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Amid Omicron alert, Maharashtra short of kits for early detection

The test detects the absence of the S-gene, which is an indicator of the presence of this variant in a Covid positive patient. Formally known as the S-gene Target Failure (SGTF) test, this proxy test can be used for early detection.

Written by Rupsa Chakraborty | Mumbai |
Updated: December 6, 2021 8:11:03 am
The genome sequencing reports of over 22 suspected Omicron patients in Maharashtra are awaited, said a state health official. (Express Photo by Amit Chakravarty)

With Omicron making its presence felt in Maharashtra, the state government has asked districts to procure the S-gene test, which enables quick detection of the variant. However, apart from Mumbai and Pune, no other district in the state has these test kits.

The test detects the absence of the S-gene, which is an indicator of the presence of this variant in a Covid positive patient. Formally known as the S-gene Target Failure (SGTF) test, this proxy test can be used for early detection.

On November 30, state Additional Chief Secretary Pradeep Vyas wrote to the districts to run the SGTF test for “efficient detection for Omicron” and instructed that specimens with SGTF should be prioritised for genomic sequencing and confirmation of Omicron. “Use of SGTF approach may lead to faster detection rate,” he instructed.

The Indian Express has learnt that out of the 36 districts in Maharashtra, only two districts-Pune and Mumbai — have the kits to run a check on S-gene. The Brihanmumbai Municipal Corporation (BMC) has procured around 1,200 kits to run SGTF tests. BMC is also partnering with private hospitals to bifurcate SGTF testing in an anticipated third wave.

“To avoid delay in identification of Omicron, we have procured the kits which are being used in KEM hospital. We have already run 5-6 SGTF tests at the hospital. We have also double checked its results to reconfirm the efficiency of the kits,” said Suresh Kakani, Additional Commissioner, BMC.

But neighbouring Kalyan-Dombivli Municipal Corporation (KDMC), where the first case in Maharashtra was detected in a marine engineer who returned from South Africa on November 24, does not have any kits. The 33-year-old’s swab sample was the first to be sent for genome sequencing for the variant. It was sent to Kasturba Gandhi Hospital, which took four days to provide the result.

The genome sequencing reports of over 22 suspected Omicron patients in Maharashtra are awaited, said a state health official.

Dr Vyas said that the directive was given suggesting conducting the SGFT test when necessary.

“SGTF test is one presumptive test, it can reduce the numbers sent for genomic sequencing. It has utility in certain situations and circumstances.”

In the districts, the government-provided RT-PCR kits detect only the E, N and Rd Rp genes, not S-gene. “Although we have got the directives, we don’t have the kits to run SGTF tests. We are sending samples for genome sequencing,” said Hingoli Collector Jitendra Papalkar.

In the first wave of the pandemic, due to the high demand, districts ran out of RT-PCR testing kits. Now laboratories across the state have put up letters of intent to purchase SGFT kits, but want more guidance from the health department on pricing and numbers while placing their orders.

“There are two ways to apply-one, if I can get the kit procurement order of a government lab, I can use their price quotation to get the fund approval from the collector office to buy kits. Secondly, through ‘short’ tendering, which will take at least 14 days for approval. To boost the procurement process, the state should facilitate the process,” said a senior health officer, who has put up intent to purchase of 2,000 S-gene kits in Aurangabad.

These kits are imported from the US. Generally, it costs Rs 250 per kit excluding GST. BMC has bought these kits at Rs 300 directly from the suppliers. Similarly, the state lab can procure the kit from local suppliers. Or else, under short tender, the suppliers can approach the state directly and provide their budget quotation which go under inspection from the purchase committee to get the fund.

There is a huge cost difference between the kits given by the state and widely used US-based TaqPath Covid-19 Detection Kits – which can check S-gene. “The kits given by the state cost Rs 40 per sample test, whereas the TaqPath kits cost Rs 200-250 per test,” said Dr Prashant Thakare, head of Amravati district’s molecular laboratory.

At present, only the US-based Thermo Fisher Scientific is importing the TaqPath kit for S-Gene testing.

In April this year, the state had tied up with the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB) for genome sequencing, where they send 100 samples from each district every month. But it is a time-consuming affair. So, BMC started its own genome sequencing facility in Kasturba Hospital in August.

Dr Prashant Thakare said that considering the high transmission rate of Omicron, the labs would get overwhelmed in case of a possible third wave. In such a situation, it would require prioritising of samples through SGTF tests.

“Generally, it takes five days to run sequencing on prioritised samples and 15 days on general samples. To channelise the testing, all districts should first run SGTF tests on suspected Omicron patients. If their report gives a red flag, then these samples should be sent on priority for genome sequencing,” he said.

Tamil Nadu and Karnataka governments have already started the procurement process of the kits to its labs.

Speaking to The Indian Express, state Health Minister Rajesh Tope said that with the identification of the first Omicron patient in the state, his department is planning to procure the kits for districts. “If the variant spreads to a large population, it will put a huge pressure on genome sequencing labs. To avoid such a situation, we are in discussion to distribute the kits among districts, especially the ones with high populations.”

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