SARS-CoV-2 and COVID-19

General
BMJ Best Practice: COVID-19 - expert advice contributions by Nick Beeching from Liverpool School of Hygiene and Tropical Medicine, Tom Fletcher and Robert Fowler : includes criteria/case definitions and treatment algorithm

This page by Nature curates key new research relevant to COVID-19

COVID-19 NICE guidelines and resources hub

Prevention and Public Health
Haug, N., Geyrhofer, L., Londei, A. et al. Ranking the effectiveness of worldwide COVID-19 government interventions. Nat Hum Behav 4, 1303–1312 (2020). https://doi.org/10.1038/s41562-020-01009-0 Note the findings in Fig. 1

Chan NC, Li K, Hirsh J. Peripheral Oxygen Saturation in Older Persons Wearing Nonmedical Face Masks in Community Settings. JAMA. 2020;324(22):2323–2324. doi:10.1001/jama.2020.21905

Stephen A. Lauer, Kyra H. Grantz, Qifang Bi, et al. TThe Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application. Ann Intern Med.2020;172:577-582. [Epub ahead of print 10 March 2020]. doi:10.7326/M20-0504

Transmission Dynamics
Shen Y, Li C, Dong H, et al. Community Outbreak Investigation of SARS-CoV-2 Transmission Among Bus Riders in Eastern China. JAMA Intern Med. 2020;180(12):1665–1671. doi:10.1001/jamainternmed.2020.5225

Pombal R, Hosegood I, Powell D. [https://jamanetwork.com/journals/jama/fullarticle/2771435. Risk of COVID-19 During Air Travel.] JAMA. 2020;324(17):1798. doi:10.1001/jama.2020.19108

Grijalva CG, Rolfes MA, Zhu Y, et al. Transmission of SARS-COV-2 Infections in Households — Tennessee and Wisconsin, April–September 2020. MMWR Morb Mortal Wkly Rep 2020;69:1631–1634. DOI: http://dx.doi.org/10.15585/mmwr.mm6944e1

Herd Immunity
Omer SB, Yildirim I, Forman HP. Herd Immunity and Implications for SARS-CoV-2 Control. JAMA. 2020;324(20):2095–2096. doi:10.1001/jama.2020.20892

Presentation
COVID Symptom Study (17 July 2020) The COVID Symptom Study reveals six distinct ‘types’ of COVID-19. COVID Symptom Study/ZOE/KCL

Sudre C. H. et al. (16 June 2020) Symptom clusters in Covid19: A potential clinical prediction tool from the COVID Symptom study app. MedRxivdoi:https://doi.org/10.1101/2020.06.12.20129056

Dermatology
Galván Casas, C. et al. (29 April 2020) Classification of the cutaneous manifestations of COVID‐19: a rapid prospective nationwide consensus study in Spain with 375 cases. British Journal of Dermatology 2020;183pg.71-77 doi: https://doi.org/10.1111/bjd.19163

Thrombo-embolic
Oxley TJ, Mocco J, Majidi S, Kellner CP, Shoirah H, Singh IP, et al. Large-Vessel Stroke as a Presenting Feature of Covid-19 in the Young. N Engl J Med. 2020 Apr 28;382(20):e60.

Host
Pairo-Castineira, E., Clohisey, S., Klaric, L. et al. Genetic mechanisms of critical illness in Covid-19. Nature (2020). https://doi.org/10.1038/s41586-020-03065-y

Virus
Nextstrain.org SARS-CoV-2 genomic data (Global data)

Microreact SARS-CoV-2 genomic data visualisation (COG-UK)

The Danish mink strain
Lassaunière R. et al. (Nov 2020) Working paper on SARS-CoV-2 spike mutations arising in Danish mink, their spread to humans and neutralization data. From Statens Serum Institute

"Omics" Resources
(pulled from this review):

SARS-CoV-2 Genome Sequencing Data, DNA Sequencing Data	https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/

SARS-CoV-2 Transcriptomic Map
 * RNA Sequencing Data	Open Science Framework: accession number doi:10.17605/OSF.IO/8F6N9


 * Kim, D et al. The Architecture of SARS-CoV-2 Transcriptome. Cell, Volume 181, Issue 4, 914 - 921.e10

SARS-CoV-2 and Human Protein Interactions, Mass Spectrometry Raw Data	http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD018117

SARS-CoV-2 Strains	https://nextstrain.org/ncov

Genomic Epidemiology   https://www.gisaid.org/

The COVID-19 Host Genetics Initiative, Host Genetics Data (GWAS, WES, WGS) https://www.covid19hg.org/

COVID-19 Cell Atlas, Single cell transcriptomics data	https://www.covid19cellatlas.org

