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

Nickbakhsh, Sema, Hughes, Joseph, Christofidis, Nicolaos, Griffiths, Emily, Shaaban, Sharif, Enright, Jessica, Smollett, Katherine, Nomikou, Kyriaki, Palmalux, Natasha, Tong, Lily, Carmichael, Stephen, Sreenu, Vattipally B., Orton, Richard, Goldstein, Emily J., Tomb, Rachael M., The COVID-19 Genomics UK (COG-UK) Consortium, Templeton, Kate, Gunson, Rory N., da Silva Filipe, Ana, Milosevic, Catriona, Thomson, Emma, Robertson, David L., Holden, Matthew T. G., Illingworth, Christopher J. R. and Smith-Palmer, Alison (2022) Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12 (1). ISSN 2045-2322

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Abstract

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.

Item Type: Article
Additional Information: Funding Information: We thank the Public Health Microbiology and Real-Time Epidemiology teams at Public Health Scotland, and the Public Health Protection Unit at NHS Greater Glasgow and Clyde, who developed and managed the surveillance infrastructure and data sharing that enabled this study as part of the COVID-19 response in Scotland. We also thank the University of Glasgow, in particular Selina Woolcott and Maureen Hood, for providing helpful contextual information. 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. Funding Information: We thank the Public Health Microbiology and Real-Time Epidemiology teams at Public Health Scotland, and the Public Health Protection Unit at NHS Greater Glasgow and Clyde, who developed and managed the surveillance infrastructure and data sharing that enabled this study as part of the COVID-19 response in Scotland. We also thank the University of Glasgow, in particular Selina Woolcott and Maureen Hood, for providing helpful contextual information. 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. Publisher Copyright: © 2022, The Author(s).
Uncontrolled Keywords: general,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1000
Faculty \ School: Faculty of Science > School of Biological Sciences
Faculty of Medicine and Health Sciences > Norwich Medical School
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Depositing User: LivePure Connector
Date Deposited: 22 Sep 2022 09:31
Last Modified: 26 Sep 2022 06:03
URI: https://ueaeprints.uea.ac.uk/id/eprint/88584
DOI: 10.1038/s41598-022-15661-1

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