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

Author

Listed:
  • Dinesh Aggarwal

    (University of Cambridge, Department of Medicine
    Public Health England
    Cambridge University Hospital NHS Foundation Trust
    Wellcome Sanger Institute, Hinxton)

  • Ben Warne

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust
    Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge)

  • Aminu S. Jahun

    (University of Cambridge, Department of Pathology, Division of Virology)

  • William L. Hamilton

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust
    Wellcome Sanger Institute, Hinxton)

  • Thomas Fieldman

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust)

  • Louis Plessis

    (University of Oxford)

  • Verity Hill

    (University of Edinburgh)

  • Beth Blane

    (University of Cambridge, Department of Medicine)

  • Emmeline Watkins

    (Cambridgeshire County Council and Peterborough City Council)

  • Elizabeth Wright

    (Cambridgeshire County Council and Peterborough City Council)

  • Grant Hall

    (University of Cambridge, Department of Pathology, Division of Virology)

  • Catherine Ludden

    (University of Cambridge, Department of Medicine
    Public Health England)

  • Richard Myers

    (Public Health England)

  • Myra Hosmillo

    (Cambridge University Hospital NHS Foundation Trust
    University of Cambridge, Department of Pathology, Division of Virology)

  • Yasmin Chaudhry

    (University of Cambridge, Department of Pathology, Division of Virology)

  • Malte L. Pinckert

    (University of Cambridge, Department of Pathology, Division of Virology)

  • Iliana Georgana

    (University of Cambridge, Department of Pathology, Division of Virology)

  • Rhys Izuagbe

    (University of Cambridge, Department of Pathology, Division of Virology)

  • Danielle Leek

    (University of Cambridge, Department of Medicine)

  • Olisaeloka Nsonwu

    (Public Health England)

  • Gareth J. Hughes

    (Public Health England)

  • Simon Packer

    (Public Health England)

  • Andrew J. Page

    (Norwich Research Park)

  • Marina Metaxaki

    (University of Cambridge, Department of Medicine)

  • Stewart Fuller

    (University of Cambridge, Department of Medicine)

  • Gillian Weale

    (University of Cambridge)

  • Jon Holgate

    (University of Cambridge)

  • Christopher A. Brown

    (Discovery Sciences, R&D, AstraZenenca
    Chesterford Research Park)

  • Rob Howes

    (Discovery Sciences, R&D, AstraZenenca)

  • Duncan McFarlane

    (University of Cambridge)

  • Gordon Dougan

    (University of Cambridge, Department of Medicine
    Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge)

  • Oliver G. Pybus

    (University of Oxford)

  • Daniela De Angelis

    (Public Health England
    University of Cambridge)

  • Patrick H. Maxwell

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust)

  • Sharon J. Peacock

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust)

  • Michael P. Weekes

    (Cambridge University Hospital NHS Foundation Trust
    University of Cambridge)

  • Chris Illingworth

    (University of Cambridge
    University of Cambridge
    MRC-University of Glasgow Centre for Virus Research)

  • Ewan M. Harrison

    (University of Cambridge, Department of Medicine
    Public Health England
    Wellcome Sanger Institute, Hinxton
    University of Cambridge)

  • Nicholas J. Matheson

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust
    Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge
    NHS Blood and Transplant)

  • Ian G. Goodfellow

    (University of Cambridge, Department of Pathology, Division of Virology)

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.

Suggested Citation

  • Dinesh Aggarwal & Ben Warne & Aminu S. Jahun & William L. Hamilton & Thomas Fieldman & Louis Plessis & Verity Hill & Beth Blane & Emmeline Watkins & Elizabeth Wright & Grant Hall & Catherine Ludden & , 2022. "Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-021-27942-w
    DOI: 10.1038/s41467-021-27942-w
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