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New double mutant COVID-19 variant found in India

The central government has announced that 771 variants of concerns (VOCs) of COVID-19 have been detected in a total of 10787 positive samples in India by the Indian SARS-CoV-2 Consortium on Genomics (INSACOG) which has been carrying out genomic sequencing and analysis of circulating COVID-19 viruses, and correlating epidemiological trends with genomic variants since December 2020. INSACOG also found a new double mutant variant after analysing samples from arriving international travellers, contacts of those positive for VOC and community samples from most of the States at INSACOG partner laboratories. 

The 771 VOCs include 736 samples of the UK (B.1.1.7) lineage, 34 samples of the South African (B.1.351) lineage and 1 sample of the Brazilian (P.1) lineage. 

The 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 and increased infectivity. These mutations have been found in about 15-20% of samples and do not match any previously catalogued VOCs. These have been categorized 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. E484Q mutation has been found in 11 countries, while L452R mutation has been detected in about 22 countries.

From Kerala 2032 samples (from all 14 districts) have 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 the UK, Denmark, Singapore, Japan and Australia. As of now these can be at best said to be variants under investigation.

The government added that though VOCs and a new double mutant variant have been found in India, these have not been detected in numbers sufficient to either establish or direct relationship or explain the rapid increase in cases in some States. Genomic sequencing and epidemiological studies are continuing to further analyze the situation.

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