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

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, Michael G. Baker, David R. Murdoch, Nigel French, Colin R. Simpson, David Welch, Alexei J. Drummond, Edward C. Holmes, Sebastián Duchêne and Joep Ligt
Additional contact information
Jemma L. Geoghegan: University of Otago
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
Michael G. Baker: University of Otago
David R. Murdoch: University of Otago
Nigel French: Massey University
Colin R. Simpson: Victoria University of Wellington
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

Nature Communications, 2020, vol. 11, issue 1, 1-7

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-20235-8

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