Abstract
Since severe acute respiratory syndrome coronavirus 2 was first eliminated in New Zealand in May 2020, a total of 13 known coronavirus disease (COVID-19) community outbreaks have occurred, 2 of which led health officials to issue stay-at-home orders. These outbreaks originated at the border via isolating returnees, airline workers, and cargo vessels. Because a public health system was informed by real-time viral genomic sequencing and complete genomes typically were available within 12 hours of community-based positive COVID-19 test results, every outbreak was well-contained. A total of 225 community cases resulted in 3 deaths. Real-time genomics were essential for establishing links between cases when epidemiologic data could not do so and for identifying when concurrent outbreaks had different origins.
Highlights
Since severe acute respiratory syndrome coronavirus 2 was first eliminated in New Zealand in May 2020, a total of 13 known coronavirus disease (COVID-19) community outbreaks have occurred, 2 of which led health officials to issue stay-at-home orders
A core part of the COVID-19 elimination strategy is a strictly controlled border where nearly every person entering the country is required to isolate for 14 days at an managed isolation and quarantine (MIQ) facility and be tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on days 0, 3, and 12 of their stay [4,5]
Of the 13 known border incursions, 7 originated in MIQ facilities (4 from MIQ workers and 3 from returnees who tested positive after leaving the facility), 3 were from airline workers, and 1 was from an infection on a visiting ship; the sources of the remaining 2, which both led to stay-at-home orders, remain unknown
Summary
We constructed a multiple sequence alignment [11] containing 225 genomes from New Zealand community outbreaks and another 663 from the rest of the world, downloaded from GISAID [12]. For the community outbreaks considered here, we had high-quality genomes for 225 (85%) of 265 case-patients (Table). Compassionate Exemption After 24 days without any recorded cases in the community or at the border and 1 week after all of New Zealand had been moved down to alert level 1, two cases were found in the community. Elevated restrictions remained until October 7 as the cluster grew to a total of 179 cases, including 3 deaths This COVID-19 cluster was the largest in New Zealand. The cluster included a healthcare worker who was infected during work at an MIQ facility where community case-patients were sent to quarantine [18].
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