Friday, August 19, 2022

New ‘alarming’ Covid-19 variant detected in India

About 10 states in India have detected a new sub-variant of Omicron BA.2.75, which may be “alarming” in nature, according to an Israeli expert on Sunday. However, the Indian Health Ministry is yet to officially confirm the detection of the sub-variant in the country.
In a series of Tweets, Dr. Shay Fleishon, with the Central Virology Laboratory at Sheba Medical Center in Tel Hashomer, said that 85 sequences from eight countries have been uploaded so far on Nextstrain, an open-source platform of genomic data. 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.
Scientists across the world have also flagged the emergence of a new coronavirus variant in India– the BA.2.75, which is said to be cropping up increasingly in samples, and may have an increased ability to infect people who have been infected before, as well as those who are vaccinated.
BA.2.75 is a sub-lineage of the Omicron variant. Sub-lineages of Omicron have become the dominant variants circulating across the globe, with new mutations continuously evolving. There has been no official communication about the variant from the Indian government, or the Indian SARS-CoV-2 Genomics Consortium (INSACOG), a genomic surveillance agency functioning under the health ministry.
Thomas Peacock, a scientist at Imperial College London, in a Twitter thread said that the variant is worth “keeping a close eye” on.
A senior genomic scientist in India, who did not wish to be named, told ThePrint that the majority of the samples of the variant have been detected in India.
Lipi Thukral, a scientist at the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB) Delhi, told ThePrint: “This lineage may require urgent attention as most of the mutations are unique and [it] has also changed its physiochemical character quite a lot.”
Thukral explained that there are nine mutations on critical interfaces of the coronavirus, including five changes in what is known as the N-terminal domain of the spike protein. The N-terminal domain plays an important role in the virus attaching itself to the host cell, and is a valuable target for neutralising antibodies.
Meanwhile, there are four mutations in the receptor binding domain region, which interacts with the ACE2 receptor in the host, Thukral said. The ACE2 is an enzyme that acts as the receptor for the SARS-CoV-2 virus and allows it to infect host cells. The BA.2.75 variant includes new mutations in the spike protein, in addition to the mutations that are already present in the Omicron variant, explained the Indian genomic scientist quoted earlier. Spike proteins are the protrusions seen on the outer surface of the novel coronavirus.
Of particular concern, said the scientist, are the mutations ‘G446S’ and ‘R493Q’, both of which are associated with significant changes in the protein structure of the spike protein, with the potential to give the variant the ability to evade several antibodies.
As a result, the variant is expected to infect people who have been vaccinated, or have been infected previously. However, currently, there is a lack of data on how fast the infection from this particular variant is spreading, owing to insufficient surveillance.
There is also not enough data currently to ascertain if the variant has the potential to cause severe infection.
But according to the scientists who have been discussing the BA.2.75 on various forums, the variant is unlikely to cause severe infection, since G446S is also better recognised by vaccine-induced T-Cells — a type of white blood cell that helps recognise and target pathogens in the body.

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