Experts call for more sequencing after new ‘Delta plus’ variant identified

Also referred to as the ‘Nepal variant’, AY.1 combines the Delta and a mutation previously found in the ‘South African’ or Beta variant

<p>A teenager receives a dose of a Covid vaccine in Ashkelon, Israel</p>

A teenager receives a dose of a Covid vaccine in Ashkelon, Israel

India’s leading virologists have called for better genome sequencing after it was confirmed that a further mutation has been detected in the already “more transmissible” Delta variant.

The Delta variant, or B.1.617.2, was first identified in India and responsible for the surge in cases and deaths during the country’s second wave. It is now also the dominant strain in the UK with up to 91 per cent of new infections, and experts say it is rising in prominence in the US too.

What do we know so far?

Referred to variously as the “Nepal variant”, the “Delta plus” variant or Delta AY.1, early data show this new lineage (B.1.617.2.1) allows the Covid virus to better resist antibody therapy treatments because it includes the K417N mutation — first found in the Beta variant that emerged in South Africa.

According to Public Health England (PHE), 63 genomes of the “Delta plus” variant have been identified so far by GISAID, a global repository of coronavirus variants.

From the data submitted by various labs across the world, we know the variant has been seen in Canada, Germany, Russia, Nepal, Switzerland, India, Poland, Portugal, Japan and the US.

The UK has 36 cases of the new variant with the majority affecting younger individuals, according to PHE. Of these 36, 27 people had taken at least one dose of vaccine, and no deaths have been reported so far.

The earliest sequence of this genome was found in Europe in March this year.

Vinod Scaria, a Delhi-based scientist with CSIR-Institute of Genomics and Integrative Biology (IGIB), said that the new mutation is in the spike protein of Sars-Cov-2, which enables the virus to enter and infect human cells.

“Understanding this continued evolution is of great importance in mapping the evolutionary landscape of emerging variants. Largely, the virus has tried to optimise for transmission and immune escape by step-wise acquisition of new mutations,” he said in a tweet.

He said one important point to consider is that the K417N mutation has shown resistance to newly developed monoclonal antibody treatment drugs, Casirivimab and Imdevimab.

The treatments have only just been approved by India’s Central Drugs Standard Control Organisation (CDSCO) for treating those with moderate and severe disease from Covid infection.

The K417N mutation in part led the previously identified Beta variant to be flagged as an international variant of concern, as it was seen as being more infectious and having significant ability to escape vaccines.

Calls for more sequencing

Speaking to The Independent, epidemiologist and public health expert Chandrakant Lahariya said the emergence of “Delta plus” and other new variants showed the need for regular genome sequencing to keep track of how the Covid virus is progressing.

He said the variant was “not a major concern immediately”.

“We know that the Delta variant is 50 to 70 per cent more transmissible than the Alpha variant (first identified in Kent) but it is yet to be known if a single major mutation, in this case K417N, will result in more transmissibility,” he said.

He confirmed that the mutation would likely make the variant resistant to antibodies therapy, but added that the method of artificially creating antibodies in a lab to fight the virus was not yet a proven treatment against Covid anyway.

He said it was crucial to conduct widespread genome sequencing in countries like the UK and India where the virus is still spreading fast.

Virologist Shahid Jameel told The Hindu: “It has all the mutations that make up the Delta variant, along with an additional concerning one [from] the South African variant.

“It is indeed a matter of concern, and we should be sequencing more to identify how widely prevalent it is in India.”

Director of CSIR-IGIB Anurag Agrawal said that the new variant was “just something to keep track of” and that, for now, it should not cause excessive concern.

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