IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-021-27942-w.html
   My bibliography  Save this article

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

Author

Listed:
  • Dinesh Aggarwal

    (University of Cambridge, Department of Medicine
    Public Health England
    Cambridge University Hospital NHS Foundation Trust
    Wellcome Sanger Institute, Hinxton)

  • Ben Warne

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust
    Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge)

  • Aminu S. Jahun

    (University of Cambridge, Department of Pathology, Division of Virology)

  • William L. Hamilton

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust
    Wellcome Sanger Institute, Hinxton)

  • Thomas Fieldman

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust)

  • Louis Plessis

    (University of Oxford)

  • Verity Hill

    (University of Edinburgh)

  • Beth Blane

    (University of Cambridge, Department of Medicine)

  • Emmeline Watkins

    (Cambridgeshire County Council and Peterborough City Council)

  • Elizabeth Wright

    (Cambridgeshire County Council and Peterborough City Council)

  • Grant Hall

    (University of Cambridge, Department of Pathology, Division of Virology)

  • Catherine Ludden

    (University of Cambridge, Department of Medicine
    Public Health England)

  • Richard Myers

    (Public Health England)

  • Myra Hosmillo

    (Cambridge University Hospital NHS Foundation Trust
    University of Cambridge, Department of Pathology, Division of Virology)

  • Yasmin Chaudhry

    (University of Cambridge, Department of Pathology, Division of Virology)

  • Malte L. Pinckert

    (University of Cambridge, Department of Pathology, Division of Virology)

  • Iliana Georgana

    (University of Cambridge, Department of Pathology, Division of Virology)

  • Rhys Izuagbe

    (University of Cambridge, Department of Pathology, Division of Virology)

  • Danielle Leek

    (University of Cambridge, Department of Medicine)

  • Olisaeloka Nsonwu

    (Public Health England)

  • Gareth J. Hughes

    (Public Health England)

  • Simon Packer

    (Public Health England)

  • Andrew J. Page

    (Norwich Research Park)

  • Marina Metaxaki

    (University of Cambridge, Department of Medicine)

  • Stewart Fuller

    (University of Cambridge, Department of Medicine)

  • Gillian Weale

    (University of Cambridge)

  • Jon Holgate

    (University of Cambridge)

  • Christopher A. Brown

    (Discovery Sciences, R&D, AstraZenenca
    Chesterford Research Park)

  • Rob Howes

    (Discovery Sciences, R&D, AstraZenenca)

  • Duncan McFarlane

    (University of Cambridge)

  • Gordon Dougan

    (University of Cambridge, Department of Medicine
    Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge)

  • Oliver G. Pybus

    (University of Oxford)

  • Daniela De Angelis

    (Public Health England
    University of Cambridge)

  • Patrick H. Maxwell

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust)

  • Sharon J. Peacock

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust)

  • Michael P. Weekes

    (Cambridge University Hospital NHS Foundation Trust
    University of Cambridge)

  • Chris Illingworth

    (University of Cambridge
    University of Cambridge
    MRC-University of Glasgow Centre for Virus Research)

  • Ewan M. Harrison

    (University of Cambridge, Department of Medicine
    Public Health England
    Wellcome Sanger Institute, Hinxton
    University of Cambridge)

  • Nicholas J. Matheson

    (University of Cambridge, Department of Medicine
    Cambridge University Hospital NHS Foundation Trust
    Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge
    NHS Blood and Transplant)

  • Ian G. Goodfellow

    (University of Cambridge, Department of Pathology, Division of Virology)

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.

