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. These case-patients had arrived on June 7 and were granted a compassionate exemption to exit MIQ early to attend a funeral on June 13. The conditions of the exemption required them to self-isolate as much as possible while traveling and to get tested. They were both positive for COVID-19 on June 16. Within 1 day, complete viral genome sequencing confirmed that virus from the 2 case-patients shared a single origin. Although there were no secondary infections, concern for public health led to the New Zealand Defence Force being put in charge of managing MIQ facilities, no returnees being allowed to leave MIQ without having a negative test result, and ending compassionate exemptions from most of the MIQ requirements.

On August 11, 2020, a 102-day period with no recorded community transmission ended when 4 cases of COVID-19 were found among workers at an Auckland cold storage facility. The city was sent into an immediate lockdown (alert level 3), and lower level restrictions were introduced for the rest of the country (alert level 2). 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.

All genomes were closely related; 44 segregating sites were found across 155 genomes (Table). The single origin gave public health officials confidence that it was a single outbreak despite several cases having no clear epidemiologic links with other cases (17). The cluster included a healthcare worker who was infected during work at an MIQ facility where community case-patients were sent to quarantine (18). Although the index case-patients worked at a cold chain supply facility linked to the border, the source of the outbreak was never established (19). Complete genomes were available for 87% of cases in this outbreak, which we believe makes it one of the most comprehensively sampled large COVID-19 outbreaks.

During the Auckland outbreak in August, there was an unusual case of COVID-19 in a maintenance worker at the Rydges MIQ facility with no known epidemiologic link to the ongoing community outbreak. Sequencing confirmed that the source of infection was not related to the main community cluster but rather to an overseas returnee under managed isolation at the Rydges MIQ facility. A follow-up investigation suggested that transmission probably occurred when the 2 case-patients used the same elevator minutes apart from each other (20) and that transmission was most likely airborne (21,22), although fomite transmission (e.g., through elevator buttons) cannot be ruled out.

The complete Crowne Plaza outbreak has been thoroughly analyzed (23), so we provide only brief detail here. In September 2020, symptoms developed in a returnee who tested positive in Auckland 4 days after leaving the Crowne Plaza MIQ facility in Christchurch. Genomic sequencing showed that this case-patient (case-patient G) and 2 household contacts were not linked to the ongoing Auckland cluster in August. Rather, they were linked to other returnees under managed isolation at the Crowne Plaza. Epidemiologic investigations show that the chain probably started with case-patients A and B, who were seated close to case-patient C on a repatriation flight from India. Case-patient C then infected case-patient D in the MIQ facility via airborne transmission between a hotel room and its adjacent hallway. Case-patient D is then thought to have infected case-patient G on a domestic flight from Christchurch to Auckland. This outbreak illustrates the power of genome sequencing—when coupled with detailed epidemiologic investigations—for identifying cryptic transmission events such as those on flights or airborne transmission between MIQ guests. The genomic evidence here is complete; all sequences in the cluster are available, and the tree is relatively well-resolved, showing 4 distinct genomes among its 9 cases.

On October 16, 2020, a group of 235 international mariners arrived in New Zealand on a charter flight from Moscow and began self-isolation at the Sudima MIQ facility in Christchurch. In the ensuing period, 31 of the mariners tested positive for COVID-19, as did 2 workers at the MIQ facility (24). Genomic sequencing produced full genomes for 24 case-patients and indicated >4 independent origins for the 33 cases; the viruses fell into 3 distinct phylogenetic clades (Figure). The 3 clades accounted for 2, 7, and 15 cases. We estimate the date of origin of the largest clade as between August 4 and October 9 (95% credible interval), but the mariners arrived on October 16, suggesting >2 separate introductions of this variant into the facility. The 2 MIQ workers were infected with 2 different variants of the virus; public health officials concluded that the 2 transmission events occurred via regular interactions with the mariners where protocols were followed but were insufficient to prevent transmission (25).

In mid-October, routine testing indicated that a border worker was positive for COVID-19. Extensive surveillance testing found 3 others who were positive: 2 were household contacts and 1 was a mariner who worked on the same cargo vessel, the Sofrana Surville (26). Genomic testing confirmed that virus isolates from the 4 case-patients shared the same origin and were part of a lineage that was novel to New Zealand, thus making residual community transmission an unlikely explanation. International crew members on the Sofrana Surville were confirmed as the source of infection when the ship arrived in Australia, and crew were tested by health officials in Queensland. One crew member tested positive, and the virus sequence reportedly matched that of the New Zealand case-patients.

