New Omicron variant on the rise amid NZ’s pre-Christmas Covid-19 wave

Another new Omicron variant is quickly gaining speed in New Zealand, just as a full-swing Christmas party season pours fuel on our fifth Covid-19 wave. Photo / NIAID-RML

Another new Omicron variant is quickly gaining traction in New Zealand, just as a full-swing Christmas party season adds to our fifth Covid-19 wave.

The subvariant JN.1, a descendant of the Omicron type BA.2.86 nicknamed “Pirola”, has emerged as the world’s fastest-growing coronavirus strain and now accounts for one in 10 cases sequenced here.

ESR’s pathogen genomics technical lead Dr David Winter said it was unclear whether it would ultimately outcompete the subvariant group - EG.5 or “Eris” - that has so far made up the bulk of cases in our pre-Christmas wave.

Now accounting for about a third of cases in the UK and US, and being increasingly seeded into New Zealand by international flights, JN.1 was separated from BA.2.86 by just a single change in its cell-hacking spike protein.

While the extraordinarily mutated Pirola itself never took off in the way scientists first suspected it would, JN.1 might have picked up some of the extra transmissibility that its close relative lost, Covid-19 modeller Professor Michael Plank said.

Importantly, there was no indication JN.1 carried a higher risk of severe disease than its Omicron counterparts, he said – and, at least for now, its contribution to our current wave was small.

The most recent data from wastewater surveillance showed the virus at its highest levels since January - albeit still well below the giant surges of 2022 - while the last update from Te Whatu Ora reported 336 people in hospital with Covid-19 as at Sunday.

Another four deaths have also been recorded, bringing New Zealand’s official toll since the start of the pandemic to 3,596.

The wave has also brought a boosting bump: the 32,734 vaccinations given in the last week of November was six times the average number administered over previous months.

“Cases were starting to come down, but now they’ve turned around and have started to go back up again, which is maybe an effect of the Christmas party season,” Plank said.

“I wouldn’t be surprised if we see cases further increase in this pre-Christmas period and possibly start to come back down again, once school holidays kick in.

“But maybe JN.1 will reverse that trend and start to send numbers upward again, perhaps after the New Year.”

When would the world see a completely new variant, as when Omicron succeeded Delta?

“Everything with Omicron has evolved from a common ancestor, whereas all the other variants before it that had Greek letters evolved independently from the initial Wuhan strain,” Otago University evolutionary virologist Dr Jemma Geoghegan said.

“So, we’d have to see a substantial leap in evolution.”