Covid 19 pandemic: Fast-rising Omicron subvariant thought to be ‘homegrown’

A rising proportion of locally-sequenced Covid-19 cases appear to be from a “homegrown child” of a long-circulating Omicron subvariant – although there’s no sign it poses any extra risk to us.

Scientists have already observed a raft of Omicron sub-types genetically linked to New Zealand, reflecting the ample opportunity the coronavirus has had to spread and evolve here.

But one of those appears to be a stand-out in our messy “subvariant soup”, with the latest ESR surveillance tying it to one third of hospital samples sequenced over recent weeks.

That’s FK.1.1 - a lineage derived from CH.1.1, which itself linked back to the BA.2 type that powered the country’s first major Omicron wave more than a year ago.

ESR’s pathogen genomics technical lead Dr David Winter said FK.1.1 included several mutations that changed proteins in the virus, including two in the spike protein, which it used for accessing our cells.

These changes weren’t “obviously linked” to increased infectivity.

“But the surveillance data does show this lineage growing and, by our best uncertain estimates, to doing so at a rate similar to the XBB sub-lineages being tracked here and overseas.”

Of XBB lineages - a family of immune-evasive hybrids originally stemming from BA.2.10.1 and BA.2.75 - the most widespread in New Zealand remained the so-called “Kraken” strain, XBB1.5, which made up 30 per cent of ESR’s latest community genome sequences.

But rates of Kraken’s cousin XBB1.16 - dubbed “Arcturus” and recently the number one source of Covid-19 in India - had shot up to the point it comprised about 13 per cent of sequenced community samples.

FK.1.1, meanwhile, made up about 22 per cent of those community samples, and Winter expected to see it circulate alongside XBB lineages for some time.

While the evidence that FK.1.1 was indeed a homegrown strain, the majority of the earliest cases in public databases happened to be from New Zealand.

“We have been quite unusual globally in CH.1.1 being common here for a long time, so perhaps it’s not surprising that this is the place a CH.1.1 virus would acquire a few extra mutations,” Winter said.

Just in: Detailed classification of #COVID19 variants in #Aotearoa New Zealand reveals XBB.1.5 as the most prevalent, while FK.1.1 & XBB.1.16 are proliferating. #Wastewater analysis confirms the prevalence of XBB & CH.1.1, consistent with WGS data
See: https://t.co/8ucqpICcLP pic.twitter.com/osGS3SQc5Q

— Rhys White 🧬 (@RhysTWhite) May 5, 2023

“We can’t be sure this lineage arose here, but widespread transmission of a virus means new mutations and changes in infectivity are always possible.

“So, we’ll keep watching this lineage and for others that others that might pop up.”

Otago University evolutionary virologist Dr Jemma Geoghegan said there were likely plenty of cases of genetic variations occurring in New Zealand - many of which may have gone undetected by genomic sequencing.

“It’s just this one happens to have increased in frequency; that’s not to say that it might take over, but that circumstances have allowed it to spread like this here.”

The factors behind its rise weren’t completely clear.

“There’s always going to be background variation in the virus population but a lineage that emerges and increases in frequency is going to have some sort of advantage,” Geoghegan said.

“It might also be that there’s a super-spreading event and that this particular lineage happened to get in first, but it’s increased to the point that it’s being continually detected.”

Meanwhile, while reported Covid-19 cases continued to trend downward around New Zealand, the virus continued to cause hundreds of hospitalisations and tens of deaths each week.

The Ministry of Health’s latest weekly update, covering the seven days to April 30, reported 306 hospital cases and 31 new deaths with the virus.

Its next update is due today.