Antibody testing
Deeks JJ.et al. (25 June 2020) [https://www.cochranelibrary.com/cdsr/doi/10.1002/14651858.CD013652/full '''Antibody tests for identification of current and past infection withSARS-CoV-2 (Review). Cochrane Database of Systematic Reviews'''], Issue 6. Art. No.: CD013652.doi: https://doi.org/10.1002/14651858.CD013652

Lisba Bastos M. et al. (1 July 2020) Diagnostic accuracy of serological tests for covid-19: systematic review and meta-analysis. BMJ370:m2516 doi:https://doi.org/10.1136/bmj.m2516

Staines H. M. et al. (9 June 2020) Dynamics of IgG seroconversion and pathophysiology of COVID-19 infections. MedRxivdoi:https://doi.org/10.1101/2020.06.07.20124636

Viral shedding, live viral culture studies, persistence and reactivation
Gousseff M. et al. (Nov 2020) Clinical recurrences of COVID-19 symptoms after recovery: Viral relapse, reinfection or inflammatory rebound? Journal of Infection, Volume 81, Issue 5, 2020, Pages 816-846, ISSN 0163-4453, https://doi.org/10.1016/j.jinf.2020.06.073.

[https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(20)30172-5/fulltext Lancet Review. SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis. Cevik et al. November 19, 2020] DOI:https://doi.org/10.1016/S2666-5247(20)30172-5 “Our findings suggest that, although patients with SARS-CoV-2 infection might have prolonged RNA shedding of up to 83 days in upper respiratory tract infection, no live virus was isolated from culture beyond day 9 of symptoms despite persistently high viral RNA loads."

[https://www.medrxiv.org/content/10.1101/2020.08.04.20167932v4 '''Viral cultures for COVID-19 infectivity assessment. Systematic review''' Tom Jefferson, Elizabeth Spencer, Jon Brassey, Carl Heneghan medRxiv 2020.08.04.20167932] doi: https://doi.org/10.1101/2020.08.04.20167932

Heading text
[https://wwwnc.cdc.gov/eid/article/26/11/20-3219_article Perera R, Tso E, Tsang O, et al. SARS-CoV-2 Virus Culture and Subgenomic RNA for Respiratory Specimens from Patients with Mild Coronavirus Disease. Emerging Infectious Diseases. 2020;26(11):2701-2704.] doi:10.3201/eid2611.203219. Also see this news article which discusses the paper above: https://www.cidrap.umn.edu/news-perspective/2020/08/those-milder-covid-19-may-not-shed-live-virus-long

Roe, K. (2020), Explanation for COVID‐19 infection neurological damage and reactivations. Transbound Emerg Dis, 67: 1414-1415. https://doi.org/10.1111/tbed.13594

Dias De Melo et al. COVID-19-associated olfactory dysfunction reveals SARS-CoV-2 neuroinvasion and persistence in the olfactory system bioRxiv 2020.11.18.388819; doi: https://doi.org/10.1101/2020.11.18.388819

Gaebler et al. Evolution of Antibody Immunity to SARS-CoV-2 bioRxiv 2020.11.03.367391; doi: https://doi.org/10.1101/2020.11.03.367391 "Analysis of intestinal biopsies obtained from asymptomatic individuals 3 months after COVID-19 onset, using immunofluorescence, electron tomography or polymerase chain reaction, revealed persistence of SARS-CoV-2 in the small bowel of 7 out of 14 volunteers. We conclude that the memory B cell response to SARS-CoV-2 evolves between 1.3 and 6.2 months after infection in a manner that is consistent with antigen persistence."

T-cell evidence
Snyder et al. Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels medRxiv 2020.07.31.20165647; doi: https://doi.org/10.1101/2020.07.31.20165647 Also see NYTimes article (free but registration required) https://www.nytimes.com/2020/11/10/health/t-cell-test-coronavirus-immunity.html

Vitamin D
Jain, A., Chaurasia, R., Sengar, N.S. et al. Analysis of vitamin D level among asymptomatic and critically ill COVID-19 patients and its correlation with inflammatory markers. Sci Rep 10, 20191 (2020). https://doi.org/10.1038/s41598-020-77093-z

WHO/COVID-NMA Summary of RCTs (Last accessed 20 Dec 2020)

RCTs
WHO/COVID-NMA consortium RCTs for pharmacologic treatments of COVID-19 with table of general characteristics of each trial

Severity
Gupta S, Hayek SS, Wang W, et al. Factors Associated With Death in Critically Ill Patients With Coronavirus Disease 2019 in the US. JAMA Intern Med. 2020;180(11):1436–1446. doi:10.1001/jamainternmed.2020.3596