fold increased risk of infection with SARS-CoV-2 compared to colleagues on non-COVID-19 wards whilst wearing fluid-resistant surgical masks, and FFP3 respirators provide up to 100% protection against infection.
67. 1. Immunology and Inflammation

    The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice

    Rafael Bayarri-Olmos, Laust Bruun Johnsen ... Mikkel-Ole Skjoedt

    Functional characterization of the alpha/B1.1.7 SARS-CoV-2 variant revealed an eightfold affinity increase of the N501Y RBD to human ACE-2 and that even a low inoculation dose of the alpha variant induces severe disease and fast progression in transgenic hACE2 mice.
68. 1. Computational and Systems Biology
    2. Immunology and Inflammation

    TCR meta-clonotypes for biomarker discovery with tcrdist3 enabled identification of public, HLA-restricted clusters of SARS-CoV-2 TCRs

    Koshlan Mayer-Blackwell, Stefan Schattgen ... Andrew Fiore-Gartland

    Distance-based TCR analysis enables grouping of biochemically similar clonotypes into meta-clonotypes that have increased publicity, and therefore statistical power, for population-level detection of antigen-specific T cells in infection and vaccination.
69. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis

    Andreas Hober, Khue Hua Tran-Minh ... Fredrik Edfors

    Immuno-affinity enrichment combined with liquid chromatography-mass spectrometry can be used to detect viral proteins to confirm the presence of SARS-CoV-2 in clinical samples.
70. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Cross-reactive antibodies after SARS-CoV-2 infection and vaccination

    Marloes Grobben, Karlijn van der Straten ... Marit J van Gils

    SARS-CoV-2 infection and vaccination elicit antibodies that cross-react with other human coronavirus spike proteins, indicating the spike S2 subdomain as a potential target strategy to develop a pan-coronavirus vaccine.
71. 1. Biochemistry and Chemical Biology
    2. Medicine

    Early prediction of in-hospital death of COVID-19 patients: a machine-learning model based on age, blood analyses, and chest x-ray score

    Emirena Garrafa, Marika Vezzoli ... Roberto Maroldi

    An early-warning model able to predict in-hospital mortality in patients affected by COVID-19 was developed and validated using common and economic tools.
72. 1. Microbiology and Infectious Disease

    Effect of SARS-CoV-2 proteins on vascular permeability

    Rossana Rauti, Meishar Shahoha ... Ben Meir Maoz

    A specific SARS-CoV-2 proteins that affect the vascular permeability and impairs the functionality of other significant organs has been identified.
73. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    mRNA vaccine-induced T cells respond identically to SARS-CoV-2 variants of concern but differ in longevity and homing properties depending on prior infection status

    Jason Neidleman, Xiaoyu Luo ... Nadia R Roan

    COVID-19 mRNA vaccine-elicited T cells recognize variants of concern and phenotypically differ depending on number of vaccine doses and prior SARS-CoV-2 infection status.
74. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    SARS-CoV-2 shedding dynamics across the respiratory tract, sex, and disease severity for adult and pediatric COVID-19

    Paul Z Chen, Niklas Bobrovitz ... Frank X Gu

    COVID-19 severity, rather than sex or age, predicts SARS-CoV-2 kinetics, and SARS-CoV-2 viral load from lower respiratory tract specimens may predict severe disease days before clinical deterioration for COVID-19 patients.
75. 1. Microbiology and Infectious Disease

    mRNA vaccination in people over 80 years of age induces strong humoral immune responses against SARS-CoV-2 with cross neutralization of P.1 Brazilian variant

    Helen Parry, Gokhan Tut ... Paul Moss

    The BNT162b2 mRNA COVID-19 vaccine is highly effective at generating immune responses in people over the age of 80 years and provides good cross neutralization of the P.1 gamma variant of concern.
76. 1. Microbiology and Infectious Disease
    2. Physics of Living Systems

    Inhibition of SARS-CoV-2 polymerase by nucleotide analogs from a single-molecule perspective

    Mona Seifert, Subhas C Bera ... David Dulin

    High-throughput and ultra-stable magnetic tweezers reveal that Remdesivir induces a long-lived backtrack pause upon incorporation by the coronavirus polymerase, and SARS-CoV-2 is able to evade interferon-induced antiviral ddhCTP.
77. 1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics

    Michael I Barton, Stuart A MacGowan ... P Anton van der Merwe

    Common variants of the SARS-CoV-2 Spike protein and its ligand, the human ACE2 receptor, increase the binding affinity, suggesting that they could increase viral transmissibility.
78. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants

