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; Alexandra Orton; Julie Douthwaite; Steve Rees; Christopher Brown; Roger Clark; Daniel R. Jones; Fred Kuenzi; Jennifer Rankin; Ian Waddell; Patrick Maxwell; Nicholas Matheson; Chris Abell; Vickie Braithwaite; Craig Brierley; Jon Crowcroft; Aastha Dahal; Kathryn Faulkner; Michael Glover; Jane Greatorex; Adam Westhorpe; Jonathan Ball; Sally Forrest

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, Alexandra Orton, Julie Douthwaite, Steve Rees, Christopher Brown, Roger Clark, Daniel R. Jones, Fred Kuenzi, Jennifer Rankin, Ian Waddell, Patrick Maxwell, Nicholas Matheson, Chris Abell, Vickie Braithwaite, Craig Brierley, Jon Crowcroft, Aastha Dahal, Kathryn Faulkner, Michael Glover, Jane Greatorex, Adam Westhorpe, Jonathan Ball, Sally Forrest

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

33 Citations (Scopus)

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
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-27942-w
Publication status	Published - 1 Dec 2022
Externally published	Yes

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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., ... Forrest, S. (2022). Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13(1), Article 751. https://doi.org/10.1038/s41467-021-27942-w

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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.",

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 Alexandra Orton and Julie Douthwaite and Steve Rees and Christopher Brown and Roger Clark and Jones, \{Daniel R.\} and Fred Kuenzi and Jennifer Rankin and Ian Waddell and Patrick Maxwell and Nicholas Matheson and Chris Abell and Vickie Braithwaite and Craig Brierley and Jon Crowcroft and Aastha Dahal and Kathryn Faulkner and Michael Glover and Jane Greatorex and Adam Westhorpe and Jonathan Ball and Sally Forrest",

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

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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, Orton, A, Douthwaite, J, Rees, S, Brown, C, Clark, R, Jones, DR, Kuenzi, F, Rankin, J, Waddell, I, Maxwell, P, Matheson, N, Abell, C, Braithwaite, V, Brierley, C, Crowcroft, J, Dahal, A, Faulkner, K, Glover, M, Greatorex, J, Westhorpe, A , Ball, J & Forrest, S 2022, 'Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission', Nature Communications, vol. 13, no. 1, 751. https://doi.org/10.1038/s41467-021-27942-w

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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 - Orton, Alexandra

AU - Douthwaite, Julie

AU - Rees, Steve

AU - Brown, Christopher

AU - Clark, Roger

AU - Jones, Daniel R.

AU - Kuenzi, Fred

AU - Rankin, Jennifer

AU - Waddell, Ian

AU - Maxwell, Patrick

AU - Matheson, Nicholas

AU - Abell, Chris

AU - Braithwaite, Vickie

AU - Brierley, Craig

AU - Crowcroft, Jon

AU - Dahal, Aastha

AU - Faulkner, Kathryn

AU - Glover, Michael

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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.

U2 - 10.1038/s41467-021-27942-w

DO - 10.1038/s41467-021-27942-w

M3 - Article

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 751

ER -

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

Abstract

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