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

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dc.contributor.authorAggarwal, Dinesh
dc.contributor.authorWarne, Ben
dc.contributor.authorJahun, Aminu
dc.contributor.authorHamilton, William L
dc.contributor.authorFieldman, Thomas
dc.contributor.authordu Plessis, Louis
dc.contributor.authorHill, Verity
dc.contributor.authorBlane, Beth
dc.contributor.authorWatkins, Emmeline
dc.contributor.authorWright, Elizabeth
dc.contributor.authorHall, Grant
dc.contributor.authorLudden, Catherine
dc.contributor.authorMyers, Richard
dc.contributor.authorHosmillo, Myra
dc.contributor.authorChaudhry, Yasmin
dc.contributor.authorPinckert, Malte L
dc.contributor.authorGeorgana, Iliana
dc.contributor.authorIzuagbe, Rhys
dc.contributor.authorLeek, Danielle
dc.contributor.authorNsonwu, Olisaeloka
dc.contributor.authorHughes, Gareth J
dc.contributor.authorPacker, Simon
dc.contributor.authorPage, Andrew J
dc.contributor.authorMetaxaki, Marina
dc.contributor.authorFuller, Stewart
dc.contributor.authorWeale, Gillian
dc.contributor.authorHolgate, Jon
dc.contributor.authorBrown, Christopher A
dc.contributor.authorCambridge Covid-19 testing Centre
dc.contributor.authorUniversity of Cambridge Asymptomatic COVID-19 Screening Programme Consortium
dc.contributor.authorCOVID-19 Genomics UK (COG-UK) Consortium
dc.contributor.authorHowes, Rob
dc.contributor.authorMcFarlane, Duncan
dc.contributor.authorDougan, Gordon
dc.contributor.authorPybus, Oliver G
dc.contributor.authorAngelis, Daniela De
dc.contributor.authorMaxwell, Patrick H
dc.contributor.authorPeacock, Sharon
dc.contributor.authorWeekes, Michael
dc.contributor.authorIllingworth, Christopher
dc.contributor.authorHarrison, Ewan
dc.contributor.authorMatheson, Nicholas
dc.contributor.authorGoodfellow, Ian
dc.contributor.orcidAggarwal, Dinesh [0000-0002-5938-8172]
dc.contributor.orcidWarne, Ben [0000-0003-1326-0373]
dc.contributor.orcidJahun, Aminu [0000-0002-4585-1701]
dc.contributor.orcidHamilton, William L [0000-0002-3330-353X]
dc.contributor.orciddu Plessis, Louis [0000-0003-0352-6289]
dc.contributor.orcidHill, Verity [0000-0002-3509-8146]
dc.contributor.orcidBlane, Beth [0000-0002-0996-9091]
dc.contributor.orcidWright, Elizabeth [0000-0002-8378-9072]
dc.contributor.orcidHall, Grant [0000-0003-3928-3979]
dc.contributor.orcidHosmillo, Myra [0000-0002-3514-7681]
dc.contributor.orcidChaudhry, Yasmin [0000-0002-2386-3269]
dc.contributor.orcidPinckert, Malte L [0000-0002-6072-5949]
dc.contributor.orcidIzuagbe, Rhys [0000-0001-8080-2510]
dc.contributor.orcidNsonwu, Olisaeloka [0000-0002-3024-700X]
dc.contributor.orcidHughes, Gareth J [0000-0002-3781-0117]
dc.contributor.orcidPacker, Simon [0000-0002-9157-3650]
dc.contributor.orcidPage, Andrew J [0000-0001-6919-6062]
dc.contributor.orcidMetaxaki, Marina [0000-0002-4552-1622]
dc.contributor.orcidWeale, Gillian [0000-0003-4728-5915]
dc.contributor.orcidBrown, Christopher A [0000-0001-7773-0878]
dc.contributor.orcidMcFarlane, Duncan [0000-0002-1558-7823]
dc.contributor.orcidDougan, Gordon [0000-0003-0022-965X]
dc.contributor.orcidPybus, Oliver G [0000-0002-8797-2667]
dc.contributor.orcidPeacock, Sharon [0000-0002-1718-2782]
dc.contributor.orcidWeekes, Michael [0000-0003-3196-5545]
dc.contributor.orcidIllingworth, Christopher [0000-0002-0030-2784]
dc.contributor.orcidHarrison, Ewan [0000-0003-2720-0507]
dc.contributor.orcidMatheson, Nicholas [0000-0002-3318-1851]
dc.contributor.orcidGoodfellow, Ian [0000-0002-9483-510X]
dc.description.abstractUnderstanding 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.
dc.description.sponsorshipDA is a Wellcome Clinical PhD Fellow and gratefully supported by the Wellcome Trust (Grant number: 222903/Z/21/Z). BW 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. IG is a Wellcome Senior Fellow and is supported by the Wellcome Trust (Grant number: 207498/Z/17/Z and 206298/B/17/Z). EMH is supported by a UK Research and Innovation (UKRI) Fellowship: MR/S00291X/1. CJRI 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). AJP 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). LdP and OGP 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.
dc.publisherNature Research
dc.publisher.departmentDepartment of Clinical Biochemistry
dc.publisher.departmentDepartment of Engineering
dc.publisher.departmentDepartment of Medicine
dc.rightsAttribution 4.0 International
dc.titleGenomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.
prism.publicationNameNat Commun
pubs.funder-project-idMedical Research Council (MC_PC_19027)
pubs.funder-project-idMedical Research Council (MR/P008801/1)
pubs.funder-project-idWellcome Trust (206298/B/17/Z)
pubs.funder-project-idWellcome Trust (207498/Z/17/Z)
pubs.licence-display-nameApollo Repository Deposit Licence Agreement
rioxxterms.typeJournal Article/Review
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