    Elizabeth Jaworski, Rose M Langsjoen ... Andrew L Routh

    Tiled-ClickSeq provides a simple and novel next-generation sequencing approach for complete genome sequencing of viruses including SARS-CoV-2, whilst capturing RNA recombination events and minority variants.
79. 1. Microbiology and Infectious Disease

    Quantifying the relationship between SARS-CoV-2 viral load and infectiousness

    Aurélien Marc, Marion Kerioui ... Jeremie Guedj

    Viral dynamic modeling reveals the relationship between SARS-CoV-2 viral load and infectiousness and allows to anticipate the effects of variants of concern and of vaccination on transmission.
80. 1. Medicine
    2. Stem Cells and Regenerative Medicine

    Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19

    Courtney Tindle, MacKenzie Fuller ... Soumita Das

    An integrated stem cell-based disease modeling and computational approach demonstrates how proximal airway epithelium is critical for SARS-CoV-2 infectivity and distal alveolar cells are critical for simulating the host responses.
81. 1. Epidemiology and Global Health
    2. Genetics and Genomics

    A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance

    Mohd Anisul, Jarrod Shilts ... Ian Dunham

    Genetic integration of human protein abundance variation and COVID-19 susceptibility identifies proteins with potential causal roles in antiviral responses, coagulation, cytokine activation, and direct receptor interactions with SARS-CoV-2.
82. 1. Structural Biology and Molecular Biophysics

    N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2

    Fang Tian, Bei Tong ... Peng Zheng

    Spike protein of SARS-CoV-2 with mutation N501Y shows a faster association rate, slower dissociation rate, and higher binding probability and unbinding force to its human receptor protein ACE2, leading to higher transmission.
83. 1. Structural Biology and Molecular Biophysics

    Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion

    Esteban Dodero-Rojas, Jose N Onuchic, Paul Charles Whitford

    SARS-CoV-2 entry mechanism through membrane fusion is regulated by the spike protein glycosylation state.
84. 1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

    Christopher JR Illingworth, William L Hamilton ... M Estée Török

    Outbreaks of SARS-CoV-2 transmission in a hospital environment show evidence of superspreading, with 80% of infections caused by 21% of infected individuals.
85. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Integrated single-cell analysis unveils diverging immune features of COVID-19, influenza, and other community-acquired pneumonia

    Alex R Schuurman, Tom DY Reijnders ... Tom van der Poll

    Different etiologies of community-acquired pneumonia evoke both shared and diverging immunological responses.
86. 1. Computational and Systems Biology
    2. Immunology and Inflammation

    Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy

    Sierra M Barone, Alberta GA Paul ... Jonathan M Irish

    Rare, virus-specific immune cells in human blood are automatically identified by machine learning algorithm T-REX and characterized for signature features needed for tracking and isolation.
87. 1. Epidemiology and Global Health
    2. Genetics and Genomics

    Patterns of within-host genetic diversity in SARS-CoV-2

    Gerry Tonkin-Hill, Inigo Martincorena ... Wellcome Sanger Institute COVID-19 Surveillance Team

    Characterisation of within-host diversity of SARS-CoV-2 provides insights into the mutational and selective mechanisms driving its evolution and has important implications for using within-host variation to inform transmission inference efforts.
88. 1. Microbiology and Infectious Disease

    The development of Nanosota-1 as anti-SARS-CoV-2 nanobody drug candidates

    Gang Ye, Joseph Gallant ... Fang Li

    Potent and low-cost Nanosota-1 drug candidates block SARS-CoV-2 infections in vitro and in animal models and act preventively and therapeutically.
89. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains

    Nikhil Faulkner, Kevin W Ng ... George Kassiotis

    Heterotypic immunity, the ability of immunity induced by one SARS-CoV-2 variant to protect against another, is asymmetric, with the UK (B.1.1.7) variant, eliciting weaker heterotypic immunity than other variants.
90. 1. Computational and Systems Biology
    2. Medicine

    NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism

    Homa MohammadiPeyhani, Anush Chiappino-Pepe ... Vassily Hatzimanikatis

    NICEdrug.ch is a resource allowing systematic and large-scale computational analysis of drug biochemistry, enzymatic targets, and toxicity in the context of cellular metabolism.
91. 1. Epidemiology and Global Health

    Tracking excess mortality across countries during the COVID-19 pandemic with the World Mortality Dataset

