Missing ‘S’ gene in RT-PCR test can point to Omicron, Health News, ET HealthWorld
Maharashtra state task force member Dr Shashank Joshi on Monday told TOI that a complete RT-PCR report for Covid included that of the ‘N’ , ‘S’ , ‘E’ and ‘ORF’ genes.
“If the ‘S’ gene is absent in a person and the other genes are positive, it is an indirect way to know that the Omicron variant may be present in him or her even without conducting genome sequencing. Unfortunately, not all laboratories conducting RT-PCR tests are checking for the ‘S’ gene,” he said.
“A directive may soon come for all laboratories to additionally check for the ‘S’ gene in a sample. Deletion of the ‘S’ gene will red-flag Omicron ahead of genome sequencing,” said the task force member
The World Health Organisation (WHO) has stated that countries using PCR tests containing the ‘S’ gene could also utilize the ‘S’ gene target failure as a proxy marker for infection with the Omicron variant of Covid. “Similarly, PCR tests are under development to test for this variant without the need for full sequencing” a WHO statement read.
Dr Rahul Pandit, a member of the state task force and also the national Covid task force, said with Omicron being stated as a cause for concern across the world, maintaining caution was instrumental. “The Technical Advisory Group (TAG) on SARS-CoV-2 Virus Evolution (TAG-VE) is continuously monitoring the evolution of the virus. Based on this, TAG-VE has advised WHO to designate Omicron as a virus of concern and will communicate new findings with the member states and public,” said Dr Pandit, who is the director (critical care) in Fortis Hospitals Mumbai.
Dr Rajesh Karyakarte, state coordinator for genome sequencing and head of B J Medical College’s microbiology department, said the current testing kits included detection of two different genes, that could be either ‘ORF’, ‘RdRp’, ‘N’ or ‘S’.