Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

Sema Nickbakhsh*, Joseph Hughes, Nicolaos Christofidis, Emily Griffiths, Sharif Shaaban, Jessica Enright, Katherine Smollett, Kyriaki Nomikou, Natasha Palmalux, Lily Tong, Stephen Carmichael, Vattipally B. Sreenu, Richard Orton, Emily J. Goldstein, Rachael M. Tomb, The COVID-19 Genomics UK (COG-UK) Consortium, Kate Templeton, Rory N. Gunson, Ana da Silva Filipe, Catriona MilosevicEmma Thomson, David L. Robertson, Matthew T.G. Holden, Christopher J.R. Illingworth*, Alison Smith-Palmer , Darren L. Smith, Matthew Bashton, Gregory R. Young, Clare M. McCann, Andrew Nelson, Matthew R. Crown, John H. Henderson, Wen C. Yew

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)
9 Downloads (Pure)


Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These four outbreaks were curtailed within a week following implementation of control measures. The impact of student infections on the local community was short-term despite an underlying increase in community infections. Our study highlights the need for context-specific information in the formation of public health policy for higher educational settings.

Original languageEnglish
Article number11735
Pages (from-to)1-17
Number of pages17
JournalScientific Reports
Issue number1
Early online date19 Jul 2022
Publication statusPublished - Dec 2022


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