COVID-19: A collection of articles

Collection

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 1. Epidemiology and Global Health

   Quantifying the impact of quarantine duration on COVID-19 transmission

   Peter Ashcroft et al.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. 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.
37. 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.
38. 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.
39. 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.