Omicron Sibling Updates: Pune: Researchers investigating the Omicron variant in India reported on Sunday that the virus’s elusive brother (sub-lineage), BA.2, cannot be detected using an imported RT-PCR kit with an S gene drop. “This indicates that for Omicron identification, we’ll have to rely primarily on whole-genome sequencing,” the expert stated. Along with the original B.1.1.529 strain, the variation has three sublineages: BA.1, BA.2, and BA.3. While they share a number of similar defining mutations and appear to be cocirculating, the BA.2 sub-lineage does not possess the Spike del6970 mutation, according to a senior ICMR virologist.
As a result, it may make it more difficult to diagnose probable Omicron cases from positive clinical samples based on Scene drop or Scene target failure using commercially available imported RTPCR kits. “This indicates that for Omicron identification, we’ll have to rely primarily on whole-genome sequencing,” the expert stated. The discovery is expected to shake up the current dual RTPCR testing technique, which has been used by states with proven Omicron cases to speed up detection.
Suspected patients’ throat/nasal swab samples are tested with a conventional RTPCR kit, and if found positive, the same sample is examined again with an imported RTPCR kit that includes a Scene drop. Only samples that test positive for Scene drop or Scene target failure (SGTF) are genomically sequenced first, allowing Omicron confirmation to be completed quickly. Aside from cost savings, the dual testing technique was intended to aid in the detection of highly likely Omicron instances and the conservation of resources.
Experts Say Foreign Kits Can’t Detect Omicron Sibling BA.2.
Differentiation between the Omicron variant and other SARSCoV2 variations is based on mutations in the S gene of the Omicron variant. A deletion at amino acid position 69-70 exists in the Omicron variation and its sub-lineages BA.1 and BA.3. These are the positions that will be used to perform the imported RTPCR with SGTF.” However, the loss of amino acids 6970 is not found in the BA.2 sub-lineage. As a result, the sub-lineage BA.2 can be misinterpreted as a SARSCoV2 variety other than Omicron, despite being an Omicron variant.
As a result, the RTPCRSGTF kit should be used with caution when screening samples for the Omicron variation, according to a virologist involved in whole-genome sequencing. The Maharashtra government was one of the first to utilize the dual testing technique. The imported kits have already been delivered to a number of districts with large floating populations. In India, the cost of genome sequencing per Covid positive sample might reach Rs 5,000, including transportation, human resources, and other overheads.
A conventional RTPCR kit costs Rs 19 and an imported RT-PCR kit with SGTF costs Rs 240 per kit, respectively. As a result, the overall cost of the dual RTPCR is less than Rs 260. These RTPCR kits with SGTF are also being used at government-run laboratories for routine Covid tests to rule out community spread from the daily caseload with high viral load or below 25 cycle threshold (CT) value, in addition to testing individuals with an international travel history and their close contacts.
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