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

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Nickbakhsh_2022_SR_Genomic_epidemiology_SARS_CoV_2_CC.pdf (3.530Mb)
Date
19/07/2022
Author
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
Illingworth, Christopher J. R.
Smith-Palmer, Alison
Keywords
QH426 Genetics
RA0421 Public health. Hygiene. Preventive Medicine
3rd-DAS
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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.
Citation
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
Publication
Scientific Reports
Status
Peer reviewed
DOI
https://doi.org/10.1038/s41598-022-15661-1
ISSN
2045-2322
Type
Journal article
Rights
Copyright © The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Description
Funding: 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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  • University of St Andrews Research
URI
http://hdl.handle.net/10023/25737

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