The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities

Aggarwal, Dinesh, Myers, Richard, Hamilton, William L, Bharucha, Tehmina, Tumelty, Niamh M, Brown, Colin S, Meader, Emma J, Connor, Tom, Smith, Darren L, Bradley, Declan T, Robson, Samuel, Bashton, Matthew, Shallcross, Laura, Zambon, Maria, Goodfellow, Ian, Chand, Meera, O'Grady, Justin, Török, M Estée, Peacock, Sharon J, Page, Andrew J, The COVID-19 Genomics UK (COG-UK) Consortium, , Allan, John, Loh, Joshua, Nelson, Andrew, Yew, Wen C. and Young, Gregory R. (2021) The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. The Lancet Microbe. pp. 1-9. ISSN 2666-5247 (In Press)

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Official URL: https://doi.org/10.1016/S2666-5247(21)00208-1

Abstract

We reviewed all genomic epidemiology studies on COVID-19 in long-term care facilities (LTCFs) that had been published to date. We found that staff and residents were usually infected with identical, or near identical, SARS-CoV-2 genomes. Outbreaks usually involved one predominant cluster, and the same lineages persisted in LTCFs despite infection control measures. Outbreaks were most commonly due to single or few introductions followed by a spread rather than a series of seeding events from the community into LTCFs. The sequencing of samples taken consecutively from the same individuals at the same facilities showed the persistence of the same genome sequence, indicating that the sequencing technique was robust over time. When combined with local epidemiology, genomics allowed probable transmission sources to be better characterised. The transmission between LTCFs was detected in multiple studies. The mortality rate among residents was high in all facilities, regardless of the lineage. Bioinformatics methods were inadequate in a third of the studies reviewed, and reproducing the analyses was difficult because sequencing data were not available in many facilities

Item Type: Article
Additional Information: Funding information: We thank members of the COVID-19 Genomics UK Consortium for their contributions to generating the data used in some of these studies. We thank Judith Pell for critically assessing and improving this manuscript. DA is a Clinical PhD Fellow and gratefully supported by the Wellcome Trust (grant number 222903/Z/21/Z). AJP and JO'G gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain (project number BB/R012504/1) and its constituent project (project number BBS/E/F/000PR10352), and also the Quadram Institute Bioscience BBSRC-funded Core Capability grant (project number BB/CCG1860/1). SR, DLS, and MB gratefully acknowledge support from Research England's Expanding Excellence in England Fund. IG is a Wellcome Senior Fellow and supported by the Wellcome Trust (grant number 207498/Z/17/Z). MET was supported by a Clinician Scientist Fellowship (funded by the Academy of Medical Sciences and the Health Foundation) and by the National institutes of Health Research Cambridge Biomedical Research Centre. The COVID-19 Genomics UK Consortium is supported by funding from the Medical Research Council part of UK Research & Innovation and the National Institute of Health Research and Genome Research, operating as the Wellcome Sanger Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The UK studies were done as part of surveillance for COVID-19 infections under the auspices of Section 251 of the National Health Service Act 2006 or Regulation 3 of The Health Service (Control of Patient Information) Regulations 2002, or both. They therefore did not require individual patient consent or ethical approval. The COVID-19 Genomics UK Consortium study protocol was approved by the Public Health England Research Ethics Governance Group (reference number R&D NR0195).
Subjects: B900 Others in Subjects allied to Medicine
C500 Microbiology
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: John Coen
Date Deposited: 19 Oct 2021 10:00
Last Modified: 19 Oct 2021 10:00
URI: http://nrl.northumbria.ac.uk/id/eprint/47512

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