Suggested Citation

  • Dinesh Aggarwal & Ben Warne & Aminu S. Jahun & William L. Hamilton & Thomas Fieldman & Louis Plessis & Verity Hill & Beth Blane & Emmeline Watkins & Elizabeth Wright & Grant Hall & Catherine Ludden & , 2022. "Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-021-27942-w
    DOI: 10.1038/s41467-021-27942-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-27942-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-021-27942-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Jemma L. Geoghegan & Xiaoyun Ren & Matthew Storey & James Hadfield & Lauren Jelley & Sarah Jefferies & Jill Sherwood & Shevaun Paine & Sue Huang & Jordan Douglas & Fábio K. Mendes & Andrew Sporle & Mi, 2020. "Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand," Nature Communications, Nature, vol. 11(1), pages 1-7, December.
    2. Torsten Seemann & Courtney R. Lane & Norelle L. Sherry & Sebastian Duchene & Anders Gonçalves da Silva & Leon Caly & Michelle Sait & Susan A. Ballard & Kristy Horan & Mark B. Schultz & Tuyet Hoang & M, 2020. "Tracking the COVID-19 pandemic in Australia using genomics," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    3. Erik Volz & Swapnil Mishra & Meera Chand & Jeffrey C. Barrett & Robert Johnson & Lily Geidelberg & Wes R. Hinsley & Daniel J. Laydon & Gavin Dabrera & Áine O’Toole & Robert Amato & Manon Ragonnet-Cron, 2021. "Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England," Nature, Nature, vol. 593(7858), pages 266-269, May.
    4. Alexei J Drummond & Simon Y W Ho & Matthew J Phillips & Andrew Rambaut, 2006. "Relaxed Phylogenetics and Dating with Confidence," PLOS Biology, Public Library of Science, vol. 4(5), pages 1-1, March.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Haogao Gu & Ruopeng Xie & Dillon C. Adam & Joseph L.-H. Tsui & Daniel K. Chu & Lydia D. J. Chang & Sammi S. Y. Cheuk & Shreya Gurung & Pavithra Krishnan & Daisy Y. M. Ng & Gigi Y. Z. Liu & Carrie K. C, 2022. "Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    2. Valentina Marziano & Giorgio Guzzetta & Alessia Mammone & Flavia Riccardo & Piero Poletti & Filippo Trentini & Mattia Manica & Andrea Siddu & Antonino Bella & Paola Stefanelli & Patrizio Pezzotti & Ma, 2021. "The effect of COVID-19 vaccination in Italy and perspectives for living with the virus," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    3. Joachim Schmidt & Lars Opgenoorth & Steffen Höll & Ralf Bastrop, 2012. "Into the Himalayan Exile: The Phylogeography of the Ground Beetle Ethira clade Supports the Tibetan Origin of Forest-Dwelling Himalayan Species Groups," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-15, September.
    4. Iliana Bista & Jonathan M. D. Wood & Thomas Desvignes & Shane A. McCarthy & Michael Matschiner & Zemin Ning & Alan Tracey & James Torrance & Ying Sims & William Chow & Michelle Smith & Karen Oliver & , 2023. "Genomics of cold adaptations in the Antarctic notothenioid fish radiation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    5. Haitao Shang & Daniel H. Rothman & Gregory P. Fournier, 2022. "Oxidative metabolisms catalyzed Earth’s oxygenation," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    6. Patrick Munk & Christian Brinch & Frederik Duus Møller & Thomas N. Petersen & Rene S. Hendriksen & Anne Mette Seyfarth & Jette S. Kjeldgaard & Christina Aaby Svendsen & Bram Bunnik & Fanny Berglund & , 2022. "Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    7. Santiago Justo Arevalo & Carmen Sofia Uribe Calampa & Cinthy Jimenez Silva & Mauro Quiñones Aguilar & Remco Bouckaert & Joao Renato Rebello Pinho, 2023. "Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    8. Mekala Sundaram & Janna R Willoughby & Nathanael I Lichti & Michael A Steele & Robert K Swihart, 2015. "Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-16, June.
    9. Jonathon D. Gass & Nichola J. Hill & Lambodhar Damodaran & Elena N. Naumova & Felicia B. Nutter & Jonathan A. Runstadler, 2023. "Ecogeographic Drivers of the Spatial Spread of Highly Pathogenic Avian Influenza Outbreaks in Europe and the United States, 2016–Early 2022," IJERPH, MDPI, vol. 20(11), pages 1-17, June.
    10. Nico Neureiter & Peter Ranacher & Nour Efrat-Kowalsky & Gereon A. Kaiping & Robert Weibel & Paul Widmer & Remco R. Bouckaert, 2022. "Detecting contact in language trees: a Bayesian phylogenetic model with horizontal transfer," Palgrave Communications, Palgrave Macmillan, vol. 9(1), pages 1-14, December.
    11. Mello, Marco & Moscelli, Giuseppe, 2022. "Voting, contagion and the trade-off between public health and political rights: Quasi-experimental evidence from the Italian 2020 polls," Journal of Economic Behavior & Organization, Elsevier, vol. 200(C), pages 1025-1052.
    12. Michael D Nowak & Andrew B Smith & Carl Simpson & Derrick J Zwickl, 2013. "A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-13, June.
    13. Bethany L Dearlove & Simon D W Frost, 2015. "Measuring Asymmetry in Time-Stamped Phylogenies," PLOS Computational Biology, Public Library of Science, vol. 11(7), pages 1-16, July.
    14. Hoan X. Dinh & Davinder Singh & Diana Gomez de la Cruz & Goetz Hensel & Jochen Kumlehn & Martin Mascher & Nils Stein & Dragan Perovic & Michael Ayliffe & Matthew J. Moscou & Robert F. Park & Mohammad , 2022. "The barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    15. Gabriela Lobinska & Ady Pauzner & Arne Traulsen & Yitzhak Pilpel & Martin A. Nowak, 2022. "Evolution of resistance to COVID-19 vaccination with dynamic social distancing," Nature Human Behaviour, Nature, vol. 6(2), pages 193-206, February.
    16. Idrissa Nonmon Sanogo & Claire Guinat & Simon Dellicour & Mohamed Adama Diakité & Mamadou Niang & Ousmane A Koita & Christelle Camus & Mariette F. Ducatez & Mariette Ducatez, 2024. "Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa," Post-Print hal-04498485, HAL.
    17. Matheus Pontes-Nogueira & Marcio Martins & Laura R V Alencar & Ricardo J Sawaya, 2021. "The role of vicariance and dispersal on the temporal range dynamics of forest vipers in the Neotropical region," PLOS ONE, Public Library of Science, vol. 16(9), pages 1-18, September.
    18. Joel O. Wertheim & Jade C. Wang & Mindy Leelawong & Darren P. Martin & Jennifer L. Havens & Moinuddin A. Chowdhury & Jonathan E. Pekar & Helly Amin & Anthony Arroyo & Gordon A. Awandare & Hoi Yan Chow, 2022. "Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    19. Dinesh Aggarwal & Andrew J. Page & Ulf Schaefer & George M. Savva & Richard Myers & Erik Volz & Nicholas Ellaby & Steven Platt & Natalie Groves & Eileen Gallagher & Niamh M. Tumelty & Thanh Viet & Gar, 2022. "Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    20. Cristian R Altaba, 2009. "Universal Artifacts Affect the Branching of Phylogenetic Trees, Not Universal Scaling Laws," PLOS ONE, Public Library of Science, vol. 4(2), pages 1-13, February.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-021-27942-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.