New coronavirus variant emerges in West Bengal

A new Sars-Cov-2 variant has been reported in West Bengal where some of the highest numbers of genome sequencing has been carried out by Indian scientists to check for mutations. 

The variant is labelled as B.1.618, often referred to as the "double mutant".

The new variant has a major mutation called E484K — found in several of the internationally identified variants of concern like the Brazilian and South African variants of the coronavirus — that help it evade the immune system and possibly compromise vaccine efficacy.

"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 (IGIB) said on Twitter, adding "along with B.1.617 it forms a major lineage in West Bengal."

Vinod Scaria added that 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.

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%.

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 Hindu reported.

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 underway, 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.

The B.1.618 was first isolated on October 25, 2020 and most recently on March 17.

Data submitted from India to the global repository GISAID shows the B.1.618, at 12%, is the third most common variant sequenced in the last 60 days. The B.1.617, at 28%, is the most common among sequences, followed by B.1.1.7 (the UK variant), the India Mutation Report by Scripps Research showed, citing the GISAID data.

"The particular variant had appeared some time ago in West Bengal, however we did not study the mutations and its clinical significance in detail as the so-called double mutant variant (B.1.617) out-competed it. The B1.618 variant has plateaued at about 25% of the total mutations reported from Bengal; B1.617 has become predominant. Across the country, there are some districts in states such as Maharashtra where the prevalence of the variant in as many as 80% samples," said Dr Saumitra Das, director, National Institute of Biomedical Genomics, which is one of the 10 laboratories in India's consortium on Sars-CoV-2 genome sequencing (INSACOG).

"What the impact of this variant or B1.617 would be on the vaccine efficacy etc. is all a matter of predictions. It is thought to evade the immune response because it contains the E484K mutation. We will be able to tell the clinical significance of these mutations only when we test it in animal system," he told Hindustan Times

The institute is currently in the process of collecting and growing in laboratory samples of the mutated variants of the virus to establish whether they actually aid the virus in escaping the immune response from vaccines and previous natural infection.

A variant can contain multiple mutations, which are not unusual – particularly for RNA viruses such as Sars-Cov-2 – but since late last year, some of them have made the virus "fitter" – particularly the UK variant, which spreads much more readily than its ancestor – and the South African variant, which appears to cause more repeat infections and make vaccines less effective.

According to the analysis at outbreak.info, 129 of the 130 B.1.618 sequences in India were in samples from West Bengal. India accounts for 62.5% of the B.1.618 variants reported in the world. The variant was first found in a sample outside of India on April 22, 2020.
Experts tracking India's genomic surveillance said that while specific tests are required to determine the implications of the virus, India needs to sequence and share details of more samples.

"India has 8,455 publicly available genomes and around 14 million cases so far. That is 0.06% of cases sequenced. Ideally, we'd want that number to be between 2%-5%, which is in line with successful genomic surveillance programs in other countries," said G Karthik, researcher at Scripps Research Institute, which has put together the mutations tracker at outbreak.info.