Covid-19: India Finds a New Virus Variant in Three States

Manas Dasgupta

NEW DELHI, Apr 21: Concerns have been expressed if the vaccines developed by India and in some other countries will be effective for the newer mutations the Coronavirus seems to be developing frequently.

After finding two mutations, the researchers have now found three mutations located in Maharashtra, Delhi and West Bengal and the researchers are still studying if the existing vaccines will be able to battle against the new variant.

As India reports nearly three lakh cases and over 2,000 deaths in 24 hours, the biggest jump since the pandemic erupted, a new mutation in the COVID virus has emerged as the new challenge.

After the double mutation, it is now the triple mutation, meaning three different Covid strains combining to form a new variant, has been detected in some parts of the country. Researchers believe that the triple mutant variant may be partly responsible for the rapid surge in the daily cases in Maharashtra, Delhi and West Bengal. Globally too, the new variants are contributing in the new surges.

“This is a more transmissible variant. It is making lots of people sick very quickly,” a researcher of epidemiology said. “We have to keep tweaking vaccines. For that we need to understand the disease. But we need sequencing on war footing,” he said. That sets up a huge challenge for India, where genome sequencing is being done for less than one per cent of all cases, currently.

The researcher said the delay in detecting the double mutation may have contributed to the current virus spurt. Explaining mutations he pointed out that more a virus spreads, more it replicates and mutates and now three Covid variants have combined to form the triple mutation.

Experts believe mutations are driving the fresh infection spikes, not just in India but across the world.

How infectious the triple mutation is, or how deadly, will be known only from more studies. For now, only 10 labs across India are involved in virus genome studies.

The double mutant shows increased transmission rate and is seen to affect children too. It has more severe pathogenicity, say scientists.

Even as study of the mutations are still on, scientists sad two of the three variants in the triple mutation have been seen to have immune escape responses, meaning they are more resistant to antibodies. Not much more is known yet on the effectiveness of vaccines. Scientists believe the new variant has some ability to escape the body’s naturally acquired immunity to Covid.

Scientists also believe that the new variant B.1.618, has a major mutation called E484K — found in several of the internationally identified variants of concern — that helps it evade the immune system and possibly compromise vaccine efficacy.

On April 8, INSACOG (Indian SARS-CoV-2 Consortium on Genomics), a group of 10 Indian labs working across the country on sequencing genomes from coronavirus patients, had named the double mutant variant as B.1.617 that contains two mutations, E484Q and another L245R. Though more studies are under way, there’s suspicion that this variant, whose mutations have also been found in variants in other countries, may be playing a significant role in the nearly month-long exponential rise in cases straining India’s health infrastructure to its seams.

The B.1.618 was first isolated on October 25, 2020 and most recently on March 17. The variants that carry some of the mutations associated with B.1.618 have also been found in the U.S., Switzerland, Singapore and Finland. While mutations occur in all parts of the coronavirus genome, key changes to the spike protein — that help the virus bind better to the body’s cells — are most closely tracked. In the case of B.1.618, there are four characteristic mutations to the spike protein associated with increased infectivity and immune escape.

“The proportion of B.1.618 has been growing significantly in recent months in West Bengal,” Vinod Scaria, who researches genome mutations at the CSIR-Insititute of Genomics and Integrative Biology said on Twitter. “Along with B.1.617, it forms a major lineage in West Bengal.” The IGIB is part of the INSACOG. The samples detailing the genetic structure of the virus was collected by the National Institute of Biomedical Genomics (NIBG), Kalyani, West Bengal — also an INSACOG lab. Though its goal is to sample 5% of coronavirus samples, the consortium has sampled around 1%.

He said at the moment there wasn’t ‘conclusive’ evidence that the lineage was driving the epidemic in West Bengal, other than the fact that the numbers and proportions were rising. Like some other states, West Bengal, helped by the election rallies on large scale, too has seen a sharp rise in cases- from 829 cases a day on April 1 to over 7,000 cases everyday with 53,000 active cases reported as of Tuesday. This has prompted some Opposition parties to announce withdrawing from campaigns and calls to club the remaining phases of the polling.

Partha Majumdar, geneticist and a former director of the NIBG, said though the variant was spreading rapidly it alone can’t be linked with the acceleration of cases in West Bengal. “Mutations play a role but as only 15% of those infected carry the B.1.618, it cannot alone explain the surge.”

The 15% only represents the number of samples whose data has been shared by Indian scientists on the global repository GISAID, a forum for researchers everywhere to collate data and track emerging variants and strains. In spite of its huge number of cases, there are relatively fewer samples and details of their genetic information regularly uploaded out of India.

Some laboratories have started testing the virus, containing these mutations, to see if vaccines are effective against mutations. Rakesh Mishra of the Centre for Cellular and Molecular Biology, Hyderabad, said the institute was testing plasma from those inoculated with Covishield and Covaxin against virus variants to check if it escaped antibodies. Studies so far have shown that the Novavax, Johnson and Johnson and Pfizer vaccines were less effective against the South African variant, that contained the E484K mutation. Some vaccine makers are already developing vaccines that reportedly account for the mutation.