TY - JOUR
T1 - Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning
AU - Nickbakhsh, Sema
AU - Hughes, Joseph
AU - Christofidis, Nicolaos
AU - Griffiths, Emily
AU - Shaaban, Sharif
AU - Enright, Jessica
AU - Smollett, Katherine
AU - Nomikou, Kyriaki
AU - Palmalux, Natasha
AU - Tong, Lily
AU - Carmichael, Stephen
AU - Sreenu, Vattipally B.
AU - Orton, Richard
AU - Goldstein, Emily J.
AU - Tomb, Rachael M.
AU - The COVID-19 Genomics UK (COG-UK) Consortium
AU - Templeton, Kate
AU - Gunson, Rory N.
AU - da Silva Filipe, Ana
AU - Milosevic, Catriona
AU - Thomson, Emma
AU - Robertson, David L.
AU - Holden, Matthew T.G.
AU - Illingworth, Christopher J.R.
AU - Smith-Palmer , Alison
AU - Smith, Darren L.
AU - Bashton, Matthew
AU - Young, Gregory R.
AU - McCann, Clare M.
AU - Nelson, Andrew
AU - Crown, Matthew R.
AU - Henderson, John H.
AU - Yew, Wen C.
N1 - 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).
PY - 2022/12
Y1 - 2022/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85134374428&partnerID=8YFLogxK
U2 - 10.1038/s41598-022-15661-1
DO - 10.1038/s41598-022-15661-1
M3 - Article
C2 - 35853960
AN - SCOPUS:85134374428
SN - 2045-2322
VL - 12
SP - 1
EP - 17
JO - Scientific Reports
JF - Scientific Reports
IS - 1
M1 - 11735
ER -
