From elimination to suppression: genomic epidemiology of a large Delta SARS-CoV-2 outbreak in Aotearoa New Zealand

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 elimination to suppression and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance.

Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border

“…However, the travel bubble was suspended in July 2021 due to Australia's difficulty in controlling the emergent Delta variant of concern (VoC). Shortly afterwards, the Delta variant entered the New Zealand community; it likely leaked from an MIQ facility via a traveller from Australia [10]. Unlike previous variants, Delta spread widely and quickly and was unable to be fully controlled, thus leading New Zealand (following a nationwide vaccine rollout, Figure 1) to abandon its elimination strategy in favour of suppression by early October 2021 [11].…”

“…Vaccination coverage is expressed as a percentage of the eligible community (5+ years of age; or 94% of the total population). The genomic epidemiology of the first three waves have been characterised elsewhere - First wave: [1]; Auckland August outbreak: [7]; Delta wave: [10].…”

“…Border controls were gradually relaxed and the MIQ system was abandoned in favour of pre-departure and on-arrival testing. The genomic epidemiology of the first three waves have been characterised elsewhere -First wave: [1]; Auckland August outbreak: [7]; Delta wave: [10].…”

Looking Further and Deeper into Environmental Protection, Regulation and Policy Using Environmental DNA (eDNA)

“…The use of real-time genomics has played a central role in Aotearoa New Zealand's ability to track and trace outbreaks of Covid-19 around the country (Jelley et al, 2022). Just a few years ago, this would not have been possible.…”