    Ariel Karlinsky, Dmitry Kobak

    The World Mortality Dataset and paper is the largest dataset of all-cause mortality currently in existence for tracking mortality and excess mortality during the COVID-19 pandemic.
92. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Identification of drugs associated with reduced severity of COVID-19 – a case-control study in a large population

    Ariel Israel, Alejandro A Schäffer ... Eytan Ruppin

    Large-scale retrospective analysis suggests medications and dietary supplements, such as rosuvastatin, ezetimibe, ubiquinone, risedronate, vitamin D, and magnesium, are associated with a lower rate of severe COVID-19 disease.
93. 1. Microbiology and Infectious Disease

    Revisiting the guidelines for ending isolation for COVID-19 patients

    Yong Dam Jeong, Keisuke Ejima ... Marco Ajelli

    Compared with the approach isolating COVID-19 patients for a fixed period, the approach using repeated PCR testing mitigates unnecessarily lengthy isolation of patients while minimizing the risk of further transmission.
94. 1. Epidemiology and Global Health

    FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip

    Manoj Kumar, Sneha Gulati ... Debojyoti Chakraborty

    A newly developed lateral flow assay can diagnose mutational signatures of major SARS CoV-2 variants in a rapid, inexpensive, and sequence-free manner.
95. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

    Oliver Stirrup, Joseph Hughes ... Judith Breuer

    Epidemiological and viral sequence data can be combined to provide standardised feedback on cases of hospital onset COVID-19 infection that would be useful for infection prevention and control.
96. 1. Epidemiology and Global Health

    Mendelian randomization analysis provides causality of smoking on the expression of ACE2, a putative SARS-CoV-2 receptor

    Hui Liu, Junyi Xin ... Xia Jiang

    Smoking, measured by both initiation and intensity, are significantly associated with an elevated expression level of ACE2 in multiple human tissues/organs, subsequently increasing the susceptibility and severity of COVID-19.
97. 1. Medicine
    2. Microbiology and Infectious Disease

    Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time

    A Sarah Walker, Emma Pritchard ... COVID-19 Infection Survey team

    Wide variation in cycle threshold (Ct) values from SARS-CoV-2 RT-PCR tests over calendar time offers the potential for their broader use in public testing programmes as an ‘early-warning’ system for shifts in infectious load and hence transmission.
98. 1. Microbiology and Infectious Disease

    Smartphone screen testing, a novel pre-diagnostic method to identify SARS-CoV-2 infectious individuals

    Rodrigo M Young, Camila J Solis ... Luis A Quiñones

    PCR testing for SARS-CoV-2 from samples taken from smartphone screens, Phone Screen Testing, provides a sensitive, cost-effective, simple, and non-invasive new method that could boost COVID-19 mass test screening.
99. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Mechanistic theory predicts the effects of temperature and humidity on inactivation of SARS-CoV-2 and other enveloped viruses

    Dylan H Morris, Kwe Claude Yinda ... James O Lloyd-Smith

    Viruses, including SARS-CoV-2, retain infectivity longer at low temperatures and extreme relative humidities because these conditions slow down the chemical reactions that inactivate those viruses.
100. 1. Epidemiology and Global Health
     2. Medicine

     Impact of COVID-19-related disruptions to measles, meningococcal A, and yellow fever vaccination in 10 countries

     Katy AM Gaythorpe, Kaja Abbas ... Mark Jit

     Routine and campaign vaccination disruption in 2020 may lead to measles outbreaks and yellow fever burden increases in some countries, but is unlikely to greatly increase meningococcal A burden.
101. 1. Immunology and Inflammation

     Ketogenic diet restrains aging-induced exacerbation of coronavirus infection in mice

     Seungjin Ryu, Irina Shchukina ... Vishwa Deep Dixit

     Ketogenic diet protects against coronavirus-infected aged mice, which, like humans, are significantly more susceptible to infections, by deactivating NLRP3 inflammasome, reducing pathogenic monotypes, and expanding γδ T cells in the lung.
102. 1. Epidemiology and Global Health

     Modeling the impact of racial and ethnic disparities on COVID-19 epidemic dynamics

     Kevin C Ma, Tigist F Menkir ... Marc Lipsitch

     Racial and ethnic disparities in SARS-CoV-2 infection rates can impact overall epidemic dynamics and herd immunity, underscoring the need to develop socially informed transmission models that account for population variability.
103. 1. Epidemiology and Global Health
     2. Medicine