After visiting several public locations in the Auckland central business district, a New Zealand Defence Force member tested positive for COVID-19 (November 2020). Genomic sequencing confirmed that his infection was acquired from the quarantine facility where he worked. Contact tracing identified 3 additional cases in Wellington (500 km from Auckland, where the Defence Force member’s close contact resided), and surveillance testing identified 1 community case in the Auckland central business district. The only known connection to the rest of the outbreak was that this case-patient worked at a retail outlet ≈50 m from one of the locations visited by the index case-patient (27). The case was quickly linked to the rest of the cluster through whole-genome sequencing, providing reassurance that widespread undetected community transmission was unlikely (28). The circumstances of the transmission event remain unknown. Because the genomic link was established, the alert level was not changed. However, the general public was asked to avoid the Auckland central business district, if possible, for ≈3 days.

In December 2020, an airline crew member tested positive for COVID-19. The worker was self-isolating at an airline hotel-based facility (as opposed to a dedicated MIQ facility) because of return from a high-risk country (United States). The crew member tested positive within the first 48 hours of self-isolation, and there were no recorded secondary infections (29). Genomic sequencing indicated that the infection had been acquired abroad. Although this case meets our definition of a community case in that it occurred outside one of the MIQ facilities, the wider community was at little risk, and the case was managed according to aircrew protocols (30).

A returnee (case-patient A) tested positive for COVID-19 1 week after completing managed isolation at the Pullman MIQ facility (January 2021). Despite extensive travel across the Northland region while infected with the B.1.351 lineage (Beta variant) of SARS-CoV-2 (H. Tegally et al., unpub. data, https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v) (31), no secondary infections were reported, including in case-patient A’s traveling companion. Shortly thereafter, 2 additional cases (case-patients B and C) with the same variant (and their household contact) were found in the community; case-patients B and C had completed self-isolation at Pullman (32). The outbreak was successfully limited to these 4 community cases, which were genomically linked to a returnee under isolation at Pullman. Case-patient A had occupied a room on the same floor as the source case-patient and may have been infected through the air circulation system; whereas, case-patient B was most likely infected from using an elevator 3 minutes after the source case-patient, despite their use of face masks (33). New arrivals at the MIQ facility were suspended, and its air filtration systems were improved.

On February 13, 2021, a total of 3 household members in Auckland tested positive for SARS-CoV-2. The genomes were identical and of the highly transmissible B.1.1.7 (Alpha) variant (34,35). Although 1 case-patient worked at an airline services company, that person had no obvious contact with persons coming through the border. Auckland was immediately sent into its third alert level 3 lockdown for 3 days, and widescale surveillance testing commenced. Other cases with closely related virus genomes were found; however, the epidemiologic links were not always strong (36). A fourth alert level 3 lockdown followed shortly after, when another case was found that could not immediately be linked to the cluster.

The known outbreak was restricted to 4 households and 15 cases, although epidemiologic gaps suggest that there may have been undetected cases. Genetic evidence showed 4 distinct genomes among 14 cases, which was not informative beyond confirming a single origin; the B.1.1.7 variant’s global overrepresentation presented further difficulties at pinpointing an overseas origin. The outbreak has not been traced back beyond the original 3 cases, and its origin remains unknown.

During the Auckland February outbreak, an airline crew member tested positive 1 week after arriving from Japan (37). Self-isolation was not required because the worker did not arrive from a high-risk location. There were no known secondary infections, including household contacts. Genomic sequencing suggested that the infection was most likely acquired overseas.

In late March 2021, a cleaner at the Grand Millennium MIQ facility tested positive. Despite this person being infected with the more transmissible B.1.1.7 lineage, there were no known secondary infections in the community. Two weeks later, 2 other workers from the same facility tested positive. All 3 cases were genomically linked back to a returnee isolating at the Grand Millennium.

A worker at Auckland International Airport tested positive for the B.1.1.7 variant in April 2020. No onward transmission was detected. Genomic sequencing linked the case to a recent returnee, and a follow-up investigation showed that the infected worker had cleaned the airplane on which the returnee had arrived, so it was likely a case of fomite or airborne transmission, despite the worker wearing personal protective equipment (38).