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

  1. Lauren Jelley
  2. Jordan Douglas
  3. Xiaoyun Ren
  4. David Winter
  5. Andrea McNeill
  6. Sue Huang
  7. Nigel French
  8. David Welch
  9. James Hadfield
  10. Joep de Ligt
  11. Jemma L. Geoghegan

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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.

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  1. Version published to 10.1038/s41467-022-31784-5
  2. ScreenIT

    SciScore for 10.1101/2022.04.04.22273376: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsField Sample Permit: Under contract for the New Zealand Ministry of Health, the Institute of Environmental Science and Research has approval to conduct genomic sequencing and phylogenetic analysis for surveillance of notifiable diseases.
    Sex as a biological variablenot detected.
    RandomizationGenomic sequencing of SARS-CoV-2: For cases reported between 17 August and 1 December 2021 a random proportion of COVID-19 community cases were referred to the Institute of Environmental Science and Research, New Zealand for genome sequencing.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    A maximum likelihood phylogenetic tree was estimated using IQ-TREE (v 1.6.8)20 using the Hasegawa-Kishino-Yano (HKY+G)21 nucleotide substitution model with a gamma distributed rate variation among sites (the best fit model was determined by ModelFinder22), and branch support was assessed using the ultrafast bootstrap method23.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Estimating the effective reproduction number: To estimate the effective reproduction number (Reff) through time for genomes with and without the ORF7a deletion, a Bayesian birth-death skyline model26 was implemented in BEAST 2.527.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    To help speed up MCMC convergence, we used the efficient tree operators in the BICEPS package27 and adaptable operator weighting28.
    BICEPS
    suggested: None

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2022.04.04.22273376v1 on medRxiv