COVID-19: A Collection of Articles

Collection

1. 1. Microbiology and Infectious Disease

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

   Lea Krutzke et al.
2. 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 et al.
3. 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 et al.

   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.
4. 1. Immunology and Inflammation

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

   Ana Carolina G Salina et al.
5. 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 et al.
6. 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 et al.

   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.
7. 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 et al.
8. 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 et al.

   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.
9. 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 et al.

   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.
10. 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 et al.

    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.
11. 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 et al.

    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.
12. 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 et al.

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

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

    Noah J Silverstein et al.

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

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

    Mohammad Afsar et al.

    Drug targeting Nsp1-ribosome interaction shows rescue of Nsp1-mediated translation inhibition and has antiviral activity against SARS-CoV-2.
15. 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 et al.

    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.
16. 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 et al.

    A replicating RNA vaccine platform generated significant immunity against SARS-CoV2 in mice and hamsters, and can be updated to target variants of concern.
17. 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 et al.

    Computer simulations explore the experimentally unknown S-protein structures, revealing novel drug binding sites.
18. 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 et al.

    The function of the SARS-CoV-2 spike is controlled by allosterically modulating the dynamics of the receptor-binding domain.
19. 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 et al.

    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.
20. 1. Epidemiology and Global Health
    2. Medicine

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

    Thomas Sonnweber et al.

    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.
21. 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 et al.

    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.
22. 1. Cell Biology
    2. Microbiology and Infectious Disease

    Vaccine-induced COVID-19 mimicry syndrome

    Eric Kowarz et al.

    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.
23. 1. Microbiology and Infectious Disease

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

    Zaigham Abbas Rizvi et al.

    SARS-CoV-2 infection in hamsters causes cardiovascular pathologies.
24. 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 et al.

    Patient outcomes, and the time spent by patients during hospital admission, showed considerable variation over the first year of the COVID-19 pandemic.
25. 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 et al.

    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.
26. 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 et al.

    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.
27. 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 et al.

    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.
28. 1. Computational and Systems Biology
    2. Medicine

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

    Xuan Xu et al.

    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.
29. 1. Epidemiology and Global Health

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

    Marius Reichardt et al.

    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.
30. 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 et al.

    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.
31. 1. Epidemiology and Global Health
    2. Medicine

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

    Wuqing Huang et al.

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

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

    Shahanshah Khan et al.

    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.
33. 1. Microbiology and Infectious Disease

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

    Farina Karim et al.

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

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

    Alexei V Tkachenko et al.

    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.
35. 1. Microbiology and Infectious Disease

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

    Fred D Mast et al.

    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.
36. 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 et al.

    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.
37. 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 et al.

    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.
38. 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 et al.

    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.
39. 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 et al.

    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.
40. 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 et al.

    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.
41. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

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

    Marloes Grobben et al.

    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.
42. 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 et al.

    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.
43. 1. Microbiology and Infectious Disease

    Effect of SARS-CoV-2 proteins on vascular permeability

    Rossana Rauti et al.

    A specific SARS-CoV-2 proteins that affect the vascular permeability and impairs the functionality of other significant organs has been identified.
44. 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 et al.

    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.
45. 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 et al.

    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.
46. 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 et al.

    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.
47. 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 et al.

    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.
48. 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 et al.

    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.
49. 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 et al.

    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.
50. 1. Microbiology and Infectious Disease

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

    Aurélien Marc et al.

    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.
51. 1. Medicine
    2. Stem Cells and Regenerative Medicine

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

    Courtney Tindle et al.

    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.
52. 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 et al.

    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.
53. 1. Structural Biology and Molecular Biophysics

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

    Fang Tian et al.

    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.
54. 1. Structural Biology and Molecular Biophysics

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

    Esteban Dodero-Rojas et al.

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

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

    Christopher JR Illingworth et al.

    Outbreaks of SARS-CoV-2 transmission in a hospital environment show evidence of superspreading, with 80% of infections caused by 21% of infected individuals.
56. 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 et al.

    Different etiologies of community-acquired pneumonia evoke both shared and diverging immunological responses.
57. 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 et al.

    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.
58. 1. Epidemiology and Global Health
    2. Genetics and Genomics

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

    Gerry Tonkin-Hill et al.

    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.
59. 1. Microbiology and Infectious Disease

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

    Gang Ye et al.

    Potent and low-cost Nanosota-1 drug candidates block SARS-CoV-2 infections in vitro and in animal models and act preventively and therapeutically.
60. 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 et al.

    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.
61. 1. Computational and Systems Biology
    2. Medicine

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

    Homa MohammadiPeyhani et al.

    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.
62. 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.
63. 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 et al.

    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.
64. 1. Microbiology and Infectious Disease

    Revisiting the guidelines for ending isolation for COVID-19 patients

    Yong Dam Jeong et al.

