Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border (preprint)

ABSTRACT

Recently there has been a surge in emergent SARS-CoV-2 lineages that are able to evade both vaccine induced immunity as well as prior infection from the founding Omicron BA.1 and BA.2 lineages. These highly transmissible and evasive lineages are on the rise and include Omicron variants BA.2.12.1, BA.4, and BA.5. Aotearoa New Zealand recently reopened its borders to many travellers, without their need to enter quarantine. By generating 10,403 complete SARS-CoV-2 genomes classified as Omicron, we show that New Zealand is observing an influx of these immune-evasive variants through the border. Specifically, there has been a recent surge of BA.5 and BA.2.12.1 introductions into the community and these can be explained by the gradual return to pre-pandemic levels of international traveller arrival rates. We estimate there is one Omicron transmission event from the border to the community for every ~5,000 passenger arrivals into the country, or around one introduction event per day at the current levels of travel. Given the waning levels of population immunity, this rate of importation presents the risk of a large wave in New Zealand during the second half of 2022. Genomic surveillance, coupled with modelling the rate at which new variants cross the border into the community, provides a lens on the rate at which new variants might gain a foothold and trigger new waves of infection.