The Omicron variant’s sub lineage, BA.1, is dominantly circulating and replacing Delta in Maharashtra and some other states, according to scientists at the Indian SARS-CoV-2 Genomics Consortium (INSACOG). The INSACOG is working on genome sequencing of Covid-positive samples, which has led to the observation that Omicron’s sibling BA.1 is increasingly present in infected patients.
“In some sequencing run of clinical samples, we get to see the presence of more BA.1 sub-lineage now than the original Omicron strain,” a senior scientist was quoted by the Times of India as saying. Since the sub-lineage belongs to the same family, the samples are considered as Omicron-positive, he said.
Omicron also has two other sub-lineages – BA.2 and BA.3. However, according to another INSACOG virologist involved in sequencing, the presence of BA.2 is far too low and and BA.3 has not been identified yet in India.
The variant is highly transmissible and is the driving force for the rapid surge of Covid-19 cases in the country. Patients have shown mild illness and relatively lesser need for hospitalization.
The INSACOG has been involved in genome surveillance of SARS-CoV-2 across the country and through sequencing of samples from sentinel sites. It puts out detailed district analysis for some states including Maharashtra and Kerala.
The diagnostic accuracy of the widely-used RT-PCR tests have not been impacted by the new variant, meaning Omicron and its sub-lineages can be detected from the standard RT-PCR tests or antigen kits. However, sifting probable Omicron cases from the daily positive cases using the RT-PCR-S-gene target method cannot be fully relied upon as available evidence shows that the BA.2 sub-lineage cannot be picked up using these RT-PCR-SGTF kits.
A Union Health Ministry official had said that according to the WHO, the BA.1 sub-lineage of Omicron variant accounts for 99% of sequences, and overall, over 95% of the variant sequences reported include a 69-70 deletion in the S gene in most countries reporting an Omicron-fuelled surge.
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