Amid the rising concerns over Omicron, the new variant of coronavirus, researchers are pitching for genome sequencing of positive samples using RT-PCR kits that employ ‘S’ Gene Target Failure (SGTF) strategy to detect the variant. Talking to PTI, scientist Krishna Khairnar, who is one of the key researchers in COVID-19 diagnostics in India, said tests target “multiple genes” of the virus so that a broad range of variants are covered.
For example, ‘S’ Gene, ORF, ‘N’ gene, Rdrp, ‘E’ gene etc are viral genes that are targeted to detect COVID-19 virus, and multiple genes make up the genetic structure of SARS-Co V-2, said Khairnar of Nagpur-based CSIR-NEERI. In case of Omicron variant, the ‘S’ gene is not getting detected in Thermofisher’s Taq Path RT-PCR test due to mutation in the gene, while other gene targets such as ORF gene and N gene are getting detected, he said.
“The occurrence is called as ‘S’ Gene Target Failure (SGTF) positive cases. Such samples can be presumptively reported as Omicron positive and can be sent for fast-track genome sequencing for confirmation,” Khairnar said.Khairnar further informed that the SGTF strategy focuses on taking those positive samples in which the RT-PCR test result shows ‘S’ Gene negative result, but ORF and N gene are positive.
The SGTF strategy will work as a kind of early detection at RT-PCR stage, and will help in screening COVID-19 positive samples of Omicron variant, he said.”Although this variant is new and incidences are less at this juncture in India, it may be a matter of days that it spreads faster among the population. It will be a wise strategy to identify Omicron patients at the RT-PCR stage itself. We can track, quarantine and contact trace cases and send samples for sequencing to confirm the infection and contain it in early stages,” Khairnar said. Both RT-PCR followed by genome sequencing will aid in early detection of Omicron cases, he added.