According to an Israeli expert, approximately ten states in India have detected a new sub-variant of Omicron BA.2.75, which may be “alarming” in nature.
However, the Indian Health Ministry has yet to officially confirm the sub-detection variant’s in the country.
Dr. Shay Fleishon of the Central Virology Laboratory at Sheba Medical Center in Tel Hashomer stated in a series of Tweets that 85 sequences from eight countries have been uploaded to Nextstrain, an open-source genomic data platform.
This included 69 from India: Delhi (1), Haryana (6), Himachal Pradesh (3), Jammu (1), Karnataka (10), Madhya Pradesh (5), Maharashtra (27), Telangana (2), Uttar Pradesh (1), and West Bengal (13).
Besides India, the strain has also been reported by seven other countries: Japan (1), Germany (2), the UK (6), Canada (2), the US (2), Australia (1), and New Zealand (2), according to the Nextstrain data.
“No transmission could be tracked based on sequences outside India yet,” Fleishon wrote on Twitter.
While it is “too early to tell” whether BA.2.75 will be the next dominant variant, he does believe the sub-variant is “alarming because it may imply a trend to come.”
Fleishon stated that there has been a recent trend of second generation variants based on Omicron sub-lineages, specifically BA.1, BA.2, BA.3, BA.4, and BA.5.
This was based on Omicron lineages that had mutations in the S1 section of the spike protein, specifically in the section of the spike protein that the virus uses to connect to and enter cells.
However, the increase in these sub-variants has been modest “at a level not seen in second-generation variants from other variants of concerns”.
Furthermore, these second-generation variants have only been discovered in a few cases within a single region. This is the first time an Omicron second-generation variant has spread to multiple regions.
“The fact that such a divergent 2nd gen variant can succeed inter-host is alarming. It means that if BA.2.75 will not succeed, and even if it will, other 2nd gen might grow better over time,” Fleishon said.
According to Thomas Peacock, a scientist at Imperial College London, the sub-variant is worth “keeping a close eye” on.
Bloom Lab at the Fred Hutch research institute in the United States also detected the BA.2.75 variant.
The institute announced the sub-variant in a tweet this week “is worth tracking, as it has appreciable antigenic change relative to its parent BA.2”.
The lab identified two key mutations: G446S and R493Q.
“G446S is at one of most potent sites of escape from antibodies elicited by current vaccines that still neutralises BA.2. So for immunity from vaccines or early infections, adding G446S to BA.2 will decrease neutralisation,” the lab said.
“However, G446S will have less effect on antibodies of people with prior BA.1 breakthrough infection. Therefore, BA.2.75’s antigenic advantage relative to BA.2 will be most pronounced in people who have not had BA.1 exposure,” it said.
This means that “BA.2.75 will have antibody escape that is similar to that for BA.4/5 with respect to the current vaccine”.
The R493Q mutation, on the other hand, appears to improve the virus’s ability to bind to ACE2, the protein used by the Covid virus to enter cells.