COVID-19: A Collection of Articles

Collection

1. 1. Epidemiology and Global Health

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

   Nightingale Health UK Biobank Initiative et al.
2. 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.
3. 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.
4. 1. Epidemiology and Global Health

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

   William Stephen Hart et al.
5. 1. Cell Biology

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

   David W Sanders et al.
6. 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.
7. 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.
8. 1. Medicine

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

   Salwa Naushin et al.
9. 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.
10. 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.
11. 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.
12. 1. Microbiology and Infectious Disease

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

    Mart M Lamers et al.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. 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.
37. 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.
38. 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.
39. 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.
40. 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.
41. 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.
42. 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.
43. 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.
44. 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.
45. 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.
46. 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.
47. 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.
48. 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.
49. 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.
50. 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.
51. 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.
52. 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.
53. 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.
54. 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.
55. 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.
56. 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.
57. 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.
58. 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.