Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Dinesh Aggarwal; Ben Warne; Aminu S. Jahun; William L. Hamilton; Thomas Fieldman; Louis du Plessis; Verity Hill; Beth Blane; Emmeline Watkins; Elizabeth Wright; Grant Hall; Catherine Ludden; Richard Myers; Myra Hosmillo; Yasmin Chaudhry; Malte L. Pinckert; Iliana Georgana; Rhys Izuagbe; Danielle Leek; Olisaeloka Nsonwu; Gareth J. Hughes; Simon Packer; Andrew J. Page; Marina Metaxaki; Stewart Fuller; Gillian Weale; Jon Holgate; Christopher A. Brown; The Cambridge Covid-19 Testing Centre; University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium; The COVID-19 Genomics UK (COG-UK) Consortium; Rob Howes; Duncan McFarlane; Gordon Dougan; Oliver G. Pybus; Daniela De Angelis; Patrick H. Maxwell; Sharon J. Peacock; Michael P. Weekes; Christopher Illingworth; Ewan M. Harrison; Nicholas J. Matheson; Ian G. Goodfellow

doi:10.1038/s41467-021-27942-w

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Dinesh Aggarwal, Ben Warne, Aminu S. Jahun, William L. Hamilton, Thomas Fieldman, Louis du Plessis, Verity Hill, Beth Blane, Emmeline Watkins, Elizabeth Wright, Grant Hall, Catherine Ludden, Richard Myers, Myra Hosmillo, Yasmin Chaudhry, Malte L. Pinckert, Iliana Georgana, Rhys Izuagbe, Danielle Leek, Olisaeloka NsonwuGareth J. Hughes, Simon Packer, Andrew J. Page, Marina Metaxaki, Stewart Fuller, Gillian Weale, Jon Holgate, Christopher A. Brown, The Cambridge Covid-19 Testing Centre, University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium, The COVID-19 Genomics UK (COG-UK) Consortium, Rob Howes, Duncan McFarlane, Gordon Dougan, Oliver G. Pybus, Daniela De Angelis, Patrick H. Maxwell, Sharon J. Peacock, Michael P. Weekes, Christopher Illingworth, Ewan M. Harrison, Nicholas J. Matheson, Ian G. Goodfellow

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Abstract

Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.

Original language	English
Article number	751
Journal	Nature Communications
Volume	13
DOIs	https://doi.org/10.1038/s41467-021-27942-w
Publication status	Published - 8 Feb 2022

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Aggarwal, D., Warne, B., Jahun, A. S., Hamilton, W. L., Fieldman, T., du Plessis, L., Hill, V., Blane, B., Watkins, E., Wright, E., Hall, G., Ludden, C., Myers, R., Hosmillo, M., Chaudhry, Y., Pinckert, M. L., Georgana, I., Izuagbe, R., Leek, D., ... Goodfellow, I. G. (2022). Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, [751]. https://doi.org/10.1038/s41467-021-27942-w

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title = "Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission",

abstract = "Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.",

author = "Dinesh Aggarwal and Ben Warne and Jahun, {Aminu S.} and Hamilton, {William L.} and Thomas Fieldman and {du Plessis}, Louis and Verity Hill and Beth Blane and Emmeline Watkins and Elizabeth Wright and Grant Hall and Catherine Ludden and Richard Myers and Myra Hosmillo and Yasmin Chaudhry and Pinckert, {Malte L.} and Iliana Georgana and Rhys Izuagbe and Danielle Leek and Olisaeloka Nsonwu and Hughes, {Gareth J.} and Simon Packer and Page, {Andrew J.} and Marina Metaxaki and Stewart Fuller and Gillian Weale and Jon Holgate and Brown, {Christopher A.} and {The Cambridge Covid-19 Testing Centre} and {University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium} and {The COVID-19 Genomics UK (COG-UK) Consortium} and Rob Howes and Duncan McFarlane and Gordon Dougan and Pybus, {Oliver G.} and {De Angelis}, Daniela and Maxwell, {Patrick H.} and Peacock, {Sharon J.} and Weekes, {Michael P.} and Christopher Illingworth and Harrison, {Ewan M.} and Matheson, {Nicholas J.} and Goodfellow, {Ian G.} and Rose Davidson",

note = "Acknowledgements: Authors A.S.J., W.H. and T.F., and authors L.d.P. and V.H. contributed equally. We thank members of the COVID-19 Genomics Consortium UK and NHS Test and Trace contact tracers for their contributions to generating data used in this study. We thank the Sanger Covid Team for assisting with Samples and Logistics. We are grateful to all students and staff at the University of Cambridge who have contributed to the COVID-19 response during Michaelmas Term. We are grateful to all staff members of the Cambridge COVID-19 Testing Centre for generating qPCR data. D.A. is a Wellcome Clinical PhD Fellow and gratefully supported by the Wellcome Trust (Grant number: 222903/Z/21/Z). B.W. receives funding from the University of Cambridge and the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre (BRC) at the Cambridge University Hospitals NHS Foundation Trust. I.G. is a Wellcome Senior Fellow and is supported by the Wellcome Trust (Grant number: 207498/Z/17/Z and 206298/B/17/Z). E.M.H. is supported by a UK Research and Innovation (UKRI) Fellowship: MR/S00291X/1. C.J.R.I. acknowledges Medical Research Council (MRC) funding (ref: MC_UU_00002/11). NJM is supported by the MRC (CSF MR/P008801/1) and NHSBT (WPA15-02). A.J.P. gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10352, also Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1). L.d.P. and O.G.P. were supported by the Oxford Martin School. This research was supported by the NIHR Cambridge BRC. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health and Social Care. The COVID-19 Genomics UK Consortium is supported by funding from the MRC part of UK Research & Innovation (UKRI), the National Institute of Health Research and Genome Research Limited, operating as the Wellcome Sanger Institute. The Cambridge Covid-19 testing Centre is funded by the Department of Health and Social Care, UK Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Rights retention statement: For the purpose of Open Access, the author has applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission.",

