Subvariant BA.2: What we know about the globally dominant 'Stealth Omicron' COVID strain

The Omicron COVID variant BA.2 accounts for half of all Omicron cases in Denmark.
The Omicron COVID variant BA.2 accounts for half of all Omicron cases in Denmark. Copyright Canva
Copyright Canva
By Ian SmithDavid Walsh with Reuters and AP
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BA.2, one of three known subvariants of Omicron, is now the most dominant form of COVID in the world, believed to be more transmissible than previous strains.


Just as governments across the world have eased COVID-19-related restrictions, the spectre of another wave of the virus is sparking concern among the scientific community.

Omicron subvariant BA.2, which is being dubbed with the moniker "Stealth Omicron," is now believed to be the dominant strain of COVID-19 in the world.

In the US, it is causing more than half of the country's weekly infections.

According to the data from the Centers for Disease Control and Prevention (CDC), infections from BA.2 have jumped 39 per cent in a week, pushing infection rates to between 51-59 per cent.

In China, too, a new wave of coronavirus has been linked to the spread of subvariant BA.2, with the country's largest city Shanghai - a city home to 26 million people - beginning a phased lockdown this week to contain it.

In January, the subvariant - which is believed to be more contagious than the original Omircon variant whose spread has begun to slow - was initially noted in over 40 countries, including the UK, Sweden and India.

It is worth noting that while BA.1 has dominated case numbers around the world, it causes less severe disease compared to the delta variant.

Recent studies from the U.K. and Denmark suggest that BA.2 may pose a similar risk of hospitalization as BA.1.

Why 'Stealth Omicron'?

Given the speed at which it has outpaced other Omicron subvariants, BA.2 is sparking fears that a more transmissible strain of coronavirus is actively spreading through the community.

Omicron, which is also referred to as B.1.1.529, has three main substrains, BA.1, BA.2, and BA.3, according to the World Health Organisation (WHO).

Up until now, it has been BA.1 that has been dominating with the WHO estimating it makes up a large majority of all Omicron cases.

However, the BA.2 has spread faster to become the dominant form of COVID-19.

The original version of Omicron had specific genetic features that allowed health officials to rapidly differentiate it from Delta using a certain PCR test because of what’s known as “S gene target failure”.

BA.2 doesn't have this same genetic quirk.

A person with BA.2 will still test positive for the coronavirus on a PCR test, but their case won't be flagged as BA.2 unless their original sample goes through genetic sequencing.

While standard PCR tests are still able to detect the BA.2 variant, they might not be able to tell it apart from the delta variant.

“It's not that the test doesn't detect it; it's just that it doesn't look like Omicron,” Dr Wesley Long, a pathologist at Houston Methodist in Texas told the Associated Press.

"Don’t get the impression that ‘stealth Omicron’ means we can’t detect it. All of our PCR tests can still detect it”.


UK watching BA.2 'closely'

BA.2 began getting attention in January when the UK Health Security Agency designated it as a variant under investigation in January.

"This sub-lineage, which was designated by Pangolin on 6 December 2021, does not have the spike gene deletion at 69-70 that causes S-gene target failure (SGTF), which has previously been used as a proxy to detect cases of Omicron," it said in a statement.

"UKHSA are continuing to monitor data on the BA.2 sub-lineage closely," it added.

According to Dr Meera Chand, Incident Director of the UKHSA, "it is the nature of viruses to evolve and mutate, so it's to be expected that we will continue to see new variants emerge as the pandemic goes on”.

“Our continued genomic surveillance allows us to detect them and assess whether they are significant," she added.


The rise in BA.2 in certain parts of the world is most likely due to a combination of its higher transmissibility, people’s waning immunity and relaxation of COVID-19 restrictions.

Should we be concerned?

The WHO has labelled Omicron as a variant of concern but it has not given any special designation to BA.2.

It says that “studies are needed to better understand the properties of BA.2, including comparative assessments of BA.2 and BA.1 for key characteristics such as transmissibility, immune escape and virulence”.

The WHO also calls on countries to increase surveillance through testing and sequencing to better understand the Omicron sub-variants.

"Initial analysis shows no differences in hospitalisations for BA.2 compared to BA.1,” said Denmark’s Statens Serum Institut, a government-run infectious disease research centre, in a statement in January.


"It is expected that vaccines also have an effect against severe illness upon BA.2 infection".

Though there may be an uptick of BA.2 infections in the coming months, protective immunity from vaccination or previous infection provides defense against severe disease.

This may make it less likely that BA.2 will cause a significant increase in hospitalisation and deaths.

Whether there will be another devastating surge depends on how many people are vaccinated or have been previously infected with BA.1.

It’s safer to generate immunity from a vaccine, however, than from getting an infection. Getting vaccinated and boosted and taking precautions like wearing an N95 mask and social distancing are the best ways to protect yourself from BA.2 and other variants.


While the natural immunity gained after COVID-19 infection may provide strong protection against reinfection from earlier variants, it weakens against omicron.

A recent preliminary study that has not yet been peer reviewed of over 1 million individuals in Qatar suggests that two doses of either the Pfizer–BioNTech or Moderna vaccines protect against symptomatic infection from BA.1 and BA.2 for several months before waning to around 10 per cent.

A booster shot, however, was able to elevate protection again close to original levels.

Importantly, both vaccines were 70 per cent to 80 per cent effective at preventing hospitalization or death, and this effectiveness increased to over 90 per cent after a booster dose.

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