According to a recent analysis that takes into account when they were detected, the so-called double-mutated coronavirus found in Maharashtra could be becoming the most common among all mutant variants in India.
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 sequenced samples in the 60 days prior to April 2 with 24%. The variant was first detected on October 5 and was relatively dark until it began appearing in a growing number of samples as of January, according to India’s status report at outbreak.info . April 1 accounted for 80% of all genome sequences analyzed of mutant variants sent by India to the global GISAID repository.
The second most frequently found variant in the last 60 days was the UK variant, or B.1.1.7, with 13% of the samples, according to the assessment of Scripps Research scientists.
Both trends could be worrisome for India and at least to some extent explain the pattern of outbreaks. 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, as of April 7, added more than half of the new registered cases in the country.
The researchers at outbreak.info added that this data may not reflect actual prevalence patterns. “SARS-CoV-2 (hCoV-19) sequencing is not a random sample of mutations. As a result, this report does not indicate the true prevalence of the mutations, but our best estimate now. “
Data can also be distorted depending on whether all sequenced genomes were loaded, although trends, where B.1.617 has grown steadily compared to other variants among the samples, support the general pattern.
But a senior official involved in coronavirus genome sequencing efforts in India said the findings were consistent with what they have observed on the ground.
“About 60 to 80% of Maharashtra samples have the variant; the prevalence should be similar in Gujarat. Elsewhere, it is less than 10-20%. Since it barely existed in December, it is now virtually everywhere we look. We now have a separate column for the variant for each state, ”said Anurag Agarwal, director of the Institute of Genomics and Integrative Biology, one of Insacog’s ten laboratories.
“We have a good idea about which mutant variant is common where; but the important thing is that everyone is increasing, ”he added.
“Variant B.1.617 is prevalent to the west in Maharashtra and Gujarat. Variant B.1.1.7 is common in the north in the Punjab. In southern India, one with an N440K mutation is common, but appears to be quiet. Finally, one of the other variants will arrive. And, in the East, we don’t have any particular variant, but the South African variant is quite common in Bangladesh, causing almost 80% of the cases, so it could happen in India. This will be problematic for the AstraZeneca vaccine. “
The double mutation refers to specific changes, among others, that are denoted by E484Q (glutamate is replaced by glutamine in the 484th spot of the ear protein) and L452R (replacement of leucine by arginine in the 452nd position).
Both are being investigated to give the virus the ability to evade immunity from a past infection, even vaccines. L452R has also been found in a variant that spread to California, USA, where it was involved in a major outbreak earlier this year. In an interview with HT on Wednesday, India’s top scientific adviser, K VijayRaghavan, said B.1.617 could now be considered a “variant of concern” or VOC.
It has been confirmed that the UK variant, B.1.1.7, is more transmissible and has been similarly 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 to case trends. “The double mutant variant is increasing in the country. But the increase in cases cannot be attributed solely to mutated variants. Human behavior plays a very important role in transmission; in the UK, when the new variant began to spread a blockade, it controlled the spread, “said Dr. Rakesh Mishra, director of the Center for Cellular and Molecular Biology (CCMB), one of the 10 laboratories in the Insacog.
Dr. Saumitra Das, director of the National Institute of Biomedical Genomics – Kalyani, said: “We have not been able to establish that the new variant is the reason for the fastest spread of the infection during the second wave; it is the people’s behavior “.
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 accounted for 9% of all genomes sequenced in the state to date. In Maharashtra, at 120, there were more samples, but they accounted for 6% of the 1,931 sequenced samples.
“To describe the prevalence of mutation sets in our mutation status reports, we rely on GISAID Initiative shared virus sequences. Although we apply filters to remove some low-quality sequences and irrational metadata such as describes 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 has been found in 408 sequences sampled worldwide. Of these, 265 were found in India out of the 8,455 sequences analyzed in the outbreak.info report.