Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.
Aggarwal D., Warne B., Jahun AS., Hamilton WL., Fieldman T., du Plessis L., Hill V., Blane B., Watkins E., Wright E., Hall G., Ludden C., Myers R., Hosmillo M., Chaudhry Y., Pinckert ML., Georgana I., Izuagbe R., Leek D., Nsonwu O., Hughes GJ., Packer S., Page AJ., Metaxaki M., Fuller S., Weale G., Holgate J., Brown CA., Cambridge Covid-19 testing Centre None., University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium None., COVID-19 Genomics UK (COG-UK) Consortium None., Howes R., McFarlane D., Dougan G., Pybus OG., Angelis DD., Maxwell PH., Peacock SJ., Weekes MP., Illingworth C., Harrison EM., Matheson NJ., Goodfellow IG.
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.