    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.
65. 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 et al.

    A newly developed lateral flow assay can diagnose mutational signatures of major SARS CoV-2 variants in a rapid, inexpensive, and sequence-free manner.
66. 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 et al.

    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.
67. 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 et al.

    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.
68. 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 et al.

    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.
69. 1. Microbiology and Infectious Disease

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

    Rodrigo M Young et al.

    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.
70. 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 et al.

    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.
71. 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 et al.

    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.
72. 1. Immunology and Inflammation

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

    Seungjin Ryu et al.

    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.
73. 1. Epidemiology and Global Health

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

    Kevin C Ma et al.

    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.
74. 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 et al.

    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.
75. 1. Epidemiology and Global Health

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

    Allison Koenecke et al.

    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.
76. 1. Epidemiology and Global Health

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

    William S Hart et al.

    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.
77. 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 et al.

    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.
78. 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 et al.

    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.
79. 1. Microbiology and Infectious Disease

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

    Mart M Lamers et al.

    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.
80. 1. Medicine

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

    Salwa Naushin et al.

    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.
81. 1. Cell Biology

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

    David W Sanders et al.

    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.
82. 1. Medicine

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

    Yuan-Po Tu et al.

    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.
83. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

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

    Nick K Jones et al.

    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.
84. 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 et al.

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

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

    Qing Yang et al.

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

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

    Alan E Mast et al.

    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.
87. 1. Immunology and Inflammation
    2. Medicine

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

    Evdoxia Kyriazopoulou et al.

    Early suPAR-guided anakinra decreases the risk for severe respiratory failure in SARS-CoV-2 pneumonia and restores the pro-/anti-inflammatory balance.
88. 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 et al.

    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.
89. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

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

    Jamie M Ellingford et al.

    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.
90. 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 et al.

    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.
91. 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 et al.

    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.
92. 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 et al.

    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.
93. 1. Epidemiology and Global Health
    2. Medicine

    Quantifying the impact of quarantine duration on COVID-19 transmission

    Peter Ashcroft et al.

    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.
94. 1. Immunology and Inflammation

    Seroconversion stages COVID19 into distinct pathophysiological states

    Matthew D Galbraith et al.

    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.
95. 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 et al.

    SARS-CoV-2 spike protein binding to receptor angiotensin-converting enzyme 2 allosterically enhances furin proteolysis at distal S1/S2 cleavage sites.
96. 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 et al.

    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.
97. 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 et al.

    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.
98. 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 et al.

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

    Antimicrobial resistance and COVID-19: Intersections and implications

    Gwenan M Knight et al.

    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.
100. 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 et al.

     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.
101. 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.
102. 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 et al.

     Longitudinal tracking of individual T-cell clones reveals the expansion of pre-existing T-cell memory in response to SARS-CoV-2 infection.
103. 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 et al.

     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.
104. 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 et al.

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

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

     Joachim Linssen et al.

     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.
106. 1. Immunology and Inflammation
     2. Microbiology and Infectious Disease

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

     Yiska Weisblum et al.

     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.
107. 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 et al.

     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.
108. 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 et al.

     A critical role for glycosylation on viral entry and methods to use this knowledge to reduce SARS-CoV-2 infectivity has been demonstrated.
109. 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 et al.

     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.
110. 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.
111. 1. Medicine
     2. Microbiology and Infectious Disease

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

     Boran Hao et al.

     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.
112. 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 et al.

     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.
113. 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 et al.

     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.
114. 1. Medicine

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

     Ilja L Kruglikov et al.

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

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

     David W Eyre et al.

     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.
116. 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 et al.

     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.
117. 1. Medicine

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

     Colin Pawlowski et al.

     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.
118. 1. Epidemiology and Global Health

     Early analysis of the Australian COVID-19 epidemic

     David J Price et al.

     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.
119. 1. Medicine

     Concentration-dependent mortality of chloroquine in overdose

     James A Watson et al.

     Most chloroquine regimens trialled for the treatment of COVID19 will not result in life-threatening cardiovascular toxicity.
120. 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 et al.

     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.
121. 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 et al.

     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.
122. 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.
123. 1. Epidemiology and Global Health

     Evidence for transmission of COVID-19 prior to symptom onset

     Lauren C Tindale et al.

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

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

     AJ Venkatakrishnan et al.

     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.
125. 1. Genetics and Genomics
     2. Medicine

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

     Roger Pique-Regi et al.

     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.
126. 1. Computational and Systems Biology
     2. Medicine

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

     Praveen Anand et al.

     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.
127. 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 et al.

     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.
128. 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 et al.

     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.
129. 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.
130. 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 et al.

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

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

     Gian Paolo Rossi et al.

     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.
132. 1. Epidemiology and Global Health
     2. Medicine

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

     Katelyn Gostic et al.

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