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

Aggarwal, Dinesh, Warne, Ben, Jahun, Aminu, Hamilton, William, Fieldman, Thomas, Plessis, Louis, Hill, Verity, Blane, Beth, Watkins, Emmeline, Wright, Elizabeth, Hall, Grant, Ludden, Catherine, Myers, Richard, Hosmillo, Myra, Goodfellow, Yasmin, Pinckert, Malte, Georgana, Iliana, Izuagbe, Rhys, Leek, Danielle, Nsonwu, Olisaeloka, Hughes, Gareth, Packer, Simon, Page, Andrew, Metaxaki, Marina, Fuller, Stewart, Weale, Gillian, Holgate, Jon, Howes, Rob, McFarlane, Duncan, Dougan, Gordon, Pybus, Oliver, Angelis, Daniela De, Maxwell, Patrick, Peacock, Sharon, Weekes, Michael, Illingworth, Chris, Harrison, Ewan, Matheson, Nicholas, Goodfellow, Ian, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg, Nelson, Andrew and McCann, Clare (2021) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Research Square Platform. pp. 1-25. (Submitted)

2d511f7c-f087-4de4-9eb6-4f16870d37d9.pdf - Submitted Version
Available under License Creative Commons Attribution 4.0.

Download (1MB) | Preview
Official URL:


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.

Item Type: Article
Additional Information: Matthew Bashton, Darren L. Smith, Gregory R. Young, Clare McCann and Andrew Nelson are member of the COVID-19 Genomics UK (COG-UK) Consortium.
Subjects: B100 Anatomy, Physiology and Pathology
C500 Microbiology
C700 Molecular Biology, Biophysics and Biochemistry
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: Elena Carlaw
Date Deposited: 09 Sep 2021 12:03
Last Modified: 09 Sep 2021 12:15

Actions (login required)

View Item View Item


Downloads per month over past year

View more statistics