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. 2021 Sep;27(9):2361-2368.
doi: 10.3201/eid2709.211097.

Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand

Jordan Douglas, Jemma L Geoghegan, James Hadfield, Remco Bouckaert, Matthew Storey, Xiaoyun Ren, Joep de Ligt, Nigel French, David Welch

Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand

Jordan Douglas et al. Emerg Infect Dis. 2021 Sep.

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.

Keywords: 2019 novel coronavirus disease; COVID-19; New Zealand; SARS-CoV-2; border incursion; community outbreak; coronavirus; coronavirus disease; epidemiology; genomics; managed isolation; quarantine; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.

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Figures

Figure
Figure
Outbreaks of coronavirus disease (COVID-19) after initial elimination in New Zealand. A) Daily COVID-19 cases, June 2020–April 2021. Alert levels in the Auckland region and across the wider country are indicated. B) Phylogenetic trees of all 13 COVID-19 postelimination community outbreaks. VoCs are indicated. Each subtree displayed is part of the larger phylogenetic tree built from genomes around the world. MIQ, managed isolation and quarantine; VoC, variant of concern.
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