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Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

Author

Listed:
  • Jemma L. Geoghegan

    (University of Otago
    Institute of Environmental Science and Research)

  • Xiaoyun Ren

    (Institute of Environmental Science and Research)

  • Matthew Storey

    (Institute of Environmental Science and Research)

  • James Hadfield

    (Fred Hutchinson Cancer Research Centre)

  • Lauren Jelley

    (Institute of Environmental Science and Research)

  • Sarah Jefferies

    (Institute of Environmental Science and Research)

  • Jill Sherwood

    (Institute of Environmental Science and Research)

  • Shevaun Paine

    (Institute of Environmental Science and Research)

  • Sue Huang

    (Institute of Environmental Science and Research)

  • Jordan Douglas

    (Centre for Computational Evolution, School of Computer Science, University of Auckland)

  • Fábio K. Mendes

    (Centre for Computational Evolution, School of Computer Science, University of Auckland)

  • Andrew Sporle

    (University of Auckland
    McDonaldSporle Ltd.)

  • Michael G. Baker

    (University of Otago)

  • David R. Murdoch

    (University of Otago)

  • Nigel French

    (Massey University)

  • Colin R. Simpson

    (Victoria University of Wellington
    University of Edinburgh)

  • David Welch

    (Centre for Computational Evolution, School of Computer Science, University of Auckland)

  • Alexei J. Drummond

    (Centre for Computational Evolution, School of Computer Science, University of Auckland)

  • Edward C. Holmes

    (Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney)

  • Sebastián Duchêne

    (The University of Melbourne at The Peter Doherty Institute for Infection and Immunity)

  • Joep Ligt

    (Institute of Environmental Science and Research)

Abstract

New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nationwide ‘lockdown’ of all non-essential services to curb the spread of COVID-19. Here, we generate 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected during the ‘first wave’, representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. These data helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number, Re of New Zealand’s largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in ongoing transmission of more than one additional case. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-20235-8
    DOI: 10.1038/s41467-020-20235-8
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    Citations

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    Cited by:

    1. John Gibson, 2022. "Hard, not early: putting the New Zealand Covid-19 response in context," New Zealand Economic Papers, Taylor & Francis Journals, vol. 56(1), pages 1-8, January.
    2. Jordan Douglas & David Winter & Andrea McNeill & Sam Carr & Michael Bunce & Nigel French & James Hadfield & Joep Ligt & David Welch & Jemma L. Geoghegan, 2022. "Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    3. 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.
    4. 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.
    5. 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.
    6. Lauren Jelley & Jordan Douglas & Xiaoyun Ren & David Winter & Andrea McNeill & Sue Huang & Nigel French & David Welch & James Hadfield & Joep Ligt & Jemma L. Geoghegan, 2022. "Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand," Nature Communications, Nature, vol. 13(1), pages 1-8, December.

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