‘Foreign test kits can’t spot Omicron’s elusive sibling’ | India News

PUNE: The elusive sibling (sub-lineage) of the Omicron variant, BA.2, cannot be picked up by the imported RT-PCR kit having an S-gene drop, researchers involved in tracking the virus in India said on Sunday. The variant has three sub-lineages BA.1, BA.2, and BA.3 along with the original B.1.1.529 strain.
A senior ICMR virologist told TOI that while they share a number of common defining mutations and appear to be co-circulating, the BA.2 sub-lineage does not carry the Spike del 69-70 mutation. As such, it may hinder the use of commercially available imported RT-PCR kits to diagnose probable Omicron cases from positive clinical samples based on S-gene drop or S-gene target failure. “This means that we have to rely mainly on the whole genome sequencing for Omicron detection,” the expert added.
The finding is likely to shake the existing dual RT-PCR testing strategy which the states with confirmed Omicron cases have adopted for faster detection. Under the dual testing, suspected patients’ throat/nasal swab samples are being tested using a standard RT-PCR kit and if detected positive, the same sample undergoes a second test with an imported RT-PCR kit having an S-gene drop.
Only those samples showing positive for S-gene drop or S-gene target failure (SGTF) are genome-sequenced, on priority, for faster Omicron confirmation. Besides cost-cutting, the dual testing strategy was expected to help in picking up the highly probable Omicron cases and save resources. The mutations in the S gene of the Omicron variant are being used for differentiating between the Omicron variant and the other SARS-CoV2 variants.
“But, in the sub-lineage BA.2, the deletion of 69-70 amino acid position is not present. Therefore, despite being an Omicron variant, the sub-lineage BA.2 can be falsely interpreted as a SARS-CoV2 variant other than Omicron. Therefore, the RT-PCR-SGTF kit should not be relied upon too much for screening of samples for Omicron variant,” the virologist involved in whole genome sequencing said.
The cost of genome sequencing goes up to Rs 5,000 per Covid positive sample in India, including the transport, human resource, and other overheads. The cost per kit of a standard RT-PCR kit and imported RT-PCR kit with SGTF is Rs 19 and Rs 240, respectively. Hence, the total cost of the dual RT-PCR costs does not exceed Rs 260.

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