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Tracking mutants: What most recent data on COVID variant spread in India tell us

The delta strain is now dominating India

coronavirus-microscope-ncov-covid19-NIAID-RML-AP Representational image

A study conducted around the first week of May in India had found that the devastating second wave of the coronavirus was driven, in large part, by the B.1.1.7 or the alpha variant which was predominantly found in the United Kingdom. The alpha strain dominated parts of North India, while the delta variant (B.1.617, most prevalent in India) could be found mostly in Maharashtra, Karnataka and Gujarat, Sujeet Singh, director of National Centre for Disease Control (NCDC), had said. 

Singh said the alpha strain dominated parts of North India, including Punjab (482 samples) and Delhi (516), followed by Telangana (192), Maharashtra (83) and Karnataka (82). The delta variant dominated Maharashtra (761), West Bengal (124), Delhi (107) and Gujarat (102). The beta variant (B.1.315, predominantly found in South Africa), was found in Telangana and Delhi. The gamma variant (P1, initially found in Brazil) was only found in Maharashtra in a negligible proportions. 

Now, the situation seems to be changing. As per the latest study conducted by INSACOG, a grouping of 10 national laboratories, the alpha lineage of the virus (UK) is declining in proportion across India and the delta strain is showing a corresponding surge. April and May witnessed a deadly second wave of coronavirus cases that swept through the country, stretching the healthcare infrastructure to its limits.

"The current surge in cases seen over the last two months in some states shows a correlation with the rise in the B.1.617 lineage of SARS CoV-2," the Indian SARS-CoV-2 Consortium on Genomics (INSACOG) said.

The delta (B.1.617) lineage of SARS CoV-2 was first reported from Maharashtra but it is now seen in other states such as West Bengal, Andhra Pradesh, Delhi, Gujarat, Telangana. B.1.617, initially termed a double mutant, has three new spike protein mutations. Two mutations, E484Q and L452R, are in the area important for antibody-based neutralisation. The third mutation, P681R in B.1.617, along with the reversion of E484Q allows its sub-lineage to be more infectious. It was found in high levels in genomes sequenced in Maharashtra (2,077), West Bengal (630), Delhi (1,458), Karnataka (225) as of May 28, and accumulates new mutations in spike and other genes, the INSACOG found in the genomes sequenced as of May 28.

Is delta variant the only cause for concern?

Not really. Take Varanasi. There are at least seven major variants of coronavirus, including B.1.617 and B.1.351 (beta), in the holy land and its adjoining areas, according to a study conducted by the Banaras Hindu University and the Centre for Cellular and Molecular Biology (CCMB).

"Among the Variants of Concern (VoC), the most predominant variant we found in our study was B.1.617. They were found among 36 per cent of the total samples. Other VoCs such as the B.1.351, detected in South Africa for the first time, was also found in this area," said Rakesh Mishra, advisor at CCMB.

"This study confirms yet again that the delta variant is the most widespread coronavirus variant in the country right now. But at the same time, it is imperative for us to keep an eye on the other emerging variants in the country to prevent another unprecedented surge of cases," he added. 

-Inputs from PTI

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