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COVID-19: Genome sequencing by INSACOG shows variants of concern and a novel variant in India: Health Ministry

The new double mutant variants ‘have not been detected in numbers sufficient to either establish or direct relationship or explain the rapid increase in cases in some States,’ it says.

Two new ‘variants of concern’ and a new ‘double mutant’ COVID-variant have been found in India, the Health Ministry said on Wednesday. Variants of concern are mutated types of coronavirus associated with either increase transmission, a reduction in neutralising antibodies or severe disease. However the government said that none of the recent spikes in Maharashtra, Punjab were attributable to the VOC.

"Genomic sequencing and epidemiological studies are continuing to further analyse the situation," the Ministry statement added.

An analysis of samples from Maharashtra has revealed that compared to December 2020, there has been an increase in the fraction of samples with the E484Q and L452R mutations. "Such mutations confer immune escape (evade neutralising antibodies) and increased inactivity," it added.

Worryingly, what the Ministry has also noted is that these mutations have been found in about 15-20% of samples and do not match any previously catalogued Variants of Concerns (VOCs).

“These have been categorised as VOCs but require the same epidemiological and public health response of increased testing, comprehensive tracking of close contacts, prompt isolation of positive cases & contacts as well as treatment as per National Treatment Protocol by the States/UTs,’’ said the Ministry.

It said that from Kerala 2,032 samples (from all 14 districts) had been sequenced. “The N440K variant that is associated with immune escape has been found in 123 samples from 11 districts. This variant was earlier found in 33% of samples from Andhra Pradesh, and in 53 of 104 samples from Telangana. This variant has also been reported from 16 other countries, including U.K., Denmark, Singapore, Japan and Australia. As of now, these can be at best said to be variant under investigation,” noted the Ministry.

It was identified by the Indian SARS-CoV-2 Consortium on Genomics (INSACOG) — a group of 10 National Laboratories established in December last. The group has been carrying out genomic sequencing and analysis of circulating COVID-19 viruses, and correlating epidemiological trends with genomic variants.

“Genomic variants of various viruses are a natural phenomenon and are found in almost all countries. Since INSACOG initiated its work, 771 variants of concerns have been detected in a total of 10,787 positive samples shared by States/UTs. These include 736 samples positive for viruses of the UK (B.1.1.7) lineage. 34 samples were found positive for viruses of the South African (B.1.351) lineage. One sample was found positive for viruses of the Brazilian (P.1) lineage. The samples with these VOCs (UK/Brazilian/South Africa) have been identified in 18 States of the country.

Genome sequencing and analysis have been carried out on samples from arriving international travellers, contacts of those positive for VOC and community samples from most of the States at INSACOG partner laboratories which are 10 in number.

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