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Reinfection is set to rise. (Image: NIAID, CC BY 2.0, additional design by Tina Tiller)

ScienceFebruary 8, 2022

What we know about the new fast-spreading omicron BA.2 sub-variant

Covid-19 virus particles
Reinfection is set to rise. (Image: NIAID, CC BY 2.0, additional design by Tina Tiller)

You’ve heard of variants – but what about sub-variants? Mirjam Guesgen answers some frequently asked questions about the omicron variant making the news. 

What are sub-variants anyway?

Think of them as different flavours of icecream in the same family. You’ve got your chocolate icecream (variant) but you can also get white, milk or dark chocolate flavours (sub-variants).

If you want to get technical, John Taylor, a senior lecturer in virology at the University of Auckland, explains that a sub-variant is “a virus with a set of mutations that define it as belonging to a distinct origin and lineage, but with a set of mutations that mark it as different from the parental variant.”

OK, so what is BA.2?

It’s a sub-variant of the omicron strain.

Usually when referring to omicron classic, people are talking about the most common BA.1 flavour. There’s also the rarer BA.3 version.

BA.2 is classed as a (sub)variant under investigation by the UK. So, not yet a variant of concern.

A queue at a vaccination hub in London on December 18. The rush for vaccines has been prompted in part by the rise of the omicron variant (Photo: Wiktor Szymanowicz/Future Publishing via Getty Images)

How common are these sub-variants?

BA.1 is still the dominant omicron type around the world right now but BA.2 has been reported in close to 50 countries, including Aotearoa.

There are a few countries where BA.2 is becoming the most common sub-variant. The UK for example has reported more than 1,000 cases of BA.2 as of 31 January. In Denmark, 65% of new cases are omicron BA.2.

BA.3 is really rare and mostly found in the UK, South Africa, Germany and Poland.

How are these sub-variants different from omicron classic?

BA.2 shares a lot of the same mutations as BA.1 but is missing others and has a couple of unique ones of its own.

In fact, the difference between BA.1 and BA.2 is more than between the original Covid-19 and alpha variants.

BA.3 is even stranger. With no specific mutations in the spike protein, it’s a franken-hybrid of the mutations found in BA.1 and BA.2.

But because the BA.2 and BA.3 sub-variants were only first reported at the end of 2021/early 2022, scientists are still characterising them and they may find other key differences later on.

How does BA.2 affect people?

At this stage it seems as though BA.2 gets passed slightly more easily from person to person than BA.1, according to UK data.

Danish researchers also estimate that the sub-variant may be one-and-a-half times more easily spread from person to person than BA.1. It’s even more easily spread between people who aren’t vaccinated. Note that this research is a preprint, meaning it hasn’t been published or reviewed by other scientists.

However, The UK Health Security Agency hasn’t found any evidence that vaccines (any of them) are less effective against the BA.2 sub-variant. According to the agency, three doses of a vaccine is 63% and 70% effective at preventing disease where you show symptoms for BA.1 and BA.2 respectively. Those numbers drop to 9% (BA.1) and 13% (BA.2) for double-dosed people.

In Denmark, researchers say that people aren’t any more or less likely to be hospitalised because of BA.2 than BA.1.

These conclusions are based on limited data, almost solely from the UK and Denmark.

headlines mentioning the "stealth variant" of omicron
Recent global headlines mentioning the so-called stealth variant of omicron, BA.2

What’s this about BA.2 being a “stealth variant”?

There’s talk that BA.2 isn’t picked up by Covid lab tests but that’s not the case.

Some overseas lab tests rely on detecting two-out-of-three target genes on the virus. The one target that fails is a mutation on the spike gene or S-gene.

That method works for BA.1 but BA.2 doesn’t have this S-gene mutation and all three target genes show up in the test.

The issue isn’t so much that overseas tests weren’t picking up BA.2, it was that it showed up like other variants including delta, which also doesn’t have the S-gene mutation.

“But it doesn’t make a difference here,” explains Jemma Geoghegan, a senior lecturer in the Department of Microbiology and Immunology at the University of Otago. “New Zealand labs don’t currently use the S-gene amplification in their PCR tests.”

And even if they did, it would still be possible to tell BA.2 apart from other variants or sub-variants if omicron was the dominant variant (get an S-gene failure and you’ve got BA.1, don’t get it and you’ve got BA.2) or if labs do full genome sequencing.

How common are BA.2 and BA.3 here in New Zealand?

It’s hard to say right now because the the Ministry of Health isn’t currently reporting the number of sub-variants identified in community cases.

It does however say that both BA.1 and BA.2 have been detected at the border and in the community through whole genome sequencing. At the time of writing, no BA.3 cases have been identified.

How do BA.2 and BA.3 fit into the bigger picture of the future of the pandemic?

The jury is still out on what this means in the short and long term.

Some experts are saying BA.2 might extend the current omicron wave in some countries, while others are saying it’s unlikely there’ll be another spike in cases.

“I don’t expect it to immediately cause a new epidemic wave or to lead to a major change in disease severity,” says James Wood, an infectious disease epidemiologist and modeller from the University of New South Wales in Australia.

Nathan Grubaugh, an epidemiologist at the Yale University School of Public Health in the US, told the New York Times that he thinks US cases of omicron will continue to decline in the coming weeks, “but I don’t yet know what that would mean for the pandemic”.

A lot more experiments are underway right now to get a clearer picture.

Virologist John Taylor says: “It’s happening almost in real time and is the focus of so many scientists around the world. The rate at which information emerges is really breathtaking.”

The Ministry of Health says: “Omicron was first detected in late November and we are still learning about the variant, and the omicron sub-variants. We will continue to carry out whole genome sequencing for the vast majority of cases to detect different variants of Covid-19 and also to understand transmission pathways.”

For now, it’s still all about keeping calm and getting vaccinated and boosted. Vaccination means there are fewer pockets of vulnerable people that the virus can sneak into and mutate into other variants or sub-variants.

The ministry also recommends wearing well-fitting face masks, physical distancing and scanning in using the Covid-19 Tracer app when out and about. Anyone with any cold or flu symptoms that could be Covid-19 is asked to get a test and isolate at home until a negative result is returned.

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