Explained: What NZ can expect from new Omicron subvariant

It's been dubbed "son of Omicrion" by the world's media, but BA.2 is better considered a close cousin to the subvariant it's overtaking around the world – and soon will here. Science reporter Jamie Morton explains.

Where did this subvariant come from?

Just as we've seen the original "wild type" of the Sars-CoV-2 virus branch into variants, variants spawn subvariants.

The B.1.1.529 variant that was first detected in South Africa just 69 days ago – and which we today know better as Omicron – has been observed in three main subtypes.

Those are BA.1, which has spread like wildfire around the world and replaced Delta in the pandemic driver's seat; BA.2; and the relatively rare BA.3.

But BA.2's star is rising fast.

It's already beating out its cousin in parts of Europe and Asia, and has so far been confirmed here in some border workers and their families.

In Denmark, it's responsible for more than 80 per cent of new infections already.

In the UK, scientists suspect a falling proportion of PCR tests with the original Omicron lineage isn't due to competition from older variants like Delta, but the ascendant BA.2.

While it shares the same 32 mutations with BA.1, some important features set it apart.

Whereas BA.1 is commonly identified because it's missing one of three target genes used in standard PCR tests, BA.2 has been nicknamed "stealth Omicron" because it doesn't have that tell-tale missing target gene.

That's left scientists to instead track it using genomic data, in the same way they did with earlier variants like Delta.

Does BA.2 pose a bigger threat?

Early studies into BA.2 have yielded good and bad news.

The good news was that, so far, it hasn't proven any more severe than the BA.1 subvariant, which itself was much less likely than Delta to make people sick enough to need to go to hospital.

"Whether or not it causes more severe disease will become apparent as more data is collected," said Professor Jonathan Ball, a molecular virologist at the UK's University of Nottingham.

The Omicron variant is more closely related to a Sars-CoV-2 ancestor discovered back in mid-2020, than the Delta variant which it rapidly replaced. Photo / CDC

"Of course, it is important to keep monitoring the situation and try to gain a better understanding of how this variant behaves, but so far there is nothing in these early analyses to worry us unduly."

It was less clear whether BA.2 was better at evading vaccine immunity than BA.1.

A new Danish study suggested it may possess immune-evasive properties that further reduce the protective effect of vaccination against infection.

Still, analyses have shown the booster shot offered a similar level of protection – up to 90 per cent – at keeping infected people out of hospital.

The bad news: it's estimated to be 1.5 times more transmissible than BA.1, which largely explained its swift path to dominance.

Even on the basis of what we know about the spreading power of BA.1, New Zealand modellers are anticipating a quick-building wave that could soon peak with tens of thousands of daily infections.

A faster-spreading Omicron might mean more cases – and more pressure on the health system.

The precise reasons for BA.2's apparent advantage remain unclear.

Scientists have so far pointed to changes within its spike protein - used by the virus to recognise and invade susceptible host cells - as well as in its receptor binding domain.

Associate Professor Stuart Turville, of the University of New South Wales, said those changes in the binding domain may increase transmissibility, but there still hadn't been enough data to compare both subvariants head-to-head in the community.

"It may turn out to be a more transmissible sub-variant to BA.1 - and not unlike what we have seen with small changes in variants that can drive the supplanting of one versus another."

Associate Professor James Wood, an infectious disease epidemiologist also of the University of New South Wales, predicted BA.2 would replace BA.1 in Australia within mere months.

Still, he didn't expect it to immediately cause a new epidemic wave, or to lead to a major change in disease severity.

Otago University virologist Dr Jemma Geoghegan said the same pattern might also play out here.

Otago University virologist Dr Jemma Geoghegan. Photo / Supplied

"We have to remember that a lot of this can depend on epidemiological factors like super-spreading, as well as genetic factors," she said.

"But all else being equal, we can still probably expect to see an increase in BA.2 cases."

What are the other big unknowns?

Geoghegan said a big unanswered question was whether BA.2 could infect someone after they'd already been infected with BA.1.

"We know that reinfections can happen and that's been reported – but not necessarily with the same variant," she said.

"What would be helpful to know is that, if you've already had BA.1, and you're fully vaccinated with the booster, if you're less likely to become infected again, either with BA.1 or BA.2."

Another question was - assuming BA.2 took over – how long its reign would last.

"Omicron has quickly become dominant and spread around the world, so whatever comes next is going to have to be even fitter."

Interestingly, she pointed out Omicron emerged not from a Delta ancestor, but from one that dated to around mid-2020.

"So, it's hard to know whether Omicron is going to produce more subvariants – or whether a whole new variant will come along that might be more closely related to something else."