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

The COVID-19 Genomics UK (COG-UK) consortium; Sema Nickbakhsh; Joseph Hughes; Nicolaos Christofidis; Emily Griffiths; Sharif Shaaban; Jessica Enright; Katherine Smollett; Kyriaki Nomikou; Natasha Palmalux; Lily Tong; Stephen Carmichael; Vattipally B. Sreenu; Richard J. Orton; Emily J. Goldstein; Rachael M. Tomb; Samuel C. Robson; Thomas R. Connor; Nicholas J. Loman; Tanya Golubchik; Rocio T.Martinez Nunez; David Bonsall; Andrew Rambaut; Luke B. Snell; Rich Livett; Catherine Ludden; Sally Corden; Eleni Nastouli; Gaia Nebbia; Ian Johnston; Katrina Lythgoe; M. Estee Torok; Ian G. Goodfellow; Jacqui A. Prieto; Kordo Saeed; David K. Jackson; Catherine Houlihan; Dan Frampton; William L. Hamilton; Adam A. Witney; Giselda Bucca; Cassie F. Pope; Catherine Moore; Emma C. Thomson; Ewan M. Harrison; Colin P. Smith; Fiona Rogan; Shaun M. Beckwith; Abigail Murray; Jonathan Edgeworth; Aaron R. Jeffries

doi:10.1038/s41598-022-15661-1

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

The COVID-19 Genomics UK (COG-UK) consortium, Sema Nickbakhsh^*, Joseph Hughes, Nicolaos Christofidis, Emily Griffiths, Sharif Shaaban, Jessica Enright, Katherine Smollett, Kyriaki Nomikou, Natasha Palmalux, Lily Tong, Stephen Carmichael, Vattipally B. Sreenu, Richard J. Orton, Emily J. Goldstein, Rachael M. Tomb, Samuel C. Robson, Thomas R. Connor, Nicholas J. Loman, Tanya GolubchikRocio T.Martinez Nunez, David Bonsall, Andrew Rambaut, Luke B. Snell, Rich Livett, Catherine Ludden, Sally Corden, Eleni Nastouli, Gaia Nebbia, Ian Johnston, Katrina Lythgoe, M. Estee Torok, Ian G. Goodfellow, Jacqui A. Prieto, Kordo Saeed, David K. Jackson, Catherine Houlihan, Dan Frampton, William L. Hamilton, Adam A. Witney, Giselda Bucca, Cassie F. Pope, Catherine Moore, Emma C. Thomson, Ewan M. Harrison, Colin P. Smith, Fiona Rogan, Shaun M. Beckwith, Abigail Murray, Jonathan Edgeworth, Aaron R. Jeffries

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

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.

Original language	English
Article number	11735
Journal	Scientific Reports
Volume	12
Issue number	1
Early online date	19 Jul 2022
DOIs	https://doi.org/10.1038/s41598-022-15661-1
Publication status	Published - 1 Dec 2022

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The COVID-19 Genomics UK (COG-UK) consortium, 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. J., Goldstein, E. J., Tomb, R. M., Robson, S. C., Connor, T. R., Loman, N. J., ... Jeffries, A. R. (2022). Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12(1), Article 11735. https://doi.org/10.1038/s41598-022-15661-1

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

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.",

author = "{The COVID-19 Genomics UK (COG-UK) consortium} and Sema Nickbakhsh and Joseph Hughes and Nicolaos Christofidis and Emily Griffiths and Sharif Shaaban and Jessica Enright and Katherine Smollett and Kyriaki Nomikou and Natasha Palmalux and Lily Tong and Stephen Carmichael and Sreenu, {Vattipally B.} and Orton, {Richard J.} and Goldstein, {Emily J.} and Tomb, {Rachael M.} and Robson, {Samuel C.} and Connor, {Thomas R.} and Loman, {Nicholas J.} and Tanya Golubchik and Nunez, {Rocio T.Martinez} and David Bonsall and Andrew Rambaut and Snell, {Luke B.} and Rich Livett and Catherine Ludden and Sally Corden and Eleni Nastouli and Gaia Nebbia and Ian Johnston and Katrina Lythgoe and Torok, {M. Estee} and Goodfellow, {Ian G.} and Prieto, {Jacqui A.} and Kordo Saeed and Jackson, {David K.} and Catherine Houlihan and Dan Frampton and Hamilton, {William L.} and Witney, {Adam A.} and Giselda Bucca and Pope, {Cassie F.} and Catherine Moore and Thomson, {Emma C.} and Harrison, {Ewan M.} and Smith, {Colin P.} and Fiona Rogan and Beckwith, {Shaun M.} and Abigail Murray and Jonathan Edgeworth and Jeffries, {Aaron R.}",

note = "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: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

day = "1",

doi = "10.1038/s41598-022-15661-1",

language = "English",

volume = "12",

journal = "Scientific Reports",

issn = "2045-2322",

publisher = "Nature Publishing Group",

number = "1",

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The COVID-19 Genomics UK (COG-UK) consortium, Nickbakhsh, S, Hughes, J, Christofidis, N, Griffiths, E, Shaaban, S, Enright, J, Smollett, K, Nomikou, K, Palmalux, N, Tong, L, Carmichael, S, Sreenu, VB, Orton, RJ, Goldstein, EJ, Tomb, RM, Robson, SC, Connor, TR, Loman, NJ, Golubchik, T, Nunez, RTM, Bonsall, D, Rambaut, A, Snell, LB, Livett, R, Ludden, C, Corden, S, Nastouli, E, Nebbia, G, Johnston, I, Lythgoe, K, Torok, ME, Goodfellow, IG, Prieto, JA, Saeed, K, Jackson, DK, Houlihan, C, Frampton, D, Hamilton, WL, Witney, AA, Bucca, G, Pope, CF, Moore, C, Thomson, EC, Harrison, EM, Smith, CP, Rogan, F, Beckwith, SM, Murray, A, Edgeworth, J & Jeffries, AR 2022, 'Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning', Scientific Reports, vol. 12, no. 1, 11735. https://doi.org/10.1038/s41598-022-15661-1

TY - JOUR

T1 - Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

AU - The COVID-19 Genomics UK (COG-UK) consortium

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 J.

AU - Goldstein, Emily J.

AU - Tomb, Rachael M.

AU - Robson, Samuel C.

AU - Connor, Thomas R.

AU - Loman, Nicholas J.

AU - Golubchik, Tanya

AU - Nunez, Rocio T.Martinez

AU - Bonsall, David

AU - Rambaut, Andrew

AU - Snell, Luke B.

AU - Livett, Rich

AU - Ludden, Catherine

AU - Corden, Sally

AU - Nastouli, Eleni

AU - Nebbia, Gaia

AU - Johnston, Ian

AU - Lythgoe, Katrina

AU - Torok, M. Estee

AU - Goodfellow, Ian G.

AU - Prieto, Jacqui A.

AU - Saeed, Kordo

AU - Jackson, David K.

AU - Houlihan, Catherine

AU - Frampton, Dan

AU - Hamilton, William L.

AU - Witney, Adam A.

AU - Bucca, Giselda

AU - Pope, Cassie F.

AU - Moore, Catherine

AU - Thomson, Emma C.

AU - Harrison, Ewan M.

AU - Smith, Colin P.

AU - Rogan, Fiona

AU - Beckwith, Shaun M.

AU - Murray, Abigail

AU - Edgeworth, Jonathan

AU - Jeffries, Aaron R.

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 - 2022/12/1

Y1 - 2022/12/1

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.

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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

JO - Scientific Reports

JF - Scientific Reports

IS - 1

M1 - 11735

ER -

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

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