     A high rate of COVID-19 vaccine hesitancy in a large-scale survey on Arabs

     Eyad A Qunaibi, Mohamed Helmy ... Iyad Sultan

     Providing important data regarding the proportion of COVID-19 vaccine hesitancy and barriers toward vaccination in Arabic-speaking people to guide addressing the problem and achievement of widespread vaccination and collective immunity.
104. 1. Epidemiology and Global Health

     Alpha-1 adrenergic receptor antagonists to prevent hyperinflammation and death from lower respiratory tract infection

     Allison Koenecke, Michael Powell ... Susan Athey

     Patients exposed to ⍺1-AR antagonists have reduced risks of mechanical ventilation and death in lower respiratory tract infection-related illnesses, highlighting the need for prospective trials assessing ⍺1-AR antagonists' effectiveness in COVID-19.
105. 1. Epidemiology and Global Health

     High infectiousness immediately before COVID-19 symptom onset highlights the importance of continued contact tracing

     William S Hart, Philip K Maini, Robin N Thompson

     Fitting a mechanistic model to data from SARS-CoV-2 source-recipient pairs generates improved estimates of changes in infectiousness during infection, indicating substantial transmission shortly before symptom onset.
106. 1. Epidemiology and Global Health
     2. Medicine

     Metabolic biomarker profiling for identification of susceptibility to severe pneumonia and COVID-19 in the general population

     Heli Julkunen, Anna Cichońska ... Nightingale Health UK Biobank Initiative

     Metabolic biomarkers measured from single blood test can identify apparently healthy people at high susceptibility for developing severe pneumonia, and may also be useful for preventive COVID-19 screening.
107. 1. Epidemiology and Global Health
     2. Microbiology and Infectious Disease

     Heterogeneity in transmissibility and shedding SARS-CoV-2 via droplets and aerosols

     Paul Z Chen, Niklas Bobrovitz ... Frank X Gu

     Broader case variation in respiratory viral load, and in shedding virus via droplets and aerosols, for SARS-CoV-2 than influenza A(H1N1)pdm09 facilitates greater transmission heterogeneity in the COVID-19 pandemic than the 2009 flu pandemic.
108. 1. Microbiology and Infectious Disease

     Human airway cells prevent SARS-CoV-2 multibasic cleavage site cell culture adaptation

     Mart M Lamers, Anna Z Mykytyn ... Bart L Haagmans

     Cell culture adaptation of SARS-CoV-2 is prevented on human airway cells with an active serine protease-mediated entry pathway, allowing the production of genetically stable virus stocks for laboratory experiments.
109. 1. Medicine

     Insights from a Pan India Sero-Epidemiological survey (Phenome-India Cohort) for SARS-CoV2

     Salwa Naushin, Viren Sardana ... Shantanu Sengupta

     Widespread asymptomatic SARS-CoV2 infection affected nearly 100 million Indians by September 2020 with a subsequent decline in new cases, which may be attributable to increased population immunity, albeit seeing reduced neutralization activity at 6 months this respite may be temporary.
110. 1. Cell Biology

     SARS-CoV-2 requires cholesterol for viral entry and pathological syncytia formation

     David W Sanders, Chanelle C Jumper ... Clifford P Brangwynne

     A high-throughput microscopy screen for drugs that modulate SARS-CoV-2 spike-mediated membrane fusion identifies an essential role for cholesterol in both virus entry and syncytia formation.
111. 1. Medicine

     Sensitivity of ID NOW and RT–PCR for detection of SARS-CoV-2 in an ambulatory population

     Yuan-Po Tu, Jameel Iqbal, Timothy O'Leary

     Although the ID NOW platform is less sensitive than RT–PCR for identification of SARS-CoV-2 infection, it provides high positive and negative predictive values in low-prevalence populations.
112. 1. Epidemiology and Global Health
     2. Microbiology and Infectious Disease

     Single-dose BNT162b2 vaccine protects against asymptomatic SARS-CoV-2 infection

     Nick K Jones, Lucy Rivett ... Michael P Weekes

     A fourfold reduction in the rate of asymptomatic SARS-CoV-2 infection in healthcare workers ≥12 days after a single dose of BNT162b2 mRNA COVID-19 vaccine (Pfizer-BioNTech) has been found.
113. 1. Immunology and Inflammation
     2. Medicine

     Longitudinal proteomic profiling of dialysis patients with COVID-19 reveals markers of severity and predictors of death

