Coronavirus | New virus lineage found in West Bengal

It has a major mutation that helps it evade immune system and possibly compromise vaccine efficacy

With elections ongoing in West Bengal, scientists report the emergence of a new lineage of coronavirus that may comprise as much as 15% of the genomes in the State from January to March. 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, named a “

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 that is now seeing over 270,000 new infections a day, the most in the world, and straining India’s health infrastructure to its seams.

Four characteristic mutations

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 other States, West Bengal too has seen a sharp spike in cases . On April 1 it was reporting 829 cases a day and that has since spiked to 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.”

Global repository

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 they 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 contains the E484K mutation. Some vaccine makers are already developing vaccines that reportedly account for the mutation.