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; 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.; Howes, Rob; McFarlane, Duncan; Dougan, Gordon; Pybus, Oliver G.; De Angelis, Daniela; Maxwell, Patrick H.; Peacock, Sharon J.; Weekes, Michael P.; Illingworth, Chris; Harrison, Ewan M.; Matheson, Nicholas J.; Goodfellow, Ian G.

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

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, Richard Myers, Myra Hosmillo, Yasmin Chaudhry, Malte L. Pinckert, Iliana Georgana, Rhys Izuagbe, Danielle Leek, Olisaeloka Nsonwu, Gareth J. Hughes, Simon Packer, Andrew J. Page, Marina Metaxaki, Stewart Fuller, Gillian Weale, Jon Holgate, Christopher A. Brown, Rob Howes, Duncan McFarlane, Gordon Dougan, Oliver G. Pybus, Daniela De Angelis, Patrick H. Maxwell, Sharon J. Peacock, Michael P. Weekes, Chris Illingworth, Ewan M. Harrison (), Nicholas J. Matheson () and Ian G. Goodfellow ()
Additional contact information
Dinesh Aggarwal: University of Cambridge, Department of Medicine
Ben Warne: University of Cambridge, Department of Medicine
Aminu S. Jahun: University of Cambridge, Department of Pathology, Division of Virology
William L. Hamilton: University of Cambridge, Department of Medicine
Thomas Fieldman: University of Cambridge, Department of Medicine
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
Richard Myers: Public Health England
Myra Hosmillo: Cambridge University Hospital NHS Foundation Trust
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
Rob Howes: Discovery Sciences, R&D, AstraZenenca
Duncan McFarlane: University of Cambridge
Gordon Dougan: University of Cambridge, Department of Medicine
Oliver G. Pybus: University of Oxford
Daniela De Angelis: Public Health England
Patrick H. Maxwell: University of Cambridge, Department of Medicine
Sharon J. Peacock: University of Cambridge, Department of Medicine
Michael P. Weekes: Cambridge University Hospital NHS Foundation Trust
Chris Illingworth: University of Cambridge
Ewan M. Harrison: University of Cambridge, Department of Medicine
Nicholas J. Matheson: University of Cambridge, Department of Medicine
Ian G. Goodfellow: University of Cambridge, Department of Pathology, Division of Virology

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-021-27942-w

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