     Jack Gisby, Candice L Clarke ... James E Peters

     Severe COVID-19 is characterised by a plasma proteomic biomarker signature, indicating innate immune activation, leucocyte–endothelial interactions, and epithelial injury.
114. 1. Microbiology and Infectious Disease

     Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers

     Qing Yang, Nicholas R Meyerson ... Sara L Sawyer

     A quick and portable test makes saliva samples turn yellow when people are carrying SARS-CoV-2, the virus that causes COVID-19.
115. 1. Epidemiology and Global Health
     2. Medicine

     SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung

     Alan E Mast, Alisa S Wolberg ... Daniel Jacobson

     Transcription changes in cells taken from bronchoalveolar fluid of COVID-19 patients indicate severe disruption of coagulation and fibrinolytic pathways in the lung and suggest similar processes in other organs.
116. 1. Immunology and Inflammation
     2. Medicine

     An open label trial of anakinra to prevent respiratory failure in COVID-19

     Evdoxia Kyriazopoulou, Periklis Panagopoulos ... Evangelos J Giamarellos-Bourboulis

     Early suPAR-guided anakinra decreases the risk for severe respiratory failure in SARS-CoV-2 pneumonia and restores the pro-/anti-inflammatory balance.
117. 1. Immunology and Inflammation
     2. Microbiology and Infectious Disease

     Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage

     Stefanie Deinhardt-Emmer, Daniel Wittschieber ... Gita Mall

     Early postmortem autopsy of COVID-19 patients shows high viral loads and damage of the lung, although extrapulmonary cells demonstrate no injury, they contribute to inflammation, hyper-coagulation, and multiple organ dysfunction.
118. 1. Genetics and Genomics
     2. Microbiology and Infectious Disease

     Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission

     Jamie M Ellingford, Ryan George ... Graeme CM Black

     Characterisation of SARS-CoV-2 genomic divergence in healthcare-associated outbreaks demonstrates that the inclusion of healthcare workers in contact networks identifies additional links in SARS-CoV-2 transmission pathways.
119. 1. Epidemiology and Global Health
     2. Genetics and Genomics

     Genomic epidemiology of COVID-19 in care homes in the east of England

     William L Hamilton, Gerry Tonkin-Hill ... COVID-19 Genomics Consortium UK

     SARS-CoV-2 can spread efficiently within care homes causing outbreaks among residents, who are at increased risk of severe disease, emphasising the importance of stringent infection control in this population.
120. 1. Genetics and Genomics
     2. Medicine

     Association of Toll-like receptor 7 variants with life-threatening COVID-19 disease in males: findings from a nested case-control study

     Chiara Fallerini, Sergio Daga ... Elisa Frullanti

     In the context of susceptibility to severe COVID-19, the observations of a study provide the basis for a personalized interferon-based therapy in patients with rare TLR7 variants.
121. 1. Epidemiology and Global Health
     2. Microbiology and Infectious Disease

     Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys

     Daniel B Larremore, Bailey K Fosdick ... Yonatan H Grad

     Integrating over multiple forms of statistical uncertainty associated with serological surveys can improve serosurvey design while also enabling that uncertainty to be appropriately propagated through epidemiological models.
122. 1. Epidemiology and Global Health
     2. Medicine

     Quantifying the impact of quarantine duration on COVID-19 transmission

     Peter Ashcroft, Sonja Lehtinen ... Sebastian Bonhoeffer

     Test-and-release quarantine strategies for traced contacts of confirmed SARS-CoV-2 cases and returning travellers can reduce average quarantine durations while remaining as effective as 10 days of quarantine without testing.
123. 1. Immunology and Inflammation

     Seroconversion stages COVID19 into distinct pathophysiological states

     Matthew D Galbraith, Kohl T Kinning ... Joaquín M Espinosa

     Stratification of COVID19 patients using quantitative metrics of seroconversion reveals distinct pathophysiological stages after SARS-CoV-2 infection, including key differences in immune cell types, inflammatory makers, and markers of organ function.
124. 1. Biochemistry and Chemical Biology
     2. Structural Biology and Molecular Biophysics

     SARS-CoV-2 S protein:ACE2 interaction reveals novel allosteric targets

     Palur V Raghuvamsi, Nikhil K Tulsian ... Ganesh S Anand

     SARS-CoV-2 spike protein binding to receptor angiotensin-converting enzyme 2 allosterically enhances furin proteolysis at distal S1/S2 cleavage sites.
125. 1. Epidemiology and Global Health
     2. Microbiology and Infectious Disease

