Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Aggarwal, Dinesh, Warne, Ben, Jahun, Aminu S., Hamilton, William L., Fieldman, Thomas, du Plessis, Louis, Hill, Verity, Blane, Beth, Watkins, Emmeline, Wright, Elizabeth, Hall, Grant, Ludden, Catherine, Myers, Richard, Hosmillo, Myra, Chaudhry, Yasmin, Pinckert, Malte L., Georgana, Iliana, Izuagbe, Rhys, Leek, Danielle, Nsonwu, Olisaeloka, Hughes, Gareth J., Packer, Simon, Page, Andrew J., Metaxaki, Marina, Fuller, Stewart, Weale, Gillian, Holgate, Jon, Brown, Christopher A., , The Cambridge Covid-19 Testing Centre, , University of Cambridge Asymptomatic COVID-19 Screening Programm, , The COVID-19 Genomics UK (COG-UK) Consortium, Howes, Rob, McFarlane, Duncan, Dougan, Gordon, Pybus, Oliver G., De Angelis, Daniela, Maxwell, Patrick H., Peacock, Sharon J., Weekes, Michael P., Illingworth, Christopher, Harrison, Ewan M., Matheson, Nicholas J. and Goodfellow, Ian G. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13. ISSN 2041-1723

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Abstract

Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.

Item Type: Article
Additional Information: Acknowledgements: Authors A.S.J., W.H. and T.F., and authors L.d.P. and V.H. contributed equally. We thank members of the COVID-19 Genomics Consortium UK and NHS Test and Trace contact tracers for their contributions to generating data used in this study. We thank the Sanger Covid Team for assisting with Samples and Logistics. We are grateful to all students and staff at the University of Cambridge who have contributed to the COVID-19 response during Michaelmas Term. We are grateful to all staff members of the Cambridge COVID-19 Testing Centre for generating qPCR data. D.A. is a Wellcome Clinical PhD Fellow and gratefully supported by the Wellcome Trust (Grant number: 222903/Z/21/Z). B.W. receives funding from the University of Cambridge and the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre (BRC) at the Cambridge University Hospitals NHS Foundation Trust. I.G. is a Wellcome Senior Fellow and is supported by the Wellcome Trust (Grant number: 207498/Z/17/Z and 206298/B/17/Z). E.M.H. is supported by a UK Research and Innovation (UKRI) Fellowship: MR/S00291X/1. C.J.R.I. acknowledges Medical Research Council (MRC) funding (ref: MC_UU_00002/11). NJM is supported by the MRC (CSF MR/P008801/1) and NHSBT (WPA15-02). A.J.P. 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 BB/R012504/1 and its constituent project BBS/E/F/000PR10352, also Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1). L.d.P. and O.G.P. were supported by the Oxford Martin School. This research was supported by the NIHR Cambridge BRC. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health and Social Care. The COVID-19 Genomics UK Consortium is supported by funding from the MRC part of UK Research & Innovation (UKRI), the National Institute of Health Research and Genome Research Limited, operating as the Wellcome Sanger Institute. The Cambridge Covid-19 testing Centre is funded by the Department of Health and Social Care, UK Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. For the purpose of Open Access, the author has applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission. Publisher Copyright: © 2022, The Author(s).
Uncontrolled Keywords: physics and astronomy(all),chemistry(all),biochemistry, genetics and molecular biology(all),sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/3100
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
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Depositing User: LivePure Connector
Date Deposited: 24 May 2022 15:00
Last Modified: 10 Jun 2022 15:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/85095
DOI: 10.1038/s41467-021-27942-w

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