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

The COVID-19 Genomics UK (COG-UK) Consortium; Dinesh Aggarwal; Ben Warne; Aminu Jahun; William Hamilton; Thomas Fieldman; Louis Plessis; Verity Hill; Beth Blane; Emmeline Watkins; Elizabeth Wright; Grant Hall; Catherine Ludden; Richard Myers; Myra Hosmillo; Yasmin Goodfellow; Malte Pinckert; Iliana Georgana; Rhys Izuagbe; Danielle Leek; Olisaeloka Nsonwu; Gareth Hughes; Simon Packer; Andrew Page; Marina Metaxaki; Stewart Fuller; Gillian Weale; Jon Holgate; Rob Howes; Duncan McFarlane; Gordon Dougan; Oliver Pybus; Daniela De Angelis; Patrick Maxwell; Sharon Peacock; Michael Weekes; Chris Illingworth; Ewan Harrison; Nicholas Matheson; Ian G. Goodfellow; Matthew Bashton; Darren Smith; Andrew Nelson; Greg Young; Clare McCann

doi:10.21203/rs.3.rs-520627/v1

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

The COVID-19 Genomics UK (COG-UK) Consortium, Dinesh Aggarwal^*, Ben Warne, Aminu Jahun, William Hamilton, Thomas Fieldman, Louis Plessis, Verity Hill, Beth Blane, Emmeline Watkins, Elizabeth Wright, Grant Hall, Catherine Ludden, Richard Myers, Myra Hosmillo, Yasmin Goodfellow, Malte Pinckert, Iliana Georgana, Rhys Izuagbe, Danielle LeekOlisaeloka Nsonwu, Gareth Hughes, Simon Packer, Andrew Page, Marina Metaxaki, Stewart Fuller, Gillian Weale, Jon Holgate, Rob Howes, Duncan McFarlane, Gordon Dougan, Oliver Pybus, Daniela De Angelis, Patrick Maxwell, Sharon Peacock, Michael Weekes, Chris Illingworth, Ewan Harrison, Nicholas Matheson, Ian G. Goodfellow, Matthew Bashton, Darren Smith, Andrew Nelson, Greg Young, Clare McCann

^*Corresponding author for this work

Applied Sciences Department

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Abstract

Understanding the drivers for spread of SARS-CoV-2 in higher education settings is important to limit transmission between students, and onward spread into at-risk populations. In this study, we prospectively sequenced 482 SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge from 5 October to 6 December 2020. We performed a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. After a limited number of viral introductions into the university, the majority of student cases were linked to a single genetic cluster, likely dispersed across the university following social gatherings at a venue outside the university. We identified considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and dramatically reduced following a national lockdown. We observed that transmission clusters were largely segregated within the university or within the community. This 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
Number of pages	25
DOIs	https://doi.org/10.21203/rs.3.rs-520627/v1
Publication status	Submitted - 19 May 2021

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The COVID-19 Genomics UK (COG-UK) Consortium, Aggarwal, D., Warne, B., Jahun, A., Hamilton, W., Fieldman, T., Plessis, L., Hill, V., Blane, B., Watkins, E., Wright, E., Hall, G., Ludden, C., Myers, R., Hosmillo, M., Goodfellow, Y., Pinckert, M., Georgana, I., Izuagbe, R., ... McCann, C. (2021). Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. https://doi.org/10.21203/rs.3.rs-520627/v1

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

abstract = "Understanding the drivers for spread of SARS-CoV-2 in higher education settings is important to limit transmission between students, and onward spread into at-risk populations. In this study, we prospectively sequenced 482 SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge from 5 October to 6 December 2020. We performed a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. After a limited number of viral introductions into the university, the majority of student cases were linked to a single genetic cluster, likely dispersed across the university following social gatherings at a venue outside the university. We identified considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and dramatically reduced following a national lockdown. We observed that transmission clusters were largely segregated within the university or within the community. This 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 = "{The COVID-19 Genomics UK (COG-UK) Consortium} and Dinesh Aggarwal and Ben Warne and Aminu Jahun and William Hamilton and Thomas Fieldman and Louis Plessis 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 Goodfellow and Malte Pinckert and Iliana Georgana and Rhys Izuagbe and Danielle Leek and Olisaeloka Nsonwu and Gareth Hughes and Simon Packer and Andrew Page and Marina Metaxaki and Stewart Fuller and Gillian Weale and Jon Holgate and Rob Howes and Duncan McFarlane and Gordon Dougan and Oliver Pybus and Angelis, {Daniela De} and Patrick Maxwell and Sharon Peacock and Michael Weekes and Chris Illingworth and Ewan Harrison and Nicholas Matheson and Goodfellow, {Ian G.} and Matthew Bashton and Darren Smith and Andrew Nelson and Greg Young and Clare McCann",

