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

The COVID-19 Genomics UK (COG-UK) Consortium, Dinesh Aggarwal*, Ben Warne, Aminu Jahun, William Hamilton, Thomas Fieldman, Louis Plessis, Verity Hill, Beth Blane, Emmeline Watkins, Elizabeth Wright, Grant Hall, Catherine Ludden, Richard Myers, Myra Hosmillo, Yasmin Goodfellow, Malte Pinckert, Iliana Georgana, Rhys Izuagbe, Danielle LeekOlisaeloka Nsonwu, Gareth Hughes, Simon Packer, Andrew Page, Marina Metaxaki, Stewart Fuller, Gillian Weale, Jon Holgate, Rob Howes, Duncan McFarlane, Gordon Dougan, Oliver Pybus, Daniela De Angelis, Patrick Maxwell, Sharon Peacock, Michael Weekes, Chris Illingworth, Ewan Harrison, Nicholas Matheson, Ian G. Goodfellow, Matthew Bashton, Darren Smith, Andrew Nelson, Greg Young, Clare McCann

*Corresponding author for this work

Research output: Working paperPreprint

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Understanding the drivers for spread of SARS-CoV-2 in higher education settings is important to limit transmission between students, and onward spread into at-risk populations. In this study, we prospectively sequenced 482 SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge from 5 October to 6 December 2020. We performed a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. After a limited number of viral introductions into the university, the majority of student cases were linked to a single genetic cluster, likely dispersed across the university following social gatherings at a venue outside the university. We identified considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and dramatically reduced following a national lockdown. We observed that transmission clusters were largely segregated within the university or within the community. This 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 languageEnglish
Number of pages25
Publication statusSubmitted - 19 May 2021


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