The reign of an Omicron subvariant that fuelled our last Covid-19 surge could be over within weeks, with two other fast-spreading lineages quickly on the rise – and another potential wave-maker waiting in the wings.

The latest ESR surveillance showed community prevalence of BA.5 - which helped push daily reported cases past 10,000 in mid-July – had fallen to about 75 per cent of sequenced genome samples.

At the same time, two sub-variants – BA.4.6 and BA.2.75 - now accounted for 15 and 10 per cent of community sampling.

While these two off-shoots appeared to be quickly on track for domination, ESR bioinformatics and genomics lead Dr Joep de Ligt said their apparent rise could be partly explained by a drop-off in PCR testing, following changes to our border settings.

"These two have sort of been slumbering in the background, but do now appear to be picking up," he said.

"It's not scary just yet, but they clearly are creating a longer tail to our winter wave."

Still, he expected BA.5 could soon be overtaken by one or several subvariants that have been causing fresh Covid-19 waves overseas.

"Probably, by the end of the month, BA.5 won't be our main variant anymore."

The latest hospital surveillance results – covering the last weeks of September – showed 90 per cent of cases were BA.5, compared with five per cent BA.2.75, four per cent BA.4.6 and one per cent BA.4.

Experts have already warned that winter surges in the Northern Hemisphere are likely to translate to another wave here before the year is out – with the possibility of several subvariants in the driver's seat.

"What will happen here is going to depend on a lot of different factors, but it's clear that we're going to be importing positive cases, because, with no pre-departure testing in place now, these will be moving directly into the community."

Just like BA.4 and BA.5 swiftly replaced the subvariants responsible for New Zealand's first Omicron wave – BA.1 and BA.2 - de Ligt expected the next changeover to play out with similar speed.

"If our borders were closed and we weren't importing anything, then this would likely happen with BA.4.6 and BA.2.75," he said.

"But the one that we're really closely watching, is BQ.1.1, which is heavily on the rise in the UK and has that potential to cause another large wave here."

While little is yet known about BQ.1.1 - a descendant of BA.5 that was discovered mere weeks ago – scientists are concerned over mutations that help it evade immunity, and also reduce the effectiveness of monoclonal antibody treatments.

According to the latest surveillance report, no cases of BQ.1.1 have yet been reported here – but with our diminished surveillance, it was possible the subvariant has already begun spreading in our communities.

"Generally, what we'd be expecting is co-circulation of several of these variants, where one is more likely to drive a peak, while the others just cause a continuous grind."

Covid-19 modeller Professor Michael Plank agreed our coming wave would be much more complex than any before it.

"We have a sort of variant soup, with different lineages growing at different rates, which makes it difficult to predict how big this wave will be," he said.

"It's unfortunate that now we can't so easily distinguish border cases from community ones in the sequencing data, as it's become harder to tell how quickly some of these variants are spreading in the community."