An Omicron variant lurking in our communities since winter now appears to be driving the majority of Covid-19 cases in New Zealand – while another that sparked initial alarm among scientists is yet to make a splash.

As health officials closely watch another late-year uptick in cases, genomic sequencing suggests our viral landscape hasn’t shifted dramatically in more than a year, with infections still being caused by an ever-evolving soup of Omicron offshoots.

While none of these strains has proven capable of causing massive waves among what’s now a highly vaccinated, well-exposed population, they’re still finding tricky new ways to infect us.

“Our last wave, and it wasn’t a big one, was six months ago now – so some of that immunity will have waned and the variants that we have now are just a bit different from what we had back then,” Covid-19 modeller Professor Michael Plank said.

“And the reason they’re able to establish is because they have some level of immune evasion that gives them just enough of a toehold to drive cases up.”

One subvariant first identified here over winter – EG.5 or “Eris” – was the most dominant, making up more than 36 per cent of sequenced virus samples.

A “descendant” within that same type, labelled HK.3, accounted for a further 25.3 per cent.

“We’ve seen plenty of variants come in, grow quickly and then hit a plateau and slow down,” ESR’s pathogen genomics technical lead Dr David Winter said.

“But EG.5 has been a bit of a freight train in its consistent, ongoing growth – and that’s because it’s been innovating and finding new mutations.”

This graph shows the distribution of Omicron subvariants among coronavirus samples genomically sequenced in New Zealand since August. The type EG.5, or "Eris", now makes up 36 per cent of samples, while its descendant lineage HK.3 accounts for a further 25 per cent. Source / ESR

When it first made itself known to the world back in February, Eris was shown to pack one new mutation in its spike protein, which the virus used to unlock host cells.

Winter said it had been “fine-tuning” itself ever since, yet still hadn’t demonstrated the potential to power big waves. Nor had any of the other Omicron subvariants circulating since last winter’s BA.5-driven surge.

These included a group of “recombinant” strains, such as XBC, XBB and its offshoots XBB.1.16 and XBB.1.15, all of which accounted for about a third of current sequenced cases.

Intriguingly, Winter added, New Zealand and Australia remained among the few places in the world where XBC – essentially a hybrid of Delta and Omicron – was still spreading.

“It makes up about 10 per cent of our cases and it seems to stick around forever, and this could be because there’s something different about the immunity here.”

New Zealand authorities recently began assessing an updated Omicron vaccine targeted at the XBB.1.5 “Kraken” strain, for which Australia’s Therapeutic Goods Administration granted full registration last month.

A Pfizer spokesperson said that, with the Covid-19 landscape continuing to evolve, it was unclear what the need for further updated vaccines would be in future.

“However, the virus that causes Covid-19 has proven itself to be highly prone to mutations, similar to influenza, so annual vaccine updates seem likely.”

Another Omicron type detected here in August – BA.2.86 or “Pirola” – accounted for just 2 per cent of cases, despite initial concern that its strikingly distinct genetic machinery could cause serious problems.

Otago University evolutionary virologist Professor Jemma Geoghegan.

Otago University evolutionary virologist Professor Jemma Geoghegan said she’d been taken aback at Omicron’s growth since it began overtaking its predecessor Delta in late 2021.

“To be honest, it continues to surprise me how much convergent evolution we’ve seen there within it – and how much space it still has to explore, to become even fitter and more transmissible.”

With the world on the verge of seven million formally reported Covid-19 deaths, the big question facing scientists such as Geoghegan and Winter is when – and how – Omicron’s successor will show up.

“We’ve already seen these huge evolutionary jumps from the ancestral strain, to Alpha, to Delta and then to Omicron,” Geoghegan said of the pandemic’s run of Greek letters to date.

“There’s no evidence of anything new like that circulating at the moment, but that doesn’t mean it won’t happen in future. That’s why it’s important we keep doing genomic surveillance.”

Jamie Morton is a specialist in science and environmental reporting. He joined the Herald in 2011 and writes about everything from conservation and climate change to natural hazards and new technology.