     Viral load and contact heterogeneity predict SARS-CoV-2 transmission and super-spreading events

     Ashish Goyal, Daniel B Reeves ... Bryan T Mayer

     A mathematical model was used to establish a simple conceptual basis for why super-spreader events fundamentally drive the spread of SARS-CoV-2 but not influenza.
126. 1. Epidemiology and Global Health
     2. Evolutionary Biology

     COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest

     Albert Tian Chen, Kevin Altschuler ... Benjamin E Deverman

     COVID-19 CG is an open source web resource that allows vaccine, therapeutics, and diagnostics developers to track SARS-CoV-2 mutations and lineages by location and time.
127. 1. Epidemiology and Global Health
     2. Microbiology and Infectious Disease

     The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

     Zharko Daniloski, Tristan X Jordan ... Neville E Sanjana

     A pervasive mutation in the Spike protein of the coronavirus that causes COVID-19 results in virions that are up to eightfold more infectious.
128. 1. Epidemiology and Global Health

     Antimicrobial resistance and COVID-19: Intersections and implications

     Gwenan M Knight, Rebecca E Glover ... Clare IR Chandler

     COVID-19 will have an ongoing impact on antimicrobial resistance acquisition, transmission, and burden, requiring the close attention of researchers globally to generate a complete evidence base for the shifted dynamics.
129. 1. Immunology and Inflammation
     2. Medicine

     Cytokine ranking via mutual information algorithm correlates cytokine profiles with presenting disease severity in patients infected with SARS-CoV-2

     Kelsey E Huntington, Anna D Louie ... Wafik S El-Deiry

     A mutual information algorithm points to macrophage activation syndrome as a specific pathogenic mechanism in COVID-19, correlated with disease severity, which could be used to monitor disease and therapeutics.
130. 1. Evolutionary Biology

     Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e

     Kathryn E Kistler, Trevor Bedford

     Phylogenetic and computational methods reveal that at least two seasonal coronaviruses are evolving adaptively in the region of the viral spike protein exposed to the human humoral immune system.
131. 1. Computational and Systems Biology
     2. Immunology and Inflammation

     Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection

     Anastasia A Minervina, Ekaterina A Komech ... Mikhail V Pogorelyy

     Longitudinal tracking of individual T-cell clones reveals the expansion of pre-existing T-cell memory in response to SARS-CoV-2 infection.
132. 1. Microbiology and Infectious Disease

     SARS-CoV-2 entry into human airway organoids is serine protease-mediated and facilitated by the multibasic cleavage site

     Anna Z Mykytyn, Tim I Breugem ... Bart L Haagmans

     Whereas SARS-CoV-2 utilizes cathepsins to enter most cell lines, human airway organoids revealed that entry into relevant cells is dependent on serine proteases, which can be targeted for treatment.
133. 1. Microbiology and Infectious Disease

     Post-acute COVID-19 associated with evidence of bystander T-cell activation and a recurring antibiotic-resistant bacterial pneumonia

     Michaela Gregorova, Daniel Morse ... Ruth C Massey

     Post-acute or long-COVID is associated with bystander T-cell activation and a recurring antimicrobial resistant, bacterial ventilator-associated pneumonia.
134. 1. Medicine

     A novel haemocytometric COVID-19 prognostic score developed and validated in an observational multicentre European hospital-based study

     Joachim Linssen, Anthony Ermens ... Andre J van der Ven

     Distinct haemocytometric parameters, including cell activation markers, combined in a prognostic score may support early identification of COVID-19 patients likely to deteriorate and thus may benefit from ICU admission.
135. 1. Immunology and Inflammation
     2. Microbiology and Infectious Disease

     Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants

     Yiska Weisblum, Fabian Schmidt ... Paul D Bieniasz

     SARS-CoV-2 spike variants that resist neutralization by therapeutic antibodies or convalescent plasma can be generated in the laboratory and exist at low frequency in natural populations.
136. 1. Developmental Biology
     2. Genetics and Genomics

     Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes

     Allen Wang, Joshua Chiou ... NHLBI LungMap Consortium

     Generation of a human lung single nucleus ATAC-seq and single nucleus RNA-seq datasets reveals candidate cis-regulatory elements that advance knowledge on gene expression control in normal and diseased lungs.
137. 1. Biochemistry and Chemical Biology
     2. Microbiology and Infectious Disease

