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Omicron concern: Maharashtra govt sanctions Rs 2.4 cr to buy S-gene testing kits

The test detects the absence of the S-gene, which is an indicator of the presence of Omicron variant in a Covid-19 patient.

Written by Rupsa Chakraborty | Mumbai |
Updated: December 22, 2021 9:47:52 am
Formally known as the S-gene Target Failure (SGTF) test, this proxy test can be used to detect samples that should be prioritised for genomic sequencing to confirm Omicron.

With a gradual rise in Omicron cases, the state health department has sanctioned Rs 2.4 crore to buy S-gene testing kits to gauge the spread of the new Covid-19 variant as a part of its 20-day study.

The test detects the absence of the S-gene, which is an indicator of the presence of Omicron variant in a Covid-19 patient. Formally known as the S-gene Target Failure (SGTF) test, this proxy test can be used to detect samples that should be prioritised for genomic sequencing to confirm Omicron.

In the last 16 days, cases of Omicron have surged to 65 in the state. Public health experts are apprehensive that as Omicron has already spread to 89 countries, of which many aren’t under the radar of “countries at risk”, several international fliers infected with Omicron arriving in India may be going undiagnosed. This increases the risk of transmission at the community-level, which may lead to a third wave as seen in European countries, said officials.

To understand the likelihood of the undetected spread of the virus, the state has instructed all the 36 districts to conduct 100 RT-PCR tests with SGTF kits to identify suspected Omicron patients.

As expected by next week, on a daily basis, 3,600 SGTF tests would be conducted on targeted populations like international fliers and their close contacts, patients with reinfection or breakthrough infection, people from Covid-19 hotspots and infected patients showing synomatic abnormalities, among others.

“The districts have been asked to procure the kits at their own level from the manufacturers, which will be quicker. The testing would be done to prioritise the samples for genome sequencing. Also, upon the completion of the study after 20 days, it will help us understand the trend of the virus,” said Dr Satish Pawar, Additional Director, National Health Mission.

Dr Prashant Thakare, head of the government molecular diagnostic laboratory in Amravati, is waiting for the final approval from the collector to place the purchase order. “Genome sequencing takes a long time to provide the reports. So, the kit will reduce the hunt for the needle in a haystack by narrowing down the search,” he said.

As the price of a SGTF kit is nearly seven times more than the government provided RT-PCR kit — which can detect only the E, N and Rd Rp genes, not S-gene — the government has sanctioned Rs 2.4 crore for purchasing purposes.

The Taqpath RT-PCR kit is made by Thermo Fisher Scientific, a pharmaceutical company headquartered in the United States. It is the only RT-PCR kit targeting the S-gene that has been approved by the World Health Organization. While the Taqpath RT-PCR kit costs Rs 240 each, one regular RT-PCR kit costs around Rs 40.

“Due to several mutations in the spike proteins of Omicron, it makes it possible to detect it through the SGTF test. But it doesn’t provide 100 per cent guarantee, so all the red-flagged samples have to undergo genome sequencing for confirmation,” said Pawar.

On November 30, the government had asked all districts to focus on SGTF test for “efficient detection for Omicron” and instructed that specimens with SGTF should be prioritised for genomic sequencing to confirm Omicron. States like Tamil Nadu, Madhya Pradesh and Gujarat have also placed orders for SGTF kits.

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