Omicron Sub-Variant BA.2: Everything You Need To Know About The 'Stealth Omicron' Outpacing Other Sub-Strains

BA.2, nicknamed 'Omicron's little brother', is believed to have emerged from a mutation of Omicron. It appears to be outpacing other sub-strains of Omicron in some regions of the world.

Representational image (Photo: Getty Images)

New Delhi: India has reported more than 500 cases of a new sub-variant of Omicron, known as BA.2. According to the UK Health Security Agency (UKHSA), India has uploaded 530 samples of BA.2 to GISAID, a global science initiative providing open-access data to genomic data of influenza viruses and SARS-CoV-2, as of January 21.

BA.2, nicknamed 'Omicron's little brother', is believed to have emerged from a mutation of Omicron, referred to as B.1.1.529. Omicron itself was a mutation of the Delta variant.

The latest Covid-19 variant accounts for the majority of the most recent cases in a number of countries, including India, Denmark and Sweden. 

The UKHSA has designated the Omicron sub-variant as a variant under investigation (VUI-22JAN-01) on Friday. 

The variant, also known as the "stealth Omicron", appears to be outpacing other sub-strains of Omicron in some regions of the world.

In Which Countries Is BA.2 Most Dominant?

The BA.2 sub-variant, detected in at least 43 countries, is believed to have become the most common variant in a number of countries. It already accounts for the majority of the most recent cases in a number of countries, such as India, Denmark, and Sweden, according to media reports.

The number of daily cases of Covid-19 has started to rise again in Denmark.  In the first 10 days of January, the UKHSA identified more than 400 cases in Britain.

The original Omicron strain, also called BA.1, is dominant in the United Kingdom, and the proportion of BA.2 cases is currently low, according to the UKHSA. 

On the basis of the increasing numbers of BA.2 sequences identified both domestically and internationally, the designation was made.

As of January 21, 426 cases of Omicron BA.2 have been confirmed by Whole Genome Sequencing (WGS). The earliest case was dated December 6, 2021.

London and the South East are the areas with the largest number of confirmed cases in the UK, with 146 and 97 cases respectively.

According to early analyses, BA.2 has an increased growth rate compared to BA.1.

A total of 40 countries have uploaded 8,040 BA.2 sequences to GISAID since November 17, 2021. The first sequences were submitted from the Philippines, and most samples have been uploaded from Denmark, according to the UKHSA.

Denmark, Sweden, and Singapore have uploaded 6,411, 181, and 127 cases of BA.2 respectively. The variant has raised fears that more transmissible strains of SARS-CoV-2 can cause a larger Covid-19 wave next.

France's Public Health Agency has said the Danish authorities have no explanation for this phenomenon, but it is being closely monitored, according to an AFP report.

Since the number of daily cases in Denmark are on the rise again, Débarre said that it suggests that BA.2 is even more transmissible.

The countries in Europe in which BA.2 has been sequenced are the UK, Germany, Belgium, Italy, and France. North America, Asia, and Australia have recorded cases as well.

Why Is BA.2 Called 'Stealth Omicron'?

The stealth Omicron lacks the genetic deletion on the spike protein at 69-70, which produces the S-gene target failure in some polymerase chain reactions. This has been used as a proxy for Omicron cases previously.

In other words, the original strain has a mutation in the form of the deletion of the S gene, while the sub-strain does not have the same mutation. Since BA.2 does not have the specific mutation seen with the original strain of Omicron which can help to easily distinguish it from the Delta variant, the sub-variant is known as stealth Omicron.

However, Cornelius Roemer, a computational biologist at Switzerland's University of Basel, said on Twitter that BA.2 is detectable by PCR and that some news reports are totally wrong. He added that depending on the PCR test used, it may not look like BA.1, but will still give a positive result. 

BA.2 _is_ detectable by PCR, these news reports are totally wrong.
Depending on the PCR test used it may not look like BA.1 (the other Omicron). But it will still give a positive result.
Frustrating to see falsehood about non-detectability still around.https://t.co/yeFzgIi84j

— Cornelius Roemer (@CorneliusRoemer) January 16, 2022

Where Was BA.2 First Detected?

The Omicron sub-variant was first identified in India and South Africa in late December 2021, according to media reports.

Though other sub-lineages, such as BA.3 or BB.2 have also been identified, they have attracted less attention from epidemiologists because the number of cases of people contracting BA.2 has dramatically increased.

BA.2 has more than 20 mutations, about half of them in the spike protein, which interacts with human cells and is key to the virus entering the body.

Is BA.2 As Dangerous As The Original Omicron Strain?

The World Health Organization (WHO) says that Omicron has three main sub-strains: BA.1, BA.2, and BA.3. The US health agency does not distinguish between BA.1 and BA.2 at this stage. 

The WHO reported that 99 per of the cases it sequenced, as of December 23, were BA.1.

Denmark, on Thursday, reported that the BA.2 sub-strain of Omicron accounts for almost half of the country's cases, according to media reports.

Oliver Véran, Minister of Solidarity and Health of France, said that BA.2 corresponds more or less to the characteristics known about Omicron, according to the AFP report. He said that the sub-variant is not a "game changer" at this stage.

The scientific community is closely studying BA.2, but there is yet no precise data on its resistance to vaccines or the severity of the cases of Covid-19 it causes.

Tom Peacock, a virologist from the Imperial College of London, tweeted that "very early observations from India and Denmark suggest there is no dramatic difference in severity compared to BA.1. He further said that the data should become more solid in the coming weeks. 

*Very* early observations from India and Denmark suggest there is no dramatic difference in severity compared to BA.1. This data should become more solid (one way or another) in the coming weeks.

— Tom Peacock (@PeacockFlu) January 19, 2022

According to Peacock, there is likely to be minimal difference in vaccine effectiveness against BA.1 and BA.2. He added that personally, he is not sure that BA.2 is going to have a substantial impact on the current Omicron wave of the pandemic.

"Several countries are near, or even past the peak of BA.1 waves. I would be very surprised if BA.2 caused a second wave at this point. Even with slightly higher transmissibility, this absolutely is not a Delta -> Omicron change and is instead likely to be slower and more subtle," Peacock wrote in the same thread.

He said he wouldn't be surprised if BA.2 slowly replaces BA.1 over the coming months with a slightly optimised mutational profile.

According to epidemiologist Antoine Flahault, director of the University of Geneva's Institute of Global Health, monitoring should make it possible to test the resistance of BA.2, in particular, if people are infected with the classic Omicron are again contaminated with the sub-variant, the AFP report said. 

According to Dr. Meera Chand, Covid-19 Incident Director at UKHSA, there is insufficient evidence so far to determine whether BA.2 causes more severe illness than Omicron BA.1. She said that it is the nature of viruses to evolve and mutate, so it is to be expected that we will continue to see new variants emerge as the pandemic goes on, according to the UKHSA. 

What Makes BA.2 Difficult To Identify?

Stealth Omicron is not easy to track. According to Florence Débarre, a biologist at the Institute of Ecology and Environmental Sciences in Paris, a variation in PCR test protocols and the fact that the type of kit varies from one laboratory to another makes it difficult to reliably identify BA.2, the AFP report said.

She said that BA.2 and Delta could not be distinguished in the UK because of the way the tests are carried out.

Genetic sequencing of the virus is a more accurate but less commonly used tool for tracking variants, the AFP report said.

With this, the exact presence of this sub-variant could be identified. However, sequencing has the drawback of being slow, which means it is not suitable for monitoring a rapidly spreading variant.