     Inhibition of SARS-CoV-2 viral entry upon blocking N- and O-glycan elaboration

     Qi Yang, Thomas A Hughes ... Sriram Neelamegham

     A critical role for glycosylation on viral entry and methods to use this knowledge to reduce SARS-CoV-2 infectivity has been demonstrated.
138. 1. Evolutionary Biology
     2. Microbiology and Infectious Disease

     Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic

     Chase W Nelson, Zachary Ardern ... Xinzhu Wei

     A novel, overlapping, putatively functional gene in SARS-CoV-2, ORF3d, is absent from close relatives of SARS-CoV-2 and may have contributed to the biology, emergence, or spread of the virus.
139. 1. Cell Biology

     ACE2: Evidence of role as entry receptor for SARS-CoV-2 and implications in comorbidities

     Natalia Zamorano Cuervo, Nathalie Grandvaux

     Despite evidence that ACE2 is the receptor for SARS-CoV-2, its limited expression in the respiratory system challenges the uniqueness of this entry route and role in the multifaceted COVID-19.
140. 1. Medicine
     2. Microbiology and Infectious Disease

     Early prediction of level-of-care requirements in patients with COVID-19

     Boran Hao, Shahabeddin Sotudian ... Ioannis Ch Paschalidis

     Using data for 2566 COVID-19 patients from five hospitals, models are developed to predict for each patient hospitalization and critical care needs, based on demographics, comorbidities, medications, and laboratory findings.
141. 1. Epidemiology and Global Health
     2. Microbiology and Infectious Disease

     The contribution of asymptomatic SARS-CoV-2 infections to transmission on the Diamond Princess cruise ship

     Jon C Emery, Timothy W Russell ... Rein MGJ Houben

     Nearly 75% of SARS-CoV-2 infections on the Diamond Princess were asymptomatic, half were never detected, and asymptomatic infections may have contributed substantially to transmission.
142. 1. Epidemiology and Global Health

     Quantifying antibody kinetics and RNA detection during early-phase SARS-CoV-2 infection by time since symptom onset

     Benny Borremans, Amandine Gamble ... James O Lloyd-Smith

     A meta-analysis shows that seroconversion of antibodies against SARS-CoV-2 is not affected by disease severity and finds higher viral RNA detection probability in lower respiratory tract and fecal samples.
143. 1. Medicine

     Obesity and diabetes as comorbidities for COVID-19: Underlying mechanisms and the role of viral–bacterial interactions

     Ilja L Kruglikov, Manasi Shah, Philipp E Scherer

     Dysfunctionaladipose tissue puts obese and type 2 diabetic patients at higher risk.
144. 1. Epidemiology and Global Health

     Differential occupational risks to healthcare workers from SARS-CoV-2 observed during a prospective observational study

     David W Eyre, Sheila F Lumley ... Timothy M Walker

     Risk factors for SARS-CoV-2 infection in healthcare workers included caring for Covid-19 patients, Black or Asian ethnicity, and Covid-19-positive household contacts, whereas a bundle of PPE-related measures protected ICU staff.
145. 1. Immunology and Inflammation
     2. Medicine

     3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography

     Marina Eckermann, Jasper Frohn ... Tim Salditt

     Phase contrast X-ray tomography based on a combination of parallel and cone beam geometry extends conventional histology by a third dimension and enables full quantication of tissue remodeling in COVID-19.
146. 1. Medicine

     Inference from longitudinal laboratory tests characterizes temporal evolution of COVID-19-associated coagulopathy (CAC)

     Colin Pawlowski, Tyler Wagner ... Venky Soundararajan

     Longitudinal laboratory testing results tied to SARS-CoV-2 diagnostic PCR results of more than 2500 patients reveal the temporal evolution of COVID-associated coagulopathy.
147. 1. Epidemiology and Global Health

     Early analysis of the Australian COVID-19 epidemic

     David J Price, Freya M Shearer ... James M McCaw

     An analysis of Australian case data demonstrates how the combined strategy of border measures, case targeted interventions, and social distancing effectively contained the first epidemic wave of COVID-19.
148. 1. Medicine

     Concentration-dependent mortality of chloroquine in overdose

     James A Watson, Joel Tarning ... Nicholas J White

     Most chloroquine regimens trialled for the treatment of COVID19 will not result in life-threatening cardiovascular toxicity.
149. 1. Computational and Systems Biology
     2. Medicine

