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

Author

Listed:
  • Lauren Jelley

    (Institute of Environmental Science and Research
    University of Otago)

  • 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
    University of Otago)

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.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31784-5
    DOI: 10.1038/s41467-022-31784-5
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    References listed on IDEAS

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    1. Yaara Finkel & Orel Mizrahi & Aharon Nachshon & Shira Weingarten-Gabbay & David Morgenstern & Yfat Yahalom-Ronen & Hadas Tamir & Hagit Achdout & Dana Stein & Ofir Israeli & Adi Beth-Din & Sharon Melam, 2021. "The coding capacity of SARS-CoV-2," Nature, Nature, vol. 589(7840), pages 125-130, January.
    2. Jordan Douglas & Rong Zhang & Remco Bouckaert, 2021. "Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model," PLOS Computational Biology, Public Library of Science, vol. 17(2), pages 1-30, February.
    3. 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.
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    1. Guilherme Dias de Melo & Victoire Perraud & Flavio Alvarez & Alba Vieites-Prado & Seonhee Kim & Lauriane Kergoat & Anthony Coleon & Bettina Salome Trüeb & Magali Tichit & Aurèle Piazza & Agnès Thierry, 2023. "Neuroinvasion and anosmia are independent phenomena upon infection with SARS-CoV-2 and its variants," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    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. Ruopeng Xie & Kimberly M. Edwards & Dillon C. Adam & Kathy S. M. Leung & Tim K. Tsang & Shreya Gurung & Weijia Xiong & Xiaoman Wei & Daisy Y. M. Ng & Gigi Y. Z. Liu & Pavithra Krishnan & Lydia D. J. C, 2023. "Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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