ABSTRACT
There have been thirteen known COVID-19 community outbreaks in Aotearoa New Zealand since the virus was first eliminated in May 2020, two of which led to stay-at-home orders being issued by health officials. These outbreaks originated at the border; via isolating returnees, airline workers, and cargo vessels. With a public health system informed by real-time viral genomic sequencing which typically had complete genomes within 12 hours after a community-based positive COVID-19 test, every outbreak was well-contained with a total of 225 community cases, resulting in three deaths. Real-time genomics were essential for establishing links between cases when epidemiological data could not, and for identifying when concurrent outbreaks had different origins. By reconstructing the viral transmission history from genomic sequences, here we recount all thirteen community outbreaks and demonstrate how genomics played a vital role in containing them.
Subject(s)
COVID-19ABSTRACT
New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nation-wide lockdown of all non-essential services to curb the spread of COVID-19. New Zealand has now effectively eliminated the virus, with low numbers of new cases limited to new arrivals in managed quarantine facilities at the border. Here, we generated 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected between 26 February and 22 May 2020, representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. The proportion of D614G variants in the virus spike protein increased over time due to an increase in their importation frequency, rather than selection within New Zealand. These data also helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number, Re, of New Zealands largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in a transmission lineage of more than one additional case. Most of the cases that resulted in a transmission lineage originated from North America, rather than from Asia where the virus first emerged or from the nearest geographical neighbour, Australia. Genomic data also helped link more infections to a major transmission cluster than through epidemiological data alone, providing probable sources of infections for cases in which the source was unclear. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation.
Subject(s)
COVID-19ABSTRACT
The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea and Iran. Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.