New Zealand's Omicron outbreak is now being dominated by multiple BA.2 lineages genetically linked to our country. Image / Supplied
New Zealand's Omicron outbreak is now being dominated by multiple BA.2 lineages genetically linked to our country. Image / Supplied
New Zealand's Omicron outbreak is now being dominated by multiple BA.2 lineages genetically linked to our country – reflecting how widely the sub-variant has been able to spread and evolve here.
An ESR scientist says it's likely our variant profile will shift again when re-opened borders bring yet more formsof Omicron to spread alongside our own.
Within just a few months, scientists have watched the original Omicron subtype BA.1 overwhelm the Delta variant - before levels of BA.1, too, were squashed by the faster-spreading BA.2.
ESR's bioinformatics and genomics lead Dr Joep de Ligt said genomic analysis of Covid-19 samples, mainly from cases picked up at our border and in hospitals, showed BA.2 continued to circulate "almost exclusively".
"And it's given rise to BA.2.10 - a local lineage that's dominated by New Zealand cases in the international data."
But that wasn't unexpected, he said, and pointed to the fact the virus had mutated enough while spreading here to branch into genetically different virus "clades".
"The fact that New Zealand are now seeing these things means we have what we call persistent transmission chains that allow the virus to accumulate these mutations," he said.
"We can now also see a BA.2.10.1 - which is the next edition down this line."
He stressed the genetic changes hadn't made the virus - responsible for another 5745 community cases today, and linked to 13 more deaths - yet more transmissible or severe.
For now, he said cases of BA.2 unlinked to our clades were rarely detected, while the most recent case of Delta was sequenced back in March.
"Global data tells us that Delta is now reported at zero per cent – so it seems the Omicron variants have suppressed it to such a level where it's become undetectable," he said.
"That doesn't mean that there aren't Delta cases out there walking around, but just that it's being out-competed by all of these other subvariants."
This graph shows what variants made up New Zealand's Covid-19 cases between late January and mid-March. Blue denotes Delta, red Omicron BA.1, yellow BA.2, and amber unclassified Omicron. Image / ESR
This graph shows variants in New Zealand since mid-March. Red denotes Omicron BA.1, yellow BA.2, amber unclassified Omicron, and green Omicron types BA.4, BA.5 or XE. Image / ESR
Infections with the high-profile BA.4 and BA.5 subvariants, meanwhile, had so far been confined to border cases.
"Because BA.4 and BA.5 appear to have a slight advantage over BA.2, it might be that it gets displaced, just as BA.1 was," he said.
"But given these have only been established in a few countries, it's still a case of wait and see."
In South Africa, the two new sub variants are suspected to have driven a six-fold jump in cases over the past few weeks – but it wasn't clear whether that was because of waning immunity, or those sub types being better able to evade immunity or infect people.
Last weekend, officials reported the first confirmed case of BA.5 in New Zealand – a traveller from South Africa – but insisted the public health settings already in place to manage BA.2 were also appropriate to manage the other Omicron types.
"The good news is that BA.4 and BA.5 also don't seem to be more severe at this point in time – and while they might have a small advantage, it's still not likely we'd see them suddenly drive a second big wave here."
Modellers expect New Zealand's next surge – perhaps as soon as late winter – to come on the back of waned immunity from either vaccination, infection or both.
With perhaps as many as three million people infected already, its trajectory is unlikely to be as dramatic as Omicron's first wave.
Could a game-changing variant entirely different from Omicron arrive before then?
"These are always very dangerous predictions to make: we only have to look back to how some people were saying Delta would be the last variant, and that the virus had exhausted its fitness," de Ligt said.
"This is a virus that's only been in humans for two or three years now, and it's still adapting to us as its hosts, and to vaccines and immunity."
