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

The Cambridge Covid-19 testing Centre; University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium; The COVID-19 Genomics UK (COG-UK) Consortium; Marta Gallis

doi:10.1038/s41467-021-27942-w

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

The Cambridge Covid-19 testing Centre, University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium, The COVID-19 Genomics UK (COG-UK) Consortium, Marta Gallis

Research output: Contribution to journal › Article › peer-review

26 Citations (Scopus)

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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.

Original language	English
Article number	751
Pages (from-to)	1-16
Number of pages	16
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-27942-w
Publication status	Published - 8 Feb 2022
Externally published	Yes

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Cite this

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title = "Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission",

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.",

author = "{The Cambridge Covid-19 testing Centre} and {University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium} and {The COVID-19 Genomics UK (COG-UK) Consortium} and Dinesh Aggarwal and Ben Warne and Jahun, {Aminu S.} and Hamilton, {William L.} and Thomas Fieldman and Plessis, {Louis du} and Verity Hill and Beth Blane and Emmeline Watkins and Elizabeth Wright and Grant Hall and Catherine Ludden and Richard Myers and Myra Hosmillo and Yasmin Chaudhry and Pinckert, {Malte L.} and Iliana Georgana and Rhys Izuagbe and Danielle Leek and Olisaeloka Nsonwu and Hughes, {Gareth J.} and Simon Packer and Page, {Andrew J.} and Marina Metaxaki and Stewart Fuller and Gillian Weale and Jon Holgate and Christopher Brown and Alexandra Orton and Julie Douthwaite and Steve Rees and Roger Clark and Jones, {Daniel R.} and Fred Kuenzi and Jennifer Rankin and Ian Waddell and Patrick Maxwell and Nicholas Matheson and Chris Abell and Vickie Braithwaite and Craig Brierley and Jon Crowcroft and Aastha Dahal and Kathryn Faulkner and Michael Glover and Jane Greatorex and Laura James and Paul Lehner and Marta Gallis and Rob Howes and Duncan McFarlane and Gordon Dougan and Pybus, {Oliver G.} and Angelis, {Daniela De} and Patrick Maxwell and Peacock, {Sharon J.} and Weekes, {Michael P.} and Illingworth, {Christopher J.R.} and Harrison, {Ewan M.} and Matheson, {Nicholas J.} and Goodfellow, {Ian G.}",

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Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. / The Cambridge Covid-19 testing Centre; University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium; The COVID-19 Genomics UK (COG-UK) Consortium et al.
In: Nature Communications, Vol. 13, No. 1, 751, 08.02.2022, p. 1-16.

Research output: Contribution to journal › Article › peer-review

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AU - Weale, Gillian

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AU - Rees, Steve

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AU - Maxwell, Patrick

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AU - Braithwaite, Vickie

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AU - Pybus, Oliver G.

AU - Angelis, Daniela De

AU - Maxwell, Patrick

AU - Peacock, Sharon J.

AU - Weekes, Michael P.

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

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