Of the virus genomes generated in real time for 78% of cases in this cluster, from August 11 through September 14, 2020, when the last case in this outbreak was reported, the maximum distance among the genome was 5 single-nucleotide polymorphisms. When we compared the genomes from patients in the August 2020 New Zealand outbreak with sequenced genomes from patients affected by the first COVID-19 wave in New Zealand and those in quarantine facilities, we found no link. Most available sequence data from case-patients in New Zealand quarantine facilities indicated virus lineages different from those of the August 2020 outbreak. However, this observation was of limited value given that only 42% of case-patients in those quarantine facilities had adequate viral RNA for successful genomic sequencing. To determine the likely origins of this outbreak, we compared genomes from the new community outbreak to the global dataset.

Figure 2

Figure 2. Genomic sequence analyses of global severe acute respiratory syndrome coronavirus 2 isolates. A) Maximum-clade credibility phylogenetic tree of 2,000 subsampled global genomes (1,996 most recently sampled B.1.1.1. plus 4 non-B.1.1.1....

An initial genomic sequence analysis found that the reemergence of COVID-19 in New Zealand was caused by a SARS-CoV-2 from the (now ancestral) lineage B.1.1.1 of the pangolin nomenclature (17). Of the countries that have contributed SARS-CoV-2 data, 30% had genomes of this lineage. Remarkably, 80% of B.1.1.1. genomes were from the United Kingdom and were generated during March 2020–January 2021; however, most samples were collected during the first wave of disease in the United Kingdom (Figure 2). Phylogenetic analysis of the most recently sampled B.1.1.1. genomes identified genomes from South Africa, England, and Switzerland in August as the most likely to be contained within the sister clade (Figure 2); these genomes were the closest sampled genomic relatives of the viruses associated with the August 2020 outbreak in New Zealand (Appendix 2). Because of the dynamic nature of the pangolin lineage nomenclature, genomes sampled from the August 2020 outbreak in New Zealand are now distinctly classified as lineage C.12, which is now extinct.

Additional Bayesian analysis estimated that the outbreak originated 10 days before the first transmission event; the 95% highest posterior density was 0–25 days. We also estimated that the first transmission event in the outbreak occurred during July 22–August 13, 2020 (95% highest posterior density mean date of August 2). Epidemiologic data showed that 2 confirmed case-patients linked to the outbreak had a symptom onset date of July 31, although the most probable sampled genomes within the sister clade were sampled later, August 6–28. Hence, it is unlikely that the currently available global genomic dataset contains the source of this outbreak.

Genomic epidemiologic analysis of the possible origins of the COVID-19 re-emergence in New Zealand in August 2020 was inconclusive, probably because of missing genomic data within the quarantine border facilities and in the global dataset. A glimpse into the genomic diversity probably omitted from the global dataset can be seen in the genomes sequenced in New Zealand from SARS-CoV-2–positive quarantined case-patients, comprising citizens and residents returning from across the globe. For example, 12 SARS-CoV-2 genomes from persons returning to New Zealand from India who arrived on the same flight fell across at least 4 genomic lineages and comprised sequence divergence of up to 34 single-nucleotide polymorphisms (https://www.nextstrain.org). This divergence represented far more genomic mutations than was observed in New Zealand during the first outbreak in March–May 2020 (7). Such a high level of diversity in just a small sample of SARS-CoV-2–positive case-patients from India suggests that the currently available genomic data fail to encompass the true diversity that existed locally, let alone globally.

The genome sequences identified after the re-emergence of SARS-CoV-2 in New Zealand in August 2020 exemplified one of the most complete genomic datasets for a specific outbreak compiled to date, comprising 78% of positive case-patients (140 of 179 total case-patients SARS-CoV-2 positive by PCR). Real-time genomic sequencing quickly informed track-and-trace efforts to control the outbreak, setting New Zealand on track to eliminate the virus from the community for the second time. The rapid genome sequencing of positive samples provided confidence to public health teams regarding links to the outbreak and identified that cases and subclusters were linked to a single genomic lineage, resulting from a single introduction event. Indeed, the timing and length of lockdown measures were partly informed on the basis of these data. Overall, real-time viral genomics has played a pivotal role in eliminating COVID-19 from New Zealand and has since helped prevent additional regional lockdowns, leading to substantial economic savings.

Nevertheless, the biased nature of global sampling, including the contribution of very few genome sequences from certain geographic locations, clearly limited the power of genomics to attribute the geographic origin of the August 2020 outbreak in New Zealand. We therefore advocate that potential sampling biases and gaps in available genomic data be carefully considered whenever attempting to determine the geographic origins of a specific SARS-CoV-2 outbreak. Analyses should consider all available evidence, including that from genomic and epidemiologic sources.