‘Stealth Omicron’: All you need to know about fast-spreading sub-strain

The BA.2 sub-strain of Omicron was detected in November last year, but it started spreading recently in recent weeks. The situation is particularly bad in Denmark, where Covid-19 infections have seen a rapid increase.
The World Health Organization has identified three sub-strains of the Omicron variant: BA.1, BA.2 and BA.3.(Representative Photo)
The World Health Organization has identified three sub-strains of the Omicron variant: BA.1, BA.2 and BA.3.(Representative Photo)
Published on Jan 22, 2022 08:37 AM IST
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By | Written by Amit Chaturvedi, Hindustan Times, New Delhi

A new sub-variant of Omicron has raised fears that more transmissible strains of the coronavirus could spark larger Covid-19 waves globally.

The health authorities in the UK have designated the sub-variant, called BA.2, as ‘variant under investigation’. It is the initial step of investigation before being designated a ‘variant of concern’ (VOC), which the original Omicron BA.1 currently is.

The sub-lineage, dubbed ‘stealth Omicron’, was designated in early December last year and as of January 10 this year, 53 sequences of BA.2 had been identified in the UK.

How many sub-strains dose the Omicron variant have?

According to World Health Organization (WHO), the Omicron variant has three sub-strains: BA.1, BA.2 and BA.3. It further said that as many as 99 per cent of the cases sequenced were found to be containing the BA.1 sub-strain.

The WHO further said that the knowledge about B.1.1.529 is still developing, but this lineage is more diverse.

But now, more sub-variants have been emerging, especially in one of the worst-affected regions by the spread of Covid-19, Europe.

Where have the cases of the BA.2 sub-variant been detected?

Apart from the UK, the BA.2 has been found in Denmark, Norway and Sweden. Scientists in France and India have also warned about the quick spread of the BA.2 sub-variant, which is expected to outpace other Omicron strains.

The situation is particularly bad in Denmark where BA.2 has gone from accounting 20 per cent of the cases to 45 per cent between late December and mid-January.

Denmark has been reporting over 30,000 cases this week, 10 times more than the peak in previous Covid-19 wave.

BA.2 vs BA.1 vs BA.3

Researchers have pointed to the probable reason why the new sub-strain is expected to become the dominant cause of Covid-19 in months to come.

Vipin M Vashishtha, Member of WHO’s Vaccine Safety Net, said on Twitter that BA.2 shares 32 mutations with BA.1 but also has 28 unique mutations of its own.

The BA.3 sub-strain is probably antigenically similar to BA.1 as it shares mutations at 417, 446, 484 and other key sites, added Vashishtha.

However, Denmark has said that it is too early to tell what the mutations of BA.2 mean. “So far there is no information as to whether BA.1 and BA.2 have different properties," said the Statens Serum Institut, a government-run infectious disease research centre.

Denmark’s government also said that their initial analysis shows there is no difference in hospitalisations for BA.2 compared to BA.1. The government announced that it is easing restrictions as the number of people needing intensive care is decreasing.

Why is it called ‘stealth Omicron’?

When the scientists discovered the Omicron variant, they noted that its original strain - the BA.1 - has a mutation in the form of a deletion in the “S” or spike gene which was detected by the PCR tests. The BA.2 sub-strain, however, does not have the same mutation, due to which it was called ‘stealth Omicron’.

But in recent weeks, many experts have claimed that the sub-strain does show up on PCR tests. “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,” Cornelius Roemer, a computational biologist at Switzerland's University of Basel, said on Twitter.

But BA.2 is currently in the news, according to virologist from the Imperial College of London Tom Peacock, because it has shown growth across multiple countries, which is the evidence that BA.2 may be some degree more transmissible than BA.1

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