Missing ‘S’ gene in RT-PCR test can point to Omicron

Missing ‘S’ gene in RT-PCR test can point to Omicron

The ‘S’ gene sequencing kits were in use in the first and second Covid wave in Karnataka

Commuters stand in a queue as others undergo RT-PCR COVID-19 testing at Talapady checkpost of the Karnataka-Kerala state border. Credit: DH Photo

The Bangalore Medical College and Research Institute (BMCRI) has procured ‘S’ gene RT-PCR test kits to identify possible Covid samples with Omicron variant of the virus.

If there are 200-odd Covid positive samples, for example, the state can prioritise those without ‘S’ gene for sequencing to determine the Omicron variant, said experts.

The ‘S’ gene sequencing kits were in use in the first and second Covid wave in Karnataka, before other kits that identify other genes (‘N’, ‘E’, ‘ORF’, and ‘RDRP’) were used.

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This kit can be used again now, say microbiologists in the state, as this can serve as a proxy marker for Omicron while waiting for sequencing results. 

Even the World Health Organisation, on November 26, said that in one widely used PCR test, the ‘S’ gene is not detected and this test can, therefore, be used as marker for the Omicron variant, pending sequencing
confirmation.

Dr V Ravi, head of the state genomic surveillance committee, told DH, “TaqPath ‘S’ gene Covid-19 diagnostic kit by Thermo Fisher has already been used by government hospital labs during the first and the second Covid wave. It can be a screening marker, but the final confirmation should come from genomic sequencing. After Indian manufacturers started providing PCR test kits, the prices started plummeting.” 

Dr Ambika R, HoD, microbiology, BMCRI, told DH, “For testing 96 samples, the company is giving us the test kit at Rs 5,000, which works out to Rs 50 per sample, to test for Omicron. We will test Covid positive samples to see if the ‘S’ gene can be detected
or not.”

“We can then know which samples to send for genomic sequencing on priority. We are expecting the kits to arrive by Wednesday. Even the Maharashtra government has procured these test kits, but only for Rs 18 per sample, as they have got them in bulk,” she said.

Dr Kala Yadav, HoD, microbiology, Bowring and Lady Curzon Hospital, said, “Initially, we used to look for ‘S’ gene, then the government included all types of kits. In the backdrop of Omicron, now the government can take the initiative to supply ‘S’
gene kits.”

The head of a private hospital diagnostic chain, requesting anonymity, said, “In places where there is no sequencing capacity, knowhow or turnaround time is several days. So, this will help. We have 2,000 kits lying with us and these can detect all genes, including ‘S’ gene. But we can’t use them as the government has capped the cost of a RT-PCR test at Rs 800. Our operational cost is Rs 1,000,” he said. 

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