‘Double mutant’ most common variant now: India’s data on genome

The so-called semi-mutated coronavirus found in Maharashtra could become the most common among all mutant variants in India, indicates genomic sequence data sent by Indian scientists to a global database, according to a recent analysis that takes into account when they were detected.

The analysis shows for the first time how the detection of various variants of the coronavirus may have changed.

The double mutation virus – now classified as B.1.617 – was the most common in the samples sequenced in the 60 days before April 2 with 24%. The variant was first detected on October 5 and was relatively obscure until it appeared during a growing number of samples January, onwards, the India situation report showed on outbreak.info. On April 1, it accounted for 80% of all analyzed genomic sequences of mutant variants sent from India to the global GISAID repository.

The second most commonly found variant in the last 60 days was the British variant, or B.1.1.7, at 13% of the samples, according to scientists from Scripps Research.

Both trends could worry India and, at least to some degree, explain the explosive model. B.1.617 was first found in a large number of samples in Maharashtra, the first hot spot region of the second wave of infections, which by 7 April had added more than half of the new cases recorded in the country.

The researchers at outbreak.info added that these data may not reflect the true prevalence patterns. “A sequence of SARS-CoV-2 (hCoV-19) is not a random sample of mutations. As a result, this report does not indicate the true prevalence of the mutations, but rather our best estimate now.”

The data can also be distorted depending on whether all sequenced genomes have been uploaded, although the trends – where B.1.617 has steadily increased compared to other variants between samples – support the overall pattern.

But a senior official involved in the efforts of India’s successive coronavirus genome said the findings match what they observed on earth.

“Almost 60 to 80% of the samples from Maharashtra have the variant; the prevalence must be similar in Gujarat. Elsewhere it is less than 10 to 20%. Since barely existing in December, it is now found almost everywhere we look. We have a separate column for the variant for each state now, ”said Anurag Agarwal, director, Institute of Genomics and Integrative Biology, one of the ten laboratories under Insacog.

“We have a pretty good idea of ​​which mutated variant rules where; but the important thing is that everyone grows, ”he added.

“Variant B.1.617 rules in the west in Maharashtra and Gujarat. Variant B.1.1.7 is common in the North in Punjab. In South India, the one with N440K mutation is common but that seems to be quiet. Finally, one of the other variants will get there. And, in the East, we do not have a particular variant, but the South African variant is quite common in Bangladesh, causing almost 80% of the cases to cross over to India. That will be annoying for the AstraZeneca vaccine. “

The double mutation refers to specific changes, among some others, that are indicated by E484Q (glutamate is replaced by glutamine at the 484th site of the stinging protein) and L452R (replacement of leucine by arginine at the 452nd position).

Both are being investigated because they have given the virus an ability to prevent immunity from past infection, even vaccines. L452R was also found in a variant spreading in California, USA, where it was involved in a major explosion earlier this year. In an interview with HT on Wednesday, India’s chief scientific adviser, K VijayRaghavan, said B.1.617 can now be considered a “critical variant”, or VOC.

The UK variant, B.1.1.7, has been confirmed to be more transferable and has similarly been involved in a large resurgence of cases across the UK.

A second scientist involved in the sequencing efforts said more evidence is needed to link mutations with case trends. “The double mutation variant is growing in the country. But the increase in cases cannot be attributed only to the mutated variants. Human behavior plays a very important role in transmission; in the UK when the new variant began to spread blockade controlled the spread, ”said Dr Rakesh Mishra, director, Center for Cellular and Molecular Biology (CCMB), one of the 10 laboratories in Insacog.

Dr Saumitra Das, director of the National Institute of Biomedical Genome – Kalyani, said: “We could not state that the new variant is the reason for the faster spread of the infection during the second wave; it is the behavior of the people. “

The analysis, published on outbreak.info, also showed that a large number of B.1.617 samples were detected in West Bengal. The 117 B.1.617 samples in Bengal represented 9% of all genomes sequenced in the state to date. In Maharashtra, at 120, there were more samples, but these represented 6% of the 1,931 samples sequenced.

“To describe the prevalence of mutation sets in our Mutation Status Reports, we rely on common virus sequences from the GISAID Initiative. While we apply filters to remove some low-quality sequences and unfair metadata as described in our methods, we rely on the accuracy of the sequences and sample metadata deposited in GISAID, ”the website outbreak.info said.

In total, variant B.1.617 was found in 408 sequences tested worldwide. Of these, 265 were found in India out of the 8,455 sequences analyzed in the report outbreak.info.