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

Auger KA, Shah SS, Richardson T, et al. Association Between Statewide School Closure and COVID-19 Incidence and Mortality in the US. JAMA. 2020;324(9):859–870. doi:10.1001/jama.2020.14348

van Doremalen N, Bushmaker T, Morris DH, Holbrook MG, Gamble A, Williamson BN, et al. Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1. N Engl J Med. 2020 Mar 17;382(16):1564–7.
 * Aerosol - up to 3 hours
 * Copper - 4 hours
 * Cardboard - 24 hours
 * Plastics, stainless steel - 72 hrs

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

Chu, Derek KChu, Derek K et al. (Jun 2020) Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: a systematic review and meta-analysis The Lancet, Volume 395, Issue 10242, 1973 - 1987

Contact tracing
John Hopkins online coursera course - COVID-19 Contact Tracing

PPE
CDC PPE FAQs

WHO - Personal protective equipment for COVID-19

Transmission Dynamics
Cheng H, Jian S, Liu D, et al. (May 2020) Contact Tracing Assessment of COVID-19 Transmission Dynamics in Taiwan and Risk at Different Exposure Periods Before and After Symptom Onset. JAMA Intern Med. 2020;180(9):1156–1163. doi:10.1001/jamainternmed.2020.2020

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

Lee S, Kim T, Lee E, et al. Clinical Course and Molecular Viral Shedding Among Asymptomatic and Symptomatic Patients With SARS-CoV-2 Infection in a Community Treatment Center in the Republic of Korea. JAMA Intern Med. 2020;180(11):1447–1452. doi:10.1001/jamainternmed.2020.3862

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

Aschwanden, C. (Oct 2020) The false promise of herd immunity for COVID-19. Nature News Feature. Nature 587, 26-28 (2020). doi: https://doi.org/10.1038/d41586-020-02948-4

Tobias S. Brett, Pejman Rohani (Oct 2020) Transmission dynamics reveal the impracticality of COVID-19 herd immunity strategies Proceedings of the National Academy of Sciences Oct 2020, 117 (41) 25897-25903; DOI: 10.1073/pnas.2008087117

Presentation and pathophysiology
Kumar R, Lee MH, Mickael C, et al. (Oct 2020) Pathophysiology and potential future therapeutic targets using preclinical models of COVID-19. ERJ Open Res. 2020;6(4):00405-2020. Published 2020 Dec 7. doi:10.1183/23120541.00405-2020

Varga, Zsuzsanna et al. Endothelial cell infection and endotheliitis in COVID-19 The Lancet, Volume 395, Issue 10234, 1417 - 1418 DOI: https://doi.org/10.1016/S0140-6736(20)30937-5

Garvin MR, Alvarez C, Miller JI, Prates ET, Walker AM, Amos BK, et al. A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm. van de Veerdonk FL, van der Meer JW, van de Veerdonk FL, Little R, editors. eLife. 2020 Jul 7;9:e59177.

Symptoms
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.

Mental health in a pandemic
Taylor, S, Landry, CA, Paluszek, MM, Fergus, TA, McKay, D, Asmundson, GJG. COVID stress syndrome: Concept, structure, and correlates. Depression and Anxiety. 2020; 37: 706– 714. https://doi.org/10.1002/da.23071

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

The UK strain Dec 2020 VUI202012/01
Baker L. (19 Dec 2020) Independent SAGE scientists share update as new mutation triggers today’s lockdown announcements. Healthcare Newsdesk.

"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

Tests, viral persistence and immunity
Dan JM et al Immunological memory to SARS-CoV-2 assessed for greater than six months after infection. bioRxiv 2020.11.15.383323; doi: https://doi.org/10.1101/2020.11.15.383323

PCR
Lauren M. Kucirka, Stephen A. Lauer, Oliver Laeyendecker, et al. Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction–Based SARS-CoV-2 Tests by Time Since Exposure. Ann Intern Med.2020;173:262-267. [Epub ahead of print 13 May 2020]. doi:10.7326/M20-1495

Woloshin S, Patel N, Kesselheim AS. False Negative Tests for SARS-CoV-2 Infection — Challenges and Implications. New England Journal of Medicine. 2020 Aug 6;383(6):e38.

Isikbay M, Henry TS, Frank JA, Hope MD. When to rule out COVID-19: How many negative RT-PCR tests are needed? Respiratory Medicine Case Reports. 2020 Jan 1;31:101192.

Lateral flow tests
[papers needed]

Antibodies and 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

Choe PG, Kang CK, Suh HJ, Jung J, Song K-H, Bang JH, et al. Waning antibody responses in asymptomatic and symptomatic SARS-CoV-2 infection. Emerg Infect Dis. 2021 Jan [published online Dec 2020]. https://doi.org/10.3201/eid2701.203515

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

[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/Cellular immunity
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

Schwarzkopf S, Krawczyk A, Knop D, Klump H, Heinold A, Heinemann FM, et al. Cellular immunity in COVID-19 convalescents with PCR-confirmed infection but with undetectable SARS-CoV-2–specific IgG. Emerg Infect Dis. 2021 Jan [original pub date Oct 2020, cited Dec 2020]. https://doi.org/10.3201/eid2701.203772

Pregnancy and perinatal
Allotey John, Stallings Elena, Bonet Mercedes, Yap Magnus, Chatterjee Shaunak, Kew Tania et al. Clinical manifestations, risk factors, and maternal and perinatal outcomes of coronavirus disease 2019 in pregnancy: living systematic review and meta-analysis BMJ 2020; 370 :m3320

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

Please note the expression of concern on the following article: Maghbooli Z, Sahraian MA, Ebrahimi M, Pazoki M, Kafan S, Tabriz HM, et al. (2020) Vitamin D sufficiency, a serum 25-hydroxyvitamin D at least 30 ng/mL reduced risk for adverse clinical outcomes in patients with COVID-19 infection. PLoS ONE 15(9): e0239799. doi:10.1371/journal.pone.0239799

WHO/COVID-NMA Summary of Vitamin D 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

Rodrigues TS et al. (cited Dec 2020) Inflammasomes are activated in response to SARS-CoV-2 infection and are associated with COVID-19 severity in patients. J Exp Med. 2021 Mar 1;218(3):e20201707. doi: 10.1084/jem.20201707. PMID: 33231615; PMCID: PMC7684031.

Curtin, K.M., Pawloski, L.R., Mitchell, P. and Dunbar, J. (2020), COVID‐19 and Morbid Obesity: Associations and Consequences for Policy and Practice. World Medical & Health Policy, 12: 512-532. https://doi.org/10.1002/wmh3.361

Michaela R. Anderson, Joshua Geleris, David R. Anderson, et al. Body Mass Index and Risk for Intubation or Death in SARS-CoV-2 Infection: A Retrospective Cohort Study. Ann Intern Med.2020;173:782-790. [Epub ahead of print 29 July 2020]. doi:10.7326/M20-3214

Sara Y. Tartof, Lei Qian, Vennis Hong, et al. Obesity and Mortality Among Patients Diagnosed With COVID-19: Results From an Integrated Health Care Organization. Ann Intern Med.2020;173:773-781. [Epub ahead of print 12 August 2020]. doi:10.7326/M20-3742