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Covid-19 virus particles
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.

Keep going!
About half of NZ reckon the red light settings have struck the right balance, according to a new poll.
About half of NZ reckon the red light settings have struck the right balance, according to a new poll.

ScienceFebruary 1, 2022

What will the next Covid variant look like?

About half of NZ reckon the red light settings have struck the right balance, according to a new poll.
About half of NZ reckon the red light settings have struck the right balance, according to a new poll.

Every time it seems the world is coming to grips with the virus, a new variant sneaks around immune systems and infects people like never before. So what form will the virus take next? Is there even any way to know? And does omicron mark the beginning of the end?

The latest variant of concern, the fifth since Covid original, is spreading around the world faster than glitter on the hands of kids at a birthday party.

With some countries once again putting travel restrictions in place, limits on gatherings in force and hospitals full, you can hear the cries of “when will it end?!”

The good news is the pandemic will end. As other pandemics have. But what that ‘end’ looks like is still somewhat mysterious.

Scientists have laid out six, main possible scenarios and one that’s looking particularly likely is that the virus becomes endemic.

Endemic means the virus is still around, circulating in communities, and that outbreaks crop up every now and again. The comparison that’s often made is to seasonal flu (read: still bad and still kills people but not world-stopping).

But how quickly we get there, and what the path there looks like, is difficult to predict. “The virus becoming endemic is likely, but the pattern that it will take is hard to predict,” Angela Rasmussen, a virologist from Georgetown University, told Nature.

Why is that pattern hard to predict? Because we’re dealing with a biological organism and, even though we’ve more or less understood the dynamics of evolution since Darwin’s time, it’s still hard to predict how that organism will change and mould itself to its surroundings.

“Predicting biological or evolutionary outcomes is really, really hard,” says Jemma Geoghegan, a senior lecturer in the department of microbiology and immunology at the University of Otago. “We don’t know how the selection pressures might play out and how that’s going to affect the evolution of the virus.”

Quick evolution recap: individual organisms look and act slightly differently. In some cases, those differences give an individual an advantage in their environment. Depending on the conditions, or selection pressures, of the environment, those traits grow in number over generations.

When it comes to the virus, it’s looking to spread to as many people as possible and it needs traits like changing the shape of its spike protein so antibodies don’t stick, to do that.

But, theoretically, if those changes mean that a person gets sicker and stays away from others or if the person dies before the virus can move on, that’s not very useful in an evolutionary sense. It’s a balance between transmissibility and virulence (how severe an infection the virus causes).

Which is why there’s been some talk about omicron being the beginning of the end of the pandemic because it’s more easily passed from person to person and doesn’t make them as sick.

But according to Geoghegan, because the SARS-Cov-2 virus is usually passed on before someone gets sick, there’s not a strong evolutionary pressure for the virus to become less virulent, or less severe.

“It’s not necessarily the case that the virus will always become avirulent. It really comes down to how it affects its transmission,” she says.

“It might also be true though that as more people get some protection from the virus, through vaccination or past infection, then infection might become milder for them since they have some immunity.”

Researchers do have some information to go on to predict what course the pandemic will take.

For one, they can look at other coronaviruses that circulate and pop up as outbreaks, such as the seasonal 229E virus. Recent research has shown that the likely reason the virus reinfects people periodically is because it’s evolving to escape our immune response (sound familiar?) rather than that our immunity is just waning.

Also, scientists can use what they know about all of the known previous SARS-Cov-2 variants to try to build predictive models of what might be around the corner. Researchers recently developed a computer model based on what mutations have helped a particular virus variant spread in the past.

When they ran it on old data, the model could predict which mutations spread up to four months in advance of it actually happening. It’s early days, but a model like this could be used to monitor how the virus is changing worldwide.

Despite having previous variants to go on, Omicron showed scientists that sometimes, mutations just seem to come out of left field. Some 13 of Omicron’s 30 spike protein mutations have very rarely been seen before in other human coronaviruses or even other animal coronaviruses. One theory is that these rare mutations formed because the virus spent a long time evolving in someone with a weak immune system, like someone with HIV.

Which is why it’s important to bolster people’s immune system and give the virus fewer opportunities to mutate, say experts.

“As long as the virus is spreading, the virus has a chance to mutate. So if you slow the spread, you’re slowing the chances of new mutations arising and therefore new variants,” says Geoghegan.

That means getting people vaccinated, and particularly getting vaccines to parts of the world with low vaccination rates, is crucial. “If 2021 was the year of vaccine production, 2022 must be the year of vaccine equity,” said WHO regional director for Europe Hans Henri Kluge in a statement.

The WHO also says that if we stick to monitoring for new variants, high vaccination rates and third doses, adding ventilation in enclosed spaces, affordable and equitable access to antivirals, targeted testing, and shielding high-risk groups, then we could be on our way to the end.

But wait there's more!