Omicron sibling BA.1 rapidly replacing Delta, says Insacog

PUNE: Scientists at the Department of Biotechnology’s Insacog (Indian SARS-CoV-2 Genomics Consortium) working on genome sequencing of Covid-positive clinical samples have said that along with the original Omicron (B.1.1.529) variant, its sibling (sub-lineage) BA.1 is dominantly co-circulating and rapidly replacing the Delta variant in Maharashtra and some other states.

Omicron also has two more sub-lineages — BA.2 and BA.3. “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 told TOI.

“Since the sub-lineage belongs to the same family, these samples are considered Omicron positive,” the scientist said.

Among the three sub-lineages of Omicron, scientists have also noticed the presence of BA.2 in genome sequencing tests. “But this presence is comparatively far too low. We have not yet identified BA.3 sub-lineage of Omicron in India,” another virologist involved in the work said.

Omicron is highly transmissible and is the main force in the current surge in cases across the country. So far, most patients have shown very mild illness and a comparatively lesser need for hospitalisation.



Insacog reports genomic surveillance of SARS CoV-2 across the country through sequencing of samples from sentinel sites and puts out a detailed district analysis for some states, including Maharashtra and Kerala.

The diagnostic accuracy of routinely used RT-PCR and antigen-based rapid diagnostic test (Ag-RDT) assays do not appear to be impacted by Omicron. It means a standard RT-PCR or antigen kit is capable of detecting Covid infection caused by Omicron and all three sub-lineages of the variant.

But 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.



"According to WHO, the BA.1 sub-lineage of Omicron accounts for 99% of sequences, and overall, over 95% of Omicron variant sequences reported include a 69-70 deletion in the S gene in most countries reporting an Omicron-fuelled surge," a Union health ministry official said.

Initial estimates of the severity of illness have, however, been lower than seen in previous outbreaks. Whether these initial observations can be generalized to older non-immune subjects is not clear and the threat level is still considered high, DBT officials have said in their latest bulletin on Omicron and its sub-lineages.