year = "2022",

month = feb,

day = "8",

doi = "10.1038/s41467-021-27942-w",

language = "English",

volume = "13",

journal = "Nature Communications",

issn = "2041-1723",

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}

Aggarwal, D, Warne, B, Jahun, AS, Hamilton, WL, Fieldman, T, du Plessis, L, Hill, V, Blane, B, Watkins, E, Wright, E, Hall, G, Ludden, C, Myers, R, Hosmillo, M, Chaudhry, Y, Pinckert, ML, Georgana, I, Izuagbe, R, Leek, D, Nsonwu, O, Hughes, GJ, Packer, S, Page, AJ, Metaxaki, M, Fuller, S, Weale, G, Holgate, J, Brown, CA, The Cambridge Covid-19 Testing Centre, University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium, The COVID-19 Genomics UK (COG-UK) Consortium, Howes, R, McFarlane, D, Dougan, G, Pybus, OG, De Angelis, D, Maxwell, PH, Peacock, SJ, Weekes, MP, Illingworth, C, Harrison, EM, Matheson, NJ & Goodfellow, IG 2022, 'Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission', Nature Communications, vol. 13, 751. https://doi.org/10.1038/s41467-021-27942-w

TY - JOUR

T1 - Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AU - Aggarwal, Dinesh

AU - Warne, Ben

AU - Jahun, Aminu S.

AU - Hamilton, William L.

AU - Fieldman, Thomas

AU - du Plessis, Louis

AU - Hill, Verity

AU - Blane, Beth

AU - Watkins, Emmeline

AU - Wright, Elizabeth

AU - Hall, Grant

AU - Ludden, Catherine

AU - Myers, Richard

AU - Hosmillo, Myra

AU - Chaudhry, Yasmin

AU - Pinckert, Malte L.

AU - Georgana, Iliana

AU - Izuagbe, Rhys

AU - Leek, Danielle

AU - Nsonwu, Olisaeloka

AU - Hughes, Gareth J.

AU - Packer, Simon

AU - Page, Andrew J.

AU - Metaxaki, Marina

AU - Fuller, Stewart

AU - Weale, Gillian

AU - Holgate, Jon

AU - Brown, Christopher A.

AU - The Cambridge Covid-19 Testing Centre

AU - University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium

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

AU - Howes, Rob

AU - McFarlane, Duncan

AU - Dougan, Gordon

AU - Pybus, Oliver G.

AU - De Angelis, Daniela

AU - Maxwell, Patrick H.

AU - Peacock, Sharon J.

AU - Weekes, Michael P.

AU - Illingworth, Christopher

AU - Harrison, Ewan M.

AU - Matheson, Nicholas J.

AU - Goodfellow, Ian G.

AU - Davidson, Rose

N1 - Acknowledgements: Authors A.S.J., W.H. and T.F., and authors L.d.P. and V.H. contributed equally. We thank members of the COVID-19 Genomics Consortium UK and NHS Test and Trace contact tracers for their contributions to generating data used in this study. We thank the Sanger Covid Team for assisting with Samples and Logistics. We are grateful to all students and staff at the University of Cambridge who have contributed to the COVID-19 response during Michaelmas Term. We are grateful to all staff members of the Cambridge COVID-19 Testing Centre for generating qPCR data. D.A. is a Wellcome Clinical PhD Fellow and gratefully supported by the Wellcome Trust (Grant number: 222903/Z/21/Z). B.W. receives funding from the University of Cambridge and the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre (BRC) at the Cambridge University Hospitals NHS Foundation Trust. I.G. is a Wellcome Senior Fellow and is supported by the Wellcome Trust (Grant number: 207498/Z/17/Z and 206298/B/17/Z). E.M.H. is supported by a UK Research and Innovation (UKRI) Fellowship: MR/S00291X/1. C.J.R.I. acknowledges Medical Research Council (MRC) funding (ref: MC_UU_00002/11). NJM is supported by the MRC (CSF MR/P008801/1) and NHSBT (WPA15-02). A.J.P. gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10352, also Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1). L.d.P. and O.G.P. were supported by the Oxford Martin School. This research was supported by the NIHR Cambridge BRC. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health and Social Care. The COVID-19 Genomics UK Consortium is supported by funding from the MRC part of UK Research & Innovation (UKRI), the National Institute of Health Research and Genome Research Limited, operating as the Wellcome Sanger Institute. The Cambridge Covid-19 testing Centre is funded by the Department of Health and Social Care, UK Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Rights retention statement: For the purpose of Open Access, the author has applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission.

PY - 2022/2/8

Y1 - 2022/2/8

N2 - Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.

AB - Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.

UR - http://www.scopus.com/inward/record.url?scp=85124325450&partnerID=8YFLogxK

U2 - 10.1038/s41467-021-27942-w

DO - 10.1038/s41467-021-27942-w

M3 - Article

VL - 13

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

M1 - 751

ER -

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Abstract

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