Stealth Omicron: What is The Fast Spreading Omicron BA.2 Sub-Variant That Can Escape RT-PCR Test?

Apart from the UK and Denmark, cases of BA.2 sub-strain have been detected in Sweden, Norway, and India.

New Delhi: A new sub-strain of the Omicron variant of coronavirus has been detected in over 40 countries and it can escape even the RT-PCR test, the UK has said. The BA.2 sub-strain, commonly called the “stealth Omicron”, has given way to fears of a stronger wave across Europe. So what is this Omicron sub-variant and how dangerous is it? Here’s what we know so far.

According to the World Health Organisation, the Omicron variant has three sub-strains — BA.1, BA.2, and BA.3. While the BA.1 sub-strain is dominant among the Omicron infections reported across the world, the BA.2 sub-strain is being said to spread quickly. It has been found in a substantial fraction in India as the Covid-19 peak is likely to come in the next fortnight.

“Omicron is now in community transmission in India and has become dominant in multiple metros, where new cases have been rising exponentially. BA.2 lineage is in a substantial fraction in India and S gene dropout based screening is thus likely to give high false negatives,” the INSACOG said.

Countries that have detected cases of ‘stealth Omicron’

Apart from the UK and Denmark, cases of BA.2 sub-strain have been detected in Sweden, Norway, and India. Scientists in India and France have also warned about the sub-strain, fearing it might outpace the BA.1 sub-strain. The UK had identified 53 sequences of the BA.2 sub-lineage as of January 10, with updated figures due to be published later on Friday.

Is ‘stealth Omicron’ a cause of concern?

According to researchers, even as the BA.2 sub-strain shares 32 strains with BA.1, there may be more than 28 unique mutations to it, read a report in Fortune. Researchers say that BA.1, has a mutation — the deletion in the “S” or spike gene — that shows up on PCR tests, making the detection of Omicron easy. BA.2, on the other hand, does not have the same mutation which makes it difficult to detect.

“However, the BA.2 sub-lineage lacks this deletion in the spike so that it can be picked by the use of most of the PCR kits being in use for the RT-PCR tests. This new sublineage BA.2 is called ‘stealth Omicron’ because it lacks the deletion that allows it to be picked up by PCR tests. BA.2 appears to be the major Omicron lineage in parts of India and the Philippines and there is evidence it is growing compared to BA.1 in Denmark, the UK and Germany,” Prof Sunit K Singh was quoted as saying by India Today.

Does that make PCR tests ineffective against stealth Omicron?

While the BA.1 sub-strain may escape RT-PCR tests sometimes, experts say these tests are still the gold standard in detecting the virus. “Lab RT-PCR test is the gold standard test and there is no difference in the sensitivity or pick-up rate between Omicron or the previous Delta while using this test. The over 30 mutations in the spike protein in the Omicron variant do not make any difference in sensitivity using the presently available testing kits,” Dr Harsh Mahajan, MD and founder, Chief Radiologist, Mahajan Imaging told India Today.