Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning
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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.
Nickbakhsh , S , Hughes , J , Christofidis , N , Griffiths , E , Shaaban , S , Enright , J , Smollett , K , Nomikou , K , Palmalux , N , Tong , L , Carmichael , S , Sreenu , V B , Orton , R , Goldstein , E J , Tomb , R M , The COVID-19 Genomics UK (COG-UK) Consortium , Templeton , K , Gunson , R N , da Silva Filipe , A , Milosevic , C , Thomson , E , Robertson , D L , Holden , M , Illingworth , C J R & Smith-Palmer , A 2022 , ' Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning ' , Scientific Reports , vol. 12 , 11735 . https://doi.org/10.1038/s41598-022-15661-1
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DescriptionFunding: The CVR authors are supported by the Medical Research Council [MC_UU_12014/12 and MC_UU_12018/12]. COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) [Grant code: MC_PC_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute.
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