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 du 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, G. Hughes, Simon Packer, Andrew J. Page, Marina Metaxaki, Stewart Fuller, Gillian Weale, Jon Holgate, Christopher Brown, Alexandra L. Orton, Julie A. Douthwaite, Steve Rees, Christopher Brown, Roger Clark, Daniel R. Jones, Fred Kuenzi, Jennifer Rankin, Ian D. Waddell, Patrick H. Maxwell, Nicholas J. Matheson, Chris Abell, Vickie Braithwaite, Craig Brierley, Jon Crowcroft, Aastha Dahal, Kathryn Faulkner, Michael Glover, Ian Goodfellow, Jane Greatorex, Laura P. James, Paul J. Lehner, Ian Leslie, Kathleen Liddell, Ben Margolis, Sally Morgan, Linda Sheridan, Sally Valletta, Anna Vignoles, Martin Vinnell, Mark R. Wills, Sarah Hilborne, Sarah Berry, Mahin Bagheri Kahkeshi, Dawn Hancock, Jennifer Winster, Jessica Enright, Richard J. Samworth, Vijay Samtani, Gabriela Ahmadi‐Assalemi, Tom Feather, Robin Goodall, Steve Hoensch, Dean Johnson, Martin Hunt, Nick Mathieson, К Е Никитина, Zara Sheldrake, Martin Keen, Aris Sato, David J. Connor, Jonathan Tolhurst, Jack Williman, Victoria Hollamby, Sinead Jordan, Tania Fatseas, Peter C. Taylor, Christine Georgiou, Michelle Caspersz, Claire McNulty, Richard B. Davies, Rebecca Clarke, Darius Danaei, Rory Dyer, Rob Glew, Oliver Lambson, Karen DiValerio Gibbs, Barbara Mozdzen, Gabor Raub, Asako Radecki, Phil White, Robert C Hughes
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.