‘Stealth Omicron’: What is subvariant BA.2 and should we be worried?

Just as governments across the world have voiced their intentions to ease 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 causing concern in the US as fears of yet another wave of COVID-19 gains pace.

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

In Denmark, it became the dominant subvariant, and now researchers in the US are bracing for a similar trend.

“A lot of us were assuming that it was going to quickly take off in the United States just like it was doing in Europe and become the new dominant variant,” Nathan Grubaugh, an associate professor of epidemiology at the Yale School of Public Health, told NPR.

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 Organization (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, in many countries, the BA.2 has begun to spread faster.

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.

“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’

The UK Health Security Agency designated the BA.2 as a variant under investigation in January while emphasizing that current case rates are very low.

The agency said they will undertake further analyses.

“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 proportion of BA.2 cases in the UK increased from 0.2 per cent of cases to 0.8 per cent between January 8 and 15, according to genomics researchers at the Wellcome Sanger Institute.

The US has also reported cases of the subvariant from coast to coast, with an infection rate of 3.9 per cent of all new cases, according to the Centers for Disease Control and Prevention (CDC). That figure is believed to be doubling. If it does, experts believe the US will be confronted with a new resurgence of the virus.

Should we be concerned?

The WHO has labeled Omron 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”.

In a press briefing, the SSI’s technical director Tyra Grove Kraus said: “There is some indication that it is more contagious, especially for the unvaccinated, but that it can also infect people who have been vaccinated to a greater extent”.

She said that this could see the peak of Denmark’s current wave extend further into February than previously forecast.

At the same briefing, Danish health minister Magnus Heunicke said the Omicron variant appears more contagious but not more severe.

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