The UK has said that a new sub-strain of the Omicron variant of coronavirus has been detected in over 40 countries which can escape even the RT-PCR test. The BA.2 sub-strain, commonly called the “stealth Omicron”, has caused fears of a stronger wave across Europe.

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 spreading quickly.

For instance, Denmark reported on January 20 that the BA.2 sub-strain accounts for almost half of the country’s active cases.

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.

Why is ‘stealth Omicron’ a 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 sublineage 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 told India Today.

So, are 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,” said Dr Harsh Mahajan, MD and founder, Chief Radiologist, Mahajan Imaging.