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Pune: The elusive sibling (sub-genus) of the Omicron variant, BA.2, cannot be sorted out by an imported RT-PCR kit with an S-gene drop, researchers involved in virus tracking in India said on Sunday. The variant has three subspecies BA.1, BA.2 and BA.3, including the original B.1.1.529 strain.
A senior ICMR virologist told TOI that while they seem to share and co-perform many commonly defined mutations, the BA.2 subgenus Spike Dale does not carry 69-70 mutations. As such, it may preclude the use of commercially available imported RT-PCR kits to diagnose potential omicron cases from positive clinical samples based on S-gene drop or S-gene target failure. “This means that we have to rely primarily on whole genome sequencing for Omicron detection,” the expert added.
This probe could shake up existing dual RT-PCR testing techniques that states have adopted for rapid detection, including confirmed omicon cases. Under dual testing, throat / nasal swab samples from suspected patients are tested using a standard RT-PCR kit and if tested positive, the same sample is subjected to a second test with an imported RT-PCR kit and an S-gene drop.
Samples shown positive for S-gene drop or S-gene target failure (SGTF) are genome-sequenced on a priority basis to ensure rapid omikron confirmation. In addition to reducing costs, the dual testing strategy was expected to help select highly potential Omicron cases and save resources. Mutations in the S gene of the Omicron variant are being used to differentiate between the Omicron variant and other SARS-CoV2 variants.
“However, in sub-genus BA.2, removal of 69-70 amino acid positions is not present. Therefore, despite being an Omicron variant, subgenus BA.2 can be misinterpreted as a SARS-CoV2 form other than Omicron. Therefore, one should not rely too heavily on RT-PCR-SGTF kits to screen samples of the Omicron variant, “said a virologist involved in whole genome sequencing.
The cost of genome sequencing goes up to Rs 5,000 per covid positive sample in India, including transportation, human resources and other overhead. The imported RT-PCR kit with a standard RT-PCR kit and SGTF costs Rs 19 and Rs 240 per kit respectively. Therefore, the total cost of dual RT-PCR does not exceed Rs.260.

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