note = "Matthew Bashton, Darren L. Smith, Gregory R. Young, Clare McCann and Andrew Nelson are member of the COVID-19 Genomics UK (COG-UK) Consortium.",

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The COVID-19 Genomics UK (COG-UK) Consortium, Aggarwal, D, Warne, B, Jahun, A, Hamilton, W, Fieldman, T, Plessis, L, Hill, V, Blane, B, Watkins, E, Wright, E, Hall, G, Ludden, C, Myers, R, Hosmillo, M, Goodfellow, Y, Pinckert, M, Georgana, I, Izuagbe, R, Leek, D, Nsonwu, O, Hughes, G, Packer, S, Page, A, Metaxaki, M, Fuller, S, Weale, G, Holgate, J, Howes, R, McFarlane, D, Dougan, G, Pybus, O, Angelis, DD, Maxwell, P, Peacock, S, Weekes, M, Illingworth, C, Harrison, E, Matheson, N, Goodfellow, IG, Bashton, M , Smith, D , Nelson, A, Young, G & McCann, C 2021 'Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission'. https://doi.org/10.21203/rs.3.rs-520627/v1

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

AU - Aggarwal, Dinesh

AU - Warne, Ben

AU - Jahun, Aminu

AU - Hamilton, William

AU - Fieldman, Thomas

AU - 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 - Goodfellow, Yasmin

AU - Pinckert, Malte

AU - Georgana, Iliana

AU - Izuagbe, Rhys

AU - Leek, Danielle

AU - Nsonwu, Olisaeloka

AU - Hughes, Gareth

AU - Packer, Simon

AU - Page, Andrew

AU - Metaxaki, Marina

AU - Fuller, Stewart

AU - Weale, Gillian

AU - Holgate, Jon

AU - Howes, Rob

AU - McFarlane, Duncan

AU - Dougan, Gordon

AU - Pybus, Oliver

AU - Angelis, Daniela De

AU - Maxwell, Patrick

AU - Peacock, Sharon

AU - Weekes, Michael

AU - Illingworth, Chris

AU - Harrison, Ewan

AU - Matheson, Nicholas

AU - Goodfellow, Ian G.

AU - Bashton, Matthew

AU - Smith, Darren

AU - Nelson, Andrew

AU - Young, Greg

AU - McCann, Clare

N1 - Matthew Bashton, Darren L. Smith, Gregory R. Young, Clare McCann and Andrew Nelson are member of the COVID-19 Genomics UK (COG-UK) Consortium.

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N2 - Understanding the drivers for spread of SARS-CoV-2 in higher education settings is important to limit transmission between students, and onward spread into at-risk populations. In this study, we prospectively sequenced 482 SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge from 5 October to 6 December 2020. We performed a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. After a limited number of viral introductions into the university, the majority of student cases were linked to a single genetic cluster, likely dispersed across the university following social gatherings at a venue outside the university. We identified considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and dramatically reduced following a national lockdown. We observed that transmission clusters were largely segregated within the university or within the community. This 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 the drivers for spread of SARS-CoV-2 in higher education settings is important to limit transmission between students, and onward spread into at-risk populations. In this study, we prospectively sequenced 482 SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge from 5 October to 6 December 2020. We performed a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. After a limited number of viral introductions into the university, the majority of student cases were linked to a single genetic cluster, likely dispersed across the university following social gatherings at a venue outside the university. We identified considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and dramatically reduced following a national lockdown. We observed that transmission clusters were largely segregated within the university or within the community. This 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.

U2 - 10.21203/rs.3.rs-520627/v1

DO - 10.21203/rs.3.rs-520627/v1

M3 - Preprint

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

ER -

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

Abstract

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