     A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm

     Michael R Garvin, Christiane Alvarez ... Daniel Jacobson

     Gene expression analysis reveals a novel, integrated molecular mechanism for much of the pathogenesis of COVID-19 that provides therapeutic intervention points that can be addressed with existing approved pharmaceuticals.
150. 1. Medicine
     2. Microbiology and Infectious Disease

     Augmented curation of clinical notes from a massive EHR system reveals symptoms of impending COVID-19 diagnosis

     Tyler Wagner, FNU Shweta ... Venky Soundararajan

     Applying deep learning technology for the large-scale curation of symptoms from unstructured EHR clinical notes accurately predicts the differential signals of COVID-19 diagnosis over the week preceding typical PCR testing.
151. 1. Medicine

     Neuropathogenesis of SARS-CoV-2 infection

     Shumayila Khan, James Gomes

     Clinical data of SARS-CoV-2 patients presenting atypical symptoms must be recorded systematically to support continuing research investigating neurological complications associated with COVID-19.
152. 1. Epidemiology and Global Health

     Evidence for transmission of COVID-19 prior to symptom onset

     Lauren C Tindale, Jessica E Stockdale ... Caroline Colijn

     Control of COVID-19 will require strong case finding and isolation of exposed individuals because transmission can occur days prior to symptom onset.
153. 1. Medicine

     Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors

     AJ Venkatakrishnan, Arjun Puranik ... Venky Soundararajan

     SARS-CoV-2 receptor ACE2 is expressed in nasal olfactory epithelia, tongue keratinocytes and small intestine enterocytes, connected with the COVID-19 patient phenotypes such as anosmia and diarrhea.
154. 1. Genetics and Genomics
     2. Medicine

     Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?

     Roger Pique-Regi, Roberto Romero ... Nardhy Gomez-Lopez

     The human placenta negligibly co-expresses the transcripts encoding the canonical cell-entry mediators for SARS-CoV-2, which explains why mothers with COVID-19 rarely transmit the virus to the fetus.
155. 1. Computational and Systems Biology
     2. Medicine

     SARS-CoV-2 strategically mimics proteolytic activation of human ENaC

     Praveen Anand, Arjun Puranik ... Venky Soundararajan

     SARS-CoV-2 has evolved to cleverly mimic the FURIN-cleavage site in human ENaC-α, unlike any prior coronavirus strain, shedding new light on the Acute Respiratory Distress Syndrome (ARDS) in COVID-19 patients.
156. 1. Epidemiology and Global Health
     2. Medicine

     Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19

     Nick K Jones, Lucy Rivett ... Michael P Weekes

     Diminished incidence of COVID-19 amongst healthcare workers in a comprehensive screening programme demonstrates how effective infection control measures and staff testing can prevent hospitals becoming independent 'hubs' of SARS-CoV-2 transmission.
157. 1. Epidemiology and Global Health
     2. Medicine

     Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission

     Lucy Rivett, Sushmita Sridhar ... Michael P Weekes

     3% of >1,000 asymptomatic healthcare workers in their workplace tested positive for SARS-CoV-2, suggesting that comprehensive screening programmes are vital to prevent acquisition of COVID-19 in hospitals.
158. 1. Microbiology and Infectious Disease

     Antibodies to SARS-CoV-2 and their potential for therapeutic passive immunization

     PJ Klasse, John P Moore

     Antibodies hold promise for breakthrough treatment of COVID-19, the disease caused by the coronavirus SARS-CoV-2.
159. 1. Medicine
     2. Immunology and Inflammation

     Kallikrein-kinin blockade in patients with COVID-19 to prevent acute respiratory distress syndrome

     Frank L van de Veerdonk, Mihai G Netea ... Hans van der Hoeven

     The kinin-kallikrein system is a crucial target for the treatment of COVID-19.
160. 1. Medicine

     Potential harmful effects of discontinuing ACE-inhibitors and ARBs in COVID-19 patients

     Gian Paolo Rossi, Viola Sanga, Matthias Barton

     Current evidence does not suggest adverse effects of ACE inhibitors or ARBs in COVID-19 patients and, to the contrary, discontinuing these drugs in these patients may potentially be harmful.
161. 1. Epidemiology and Global Health
     2. Medicine

     Estimated effectiveness of symptom and risk screening to prevent the spread of COVID-19

     Katelyn Gostic, Ana CR Gomez ... James O Lloyd-Smith

     Even in the best-case scenario, screening for COVID-19 misses well over half of infected travellers.