The heavily mutated Omicron variant of the coronavirus is now in community transmission in the country, according to India’s genome sequencing consortium. “Omicron is now in community transmission in India and has become dominant in multiple metros where new cases have been rising exponentially,” a statement from the Indian SARS-CoV-2 Genomics Consortium (Insacog) said. 

The consortium also warned against screening for the Omicron variant based on the s-gene dropout. The omicron variant has a high number of mutations, including 32 on its spike protein or the s-gene that attaches with the human ACE2 receptor—a specific protein that serves an entry point for the coronavirus—to cause infection. Due to the high number of mutations in the s-gene, the kits using it as one of the targets could not detect it, it said.  

The Omicron variant’s newly found BA.2 lineage does not lead to this s-gene target failure and could thereby lead people to believe that it is not an Omicron infection. “The BA.2 lineage is a substantial fraction in India and the s-gene dropout-based screening is thus likely to give high false negatives,” the statement was quoted by NDTV as saying.

It stated that while most Omicron cases have been asymptomatic or mild, hospitalisations and ICU admissions are increasing in the country. Hence, the threat level remains unchanged.

In a bulletin from January 3, which was also uploaded on Sunday, the consortium said that the sampling method for genomic surveillance has to be changed in view of Omicron being in community transmission and spreading internally and not through infected travellers. The consortium had prioritised sequencing of samples from international travellers in December in order to detect the variant coming into the country.

(SAM)