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

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

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)

Heading text
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

Genomic Epidemiology	https://nextstrain.org/ncov 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	www.covid19cellatlas.org

List of Clinical Trials https://clinicaltrials.gov/ct2/home

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
[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

[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