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“So we have to watch that. It’s still too early to know if this sub-variant has properties of additional immune evasion or indeed of being more clinically severe. We don’t know that,” she said.

The WHO’s Technical Advisory Group on Sars-CoV-2 Virus Evolution (TAG-VE) will now analyse the signs further and decide if this lineage requires a Variant of Concern (VOC) classification of its own.

HT reviewed realtime tracking data from the global coronavirus genome repository GISAID and discussions between virologists to piece together the early clues and the concerns they indicate.

First key signal: Mutations

The sub-lineage first caught attention of scientists in late June when they noticed particular mutations that appear to be a location in the virus that is informally described as the “supersite” for antibody binding: the N terminal domain, or NTD. This mutation, among nine unique to the BA.2.75, is classified as G446S, and scientists believe it could reduce the ability of antibodies exposed to other configurations of the virus to recognise this one, thereby making it more resistant. “G446S is at one of most potent sites of escape from antibodies elicited by current vaccines that still neutralize BA.2,” wrote Jesse Bloom, who heads one of the virology research labs at the Fred Hutch research centre, in a tweet last week.

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The assumption from this is that immunity from vaccines or early infections is likely to be less potent when faced with the BA.2.75.

Second concern: Growth rate

Genome sequences submitted to the GISAID database suggest the variant’s footprint is growing in India, where it was first found in early May. As on Thursday, there are 92 sequences submitted from around the world that can roughly be classified as belong to BA.2.75 (there isn’t a formal BA.2.75 classification on GISAID yet, which is why researchers are using a custom query to find this lineage). Of the 92, 73 are from India — and of these, 18 were collected in the past fortnight alone.

To understand how it has grown, BA.2.75 samples accounted for less than 1% of all samples submitted to GISAID in the first half of June, but that proportion grew to over 10% in the second half of June, a cov-spectrum.org query showed. An important caveat here is that this could because a state with more infections of this lineage may have submitted more samples in the second half of June than a state where this virus was still to reach. Nonetheless, the numbers are significant enough to suggest a transmission advantage over older BA.2 lineages that are at present the most widespread in India.

More clues needed

The highest number of samples, 50, appear to be from Maharashtra, a state that has not shown any worrying uptick in hospitalisations or deaths, or even a particularly rapid surge. What scientists will now watch for is if the nine mutations confer the variant any additional trait, particularly severity that has largely not been a concern with the Omicron family of the coronavirus till now. It also remains to be seen how this sub-lineage competes with the BA.4 and BA.5 sub-lineages, which are causing new waves of infections in parts of Europe and US.