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

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.

Exploring the depth and breadth of the genomics toolbox during the COVID-19 pandemic: Insights from Aotearoa New Zealand.

“…BA.2 followed soon after and its transmission advantage saw it rapidly displace BA.1. Genomics demonstrated that in the first half of 2022 approximately 85% of all New Zealand cases were BA.2 -we largely skipped the first Omicron BA.1 wave [14].…”

“…By March 2022, the MIQ system was dismantled, and New Zealand opened to citizens, permanent residents and work visa holders without the need to self-isolate until testing positive. Pre-departure tests were dropped by mid-June 2022 coinciding with the arrival of subvariants BA.4, BA.5, BA.2.12.1 and BA.2.75 -first at the border, then in the community [14]. In mid-2022, using the genomes of border detections compared to community cases we estimate that there is about one new incursion per day into the community from the ~8000 international daily arrivals.…”

“…Genomic surveillance demonstrated that BA.1 was the first Omicron variant to arrive in New Zealand [14]. BA.2 followed soon after and its transmission advantage saw it rapidly displace BA.1.…”

“…In 2022 as border restrictions were progressively scaled back across New Zealand, we were able to observe a change in state from that in which a single lineage from a single introduction spread across the country, to the situation we have today where there are regular border 'jumps'. In mid-2022 genomic surveillance estimated that there was ~1 border 'jump' per 5000 passenger arrivals, or about 2 per day [14]. These metrics provide modellers with estimates of the speed at which variants arrive, spread and their fitness advantage.…”

Modelling the impact of the Omicron BA.5 subvariant in New Zealand

“…The B.1.1.529 (Omicron) variant of SARS-CoV-2 was designated a variant of concern by the World Health Organization on 26 November 2021 [1] subsequent to a rapid growth in cases of COVID-19 in southern Africa [2]. Following transmission from cases in managed isolation facilities into the community in January 2022 [3], New Zealand experienced a large Omicron wave with a cumulative attack rate of around 220 confirmed cases per 1000 people between 1 February and 31 May 2022. This wave was dominated by the BA.2 subvariant, which accounted for an estimated 84% of cases, with BA.1 accounting for the remaining 16%.…”