A case study of extended in-flight transmission of SARS-CoV-2 en route to Aotearoa New Zealand

Background: Since the first wave of COVID-19 in March 2020, people returning to New Zealand have been required to undergo managed isolation and quarantine (MIQ) for 14 days with mandatory testing for SARS-CoV-2. As of 20 October, testing in MIQ had identified 215 cases of SARS-CoV-2 from a total of 62,698 arrivals. While the majority of infections were likely obtained in the country of origin prior to departure, there have been possible reports of in-flight transmission. Methods: Seven people who arrived in New Zealand on the same flight on 29 September tested positive during their stay in MIQ (out of 86 passengers). The seven passengers originated from five different countries before travelling on the same flight from Dubai, United Arab Emirates (UAE) to Auckland, New Zealand. Information about their journeys, disease progression and virus genomic data was used to assess possible points of infection. Findings: All seven SARS-CoV-2 genomes were genetically identical, with the exception of a single mutation in one case, and all genomes had five signature mutations seen in only six other genomes from the >155,000 genomes sequenced globally. Four of these six related genome sequences were from Switzerland, the country of origin of the suspected index case. Interpretation: By combining information on disease progression, travel dynamics and genomic analysis, we conclude that at least four in-flight transmission events of SARS-CoV-2 likely took place.