B.1.617 Covid variant has sub-lineages; B.1.617.2 more infectious, says expert

The double mutant B.1.617 variant of SARS-CoV2 is further mutating and one of its sub-lineages, the B.1.617.2, reported in India, is more infectious than its parent and fast increasing its footprint, Rakesh Mishra, former Director of the Centre for Cellular and Molecular Biology, said on Wednesday.

He also said there is nothing called the “Singapore variant”, a term that has led to a war of words between the Centre and the AAP government after Singapore objected to Chief Minister Arvind Kejriwal's tweet that a "new" coronavirus strain in the city-state is very dangerous for children.

Singapore's health ministry on Tuesday night said the strain that is prevalent in many of the Covid-19 cases in recent weeks is the B.1.617.2 variant, which was first detected in India.

Amid criticism over Kejriwal's Singapore Covid-19 variant remark, Delhi Health Minister Satyendar Jain on Wednesday claimed there was a "different strain" of coronavirus spreading in that country.

However, Mishra said B.1.617.2 has already been reported in India and is in the majority of the new cases in Karnataka and Andhra Pradesh.

Mishra is part of the INSACOG, a consortium of 10 institutes of the Centre, that is involved in the genome sequencing of coronavirus.

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Explaining about the sub-lineage, Mishra told PTI, “B.1.617 was the mutant which was increasing in some part of the country like Maharashtra, West Bengal, Karnataka and now gradually it has led to three sub-lineages (B.1) 617.1, 617.2 and 617.3.

“Among these three, B.1.617.2 is more infectious than B.1.617. That does not indicate a greater worry except the numbers are more and symptomatically. Otherwise, we have not seen any other difference. So this is now replacing others,”

He said the same thing is being observed in the UK where B.1.617 was found and the sub-lineage has started to take over. This is the same thing we are seeing in Singapore. Most of the cases in Singapore are B.1.617 and a majority is B.1.617.2.

“B.1.617.2 sub-lineage is the majority in the new cases in Karnataka and Andhra Pradesh,” Mishra said.

“Gradually it is increasing its footprint and it will be a major one replacing other variants,” he added.

Another virologist, who did not want to be quoted, said the sub-lineage was first detected in India in December.

Sujeet Singh, the Director of the National Centre for Disease Control, said in a webinar in April that in Maharashtra, the B.1.617 variant was found in over 50 per cent of samples in many cities while the UK variant was found in 28 per cent of samples in the second week of March.

B.1.617, termed as 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.

The World Health Organisation (WHO) has termed it as 'Variant of Concern'. According to the Centre for Disease Control and Prevention of the US, B.1.617.1 and B.1.617.3 sub-lineages have two receptor binding domain mutations --- L452R and E484Q. The former has seven spike mutation while the latter has 7-8.

In the case of B.1.617.3, it has 9-10 spike mutations and two receptor binding domain mutations --- L452R and T478K.

In the case of all the three sub-lineage, it has the potential to reduced antibody efficacy and potentially reduced neutralisation by vaccine sera, which, however, remains to be established.

On Tuesday, Kejriwal had tweeted, "The new form of coronavirus in Singapore is said to be very dangerous for children. It could reach Delhi in the form of a third wave. My appeal to the Central government: 1. Cancel all air services with Singapore with immediate effect 2. Work on vaccine alternatives for children on a priority basis."

Responding to Kejriwal's tweet, Singapore's health ministry on Tuesday night said: “There is no Singapore variant. The strain that is prevalent in many of the Covid-19 cases in recent weeks is the B.1.617.2 variant, which originated in India. Phylogenetic testing has shown this B.1.617.2 variant to be associated with several clusters in Singapore,” it said in a statement.