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

Nickbakhsh, S. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12, 11735. (doi: 10.1038/s41598-022-15661-1) (PMID:35853960) (PMCID:PMC9296497)

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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:Articles
Additional 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.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Robertson, Professor David and Tomb, Dr Rachael and Tong, Dr Lily and Palmalux, Natasha and Orton, Dr Richard and Da Silva Filipe, Dr Ana and Gunson, Dr Rory and Hughes, Dr Joseph and Thomson, Professor Emma and Nickbakhsh, Dr Sema and Carmichael, Dr Stephen and Nomikou, Dr Kyriaki and Illingworth, Dr Chris and Enright, Dr Jessica and Smollett, Dr Katherine
Authors: 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., 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. T.G., Illingworth, C. J.R., and Smith-Palmer, A.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
College of Medical Veterinary and Life Sciences > School of Health & Wellbeing > General Practice and Primary Care
College of Medical Veterinary and Life Sciences > School of Health & Wellbeing > MRC/CSO SPHSU
College of Science and Engineering > School of Computing Science
College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
Journal Name:Scientific Reports
Publisher:Nature Research
ISSN:2045-2322
ISSN (Online):2045-2322
Copyright Holders:Copyright © The Author(s) 2022
First Published:First published in Scientific Reports 12:11735
Publisher Policy:Reproduced under a Creative Commons Licence

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
172630014Cross-Cutting Programme – Viral Genomics and Bioinformatics (Programme 9)David RobertsonMedical Research Council (MRC)MC_UU_12014/12III - Centre for Virus Research