Once Omicron transmission is detected in the community, all of NZ will move to the red setting of the traffic light system. Video / NZ Herald
An emergent Omicron subtype appears to be swiftly rising in New Zealand – yet scientists don't expect BA.2 to eclipse its cousin as it has overseas, but spread Covid-19 alongside it.
As of Tuesday, the original type BA.1 accounted for around three-quarters of 1315 Omicron MIQ and community cases genomically sequenced since the start of the year.
But rates of BA.2 have been quickly creeping up over the past few weeks – and scientists have been closely watching to see whether it might become our dominant coronavirus strain.
That's already happened in many parts of Asia and Europe.
While rates of BA.2 in the US have been recently tripling, it still only made up less than 4 per cent of all sequenced cases there, as per the week ending February 5.
The subtype shares the same 32 mutations with BA.1 - but many others that 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 telltale missing target gene.
This graph shows the proportion of different virus lineages over time per week in 2022, with blue representing Delta, red showing Omicron's BA.1 subvariant, and yellow denoting the emerging BA.2 subtype. Image / ESR
That's left scientists to instead track it using genomic data, in the same way they did with earlier variants like Delta.
But why BA.2 appeared to have a growth advantage over BA.1 in some countries - estimates have put it at between 30 per cent to 50 per cent more contagious - still remained largely unclear.
In its latest report, the UK Health Security Agency found it was "plausible" that higher transmissibility and a shorter serial interval – a duration between when one infected person starts to show symptoms to when the next person infected becomes symptomatic – were factors behind its higher spread.
The agency also reported no great difference in vaccine effectiveness against the two types; in fact, protection against symptomatic disease was slightly higher for BA.2 (74 per cent after two to four weeks) than BA.1 (69 per cent).
While studies have suggested BA.2 may be more resistant to monoclonal antibody treatments, there wasn't yet enough firm data to show it made people sicker.
Some early "pre-print" studies, released ahead of peer review, have indicated there may be a higher risk of severe illness.
One such paper, led by Japanese researchers and using hamsters, found BA.2 may cause heavier lung infection than BA.1 - while carrying an effective reproductive number 1.4-fold higher.
"Together with a higher effective reproduction number and pronounced immune resistance of BA.2, it is evident that the spread of BA.2 can be a serious issue for global health in the near future," the researchers reported.
University of Auckland infectious diseases expert Dr David Welch nonetheless felt it was too early to say.
An emergent Omicron subtype appears to be swiftly rising in New Zealand - yet scientists don't expect BA.2 to eclipse its cousin as it has overseas, but spread Covid-19 alongside it. Image / 123rf
"Figuring out whether there's a difference in severity is very hard, but there's nothing upfront that suggests it's going to be," Welch said.
"In fact, in Denmark, where BA.2 is dominant, they aren't seeing a big difference."
University of Otago virologist Dr Jemma Geoghegan agreed it'd be premature to make inferences around disease severity.
University of Otago virologist Dr Jemma Geoghegan. Photo / Supplied
"There's nothing that's been of note yet."
Both experts also saw no reason to say BA.2 would knock out BA.1 here.
Geoghegan noted an Auckland wedding at the centre of New Zealand's initial Omicron outbreak was linked to BA.1, while a second high-profile "superspreader" event – Hamilton's Soundsplash Festival – was hit by BA.2.
"So, they seem to have got into different populations – and there's probably every reason why both would persist at the moment," she said.
"We'll see when things get more out of control, but I can see this pattern continuing for some time at least."
Welch added: "I expect both BA.1 and BA.2 numbers to increase quickly, with the proportion of BA.2 growing.
"But it is likely BA.2 won't completely dominate and we'll see numbers of both variants start falling around the same time."
Meanwhile, scientists are still keeping a sharp eye on Delta, which still accounted for most sequenced Covid-19 cases in our hospitals, along with 5 to 7 per cent of all sequenced cases in MIQ and the community.
Between Omicron and Delta, there was a much starker difference.
While Omicron could be between two to three times more infectious than Delta among vaccinated and boosted people, cases were typically milder.
One pre-print study found Omicron infections carried half the risk of hospitalisation, just a quarter of the risk of ICU admission - and 91 per cent less risk of death.
