Explainer: Why the arrival of a new sub-variant of the coronavirus requires India to keep a closer watch on COVID-19 cases

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Over recent days, India has posted a significant increase in daily COVID-19 cases and active infections.

The rise may have been caused by the possible arrival of a new SARS CoV 2 mutant, BA2.12.1, a sub-variant of Omicron BA.2 that was noticed in the third wave of the COVID-19 pandemic, according to insiders in the Indian SARS-CoV-2 Genomics Consortium (INSACOG), which monitors genomic variations in the virus.

Although neither the Union health ministry nor INSACOG have announced the detection of the new sub-variant, scientists told Moneycontrol that the new mutant is highly contagious and capable of again infecting previously infected people.

Significantly, the presence of the L452Q mutation in BA2.12.1, which was also noticed in the SARS CoV 2 Delta variant that caused the devastating second COVID-19 wave, has heightened concern.

BA2.12.1 is a sub-lineage of Omicron BA.2. According to senior virologist Dr Shahid Jameel, this mutant is spreading quickly in north-eastern United States, but doesn’t appear to be significantly more contagious that other BA.2 versions.

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“All of these sub-variants are on average about 12 times more infectious than the original virus,” he said.

BA.1—the other variant of Omicron-- is about 10 times more infectious than the original virus while BA.2 variants are about 20 percent more infectious compared to BA.1.

Some other experts said BA2.12.1 may be even more resilient and transmissible.

Dr Eric Topol, a US clinician and scientist, wrote on Twitter that in his country, the BA.2 wave was morphing into a BA2.12.1 wave.

Data from the US Centres for Disease Control shows that the new mutant caused 19 percent of new cases in the US last week, up from 11 percent a week before and 7 percent the week before that.

Back home, INSACOG sources said that in Delhi, which is currently experiencing the sharpest surge in COVID-19 cases in the country, a final analysis hasn’t been done yet, but BA2.12.1 had been found in a large number of samples that underwent whole genome sequencing this week.

In India, during the Omicron wave in January, BA.2 was the dominant sub-lineage, detected in more than 80 percent of the samples subjected to whole genome sequencing.

BA2.12.1 has the L452Q mutation that in the case of the Delta variant of the coronavirus was seem to have increased the ability of the virus to infect human cells.

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It is not yet clear how the L452Q mutation confers a growth advantage on BA.2.12.1. As the L452 position of the spike protein is critical for the virus binding to the human receptors, it is likely that the mutation could potentially enhance the transmissibility of the virus.

This also suggests that this sub-lineage could potentially have immune escape properties or the ability to infect people who have been previously immunised -- either by infections or by vaccination

Although nothing definitive can be said about the severity of BA2.12.1, a close watch needs to be kept on COVID-19 cases and hospitalisation rates, Dr. Jameel said. That’s because it has the L452Q mutation, also seen in Delta but not in BA.2.

Dr Pragya Yadav, a senior scientist at the National Institute of Virology- Indian Council of Medical Research (NIV-ICMR) said she was not yet sure of the sub-variant’s arrival in India, but stressed that concerns will arise if a cluster of cases were detected in a particular geography.

“But we will need to keep a watch on the hospitalisation patterns,” she said.

In Delhi, which has nearly 3,000 active COVID-19 cases as of now, the highest in an Indian state presently, less than 1 percent of patients are in hospital.

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“For the time being, I don’t see any reason to panic,” scientist Dr Anurag Agrawal, who has previously been associated with INSACOG and is now a senior faculty at Ashoka University, wrote on Twitter.

“With a very small truly vulnerable group (India), there should not be a big wave that stresses healthcare. Go on with life but do get your booster and do use the mask responsibly for yourself and others,” he wrote.