Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand

Lauren Jelley, Jordan Douglas, Xiaoyun Ren, David Winter, Andrea McNeill, Sue Huang, Nigel French, David Welch, James Hadfield, Joep Ligt and Jemma L. Geoghegan ()
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Lauren Jelley: Institute of Environmental Science and Research
Jordan Douglas: University of Auckland
Xiaoyun Ren: Institute of Environmental Science and Research
David Winter: Institute of Environmental Science and Research
Andrea McNeill: Institute of Environmental Science and Research
Sue Huang: Institute of Environmental Science and Research
Nigel French: Massey University
David Welch: University of Otago
James Hadfield: Fred Hutchinson Cancer Research Centre
Joep Ligt: Institute of Environmental Science and Research
Jemma L. Geoghegan: Institute of Environmental Science and Research

Nature Communications, 2022, vol. 13, issue 1, 1-8

Abstract: Abstract New Zealand’s COVID-19 elimination strategy heavily relied on the use of genomics to inform contact tracing, linking cases to the border and to clusters during community outbreaks. In August 2021, New Zealand entered its second nationwide lockdown after the detection of a single community case with no immediately apparent epidemiological link to the border. This incursion resulted in the largest outbreak seen in New Zealand caused by the Delta Variant of Concern. Here we generated 3806 high quality SARS-CoV-2 genomes from cases reported in New Zealand between 17 August and 1 December 2021, representing 43% of reported cases. We detected wide geographical spread coupled with undetected community transmission, characterised by the apparent extinction and reappearance of genomically linked clusters. We also identified the emergence, and near replacement, of genomes possessing a 10-nucleotide frameshift deletion that caused the likely truncation of accessory protein ORF7a. By early October, New Zealand moved from an elimination strategy to a suppression strategy and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance.

Date: 2022
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DOI: 10.1038/s41467-022-31784-5

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