Karnataka virologist team develop India's first Omicron testing kit

State genomic surveillance committee chairman and virologist Dr V Ravi and a team of 12 R&D personnel from Tata MD developed OmiSure, India's first indigenously developed Omicron testing kit.

The former head of Neurovirology in NIMHANS, Ravi who now heads the research and development at Tata MD, said the testing kit, developed over a month, is compatible with all RT-PCR testing machines. The USP of this testing kit is that it is the first test kit globally to employ a combination of two S gene viral targets -- one based on S gene dropout or S gene target failure (SGTF) and the other based on S gene mutation amplification (SGMA). Test kits like TaqPath from American company Thermo Fisher currently in use in the state use only the S gene drop out method.

It has two checks in place for Omicron detection without compromising on the ability to detect other SARS-CoV-2 strains. "While an S-gene dropout can only be used as a proxy marker, this can be used as a confirmatory test for Omicron and does not require genomic sequencing confirmation," he said. While TaqPath works out to Rs 300 per sample, OmiSure's price has been fixed at Rs 250 per sample, Dr Ravi added.

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With the state's Omicron tally rising, it is important to get faster results on the variant in a Covid sample to track its transmission.

He has apprised the CM about the test in the three-hour meeting held with the state Covid-19 Technical Advisory Committee (TAC) on Tuesday, he said. While ICMR approved the test on December 30, the Drugs Controller General of India's (DCGI) approval came on Wednesday. An application for a patent was also filed on December 23, he said.

“The good news is that the Omicron detecting RT-PCR kit has been developed in partnership with TataMD and ICMR, and has been approved by the Drugs Controller General of India. This new kit will test for Omicron in four hours, and will augment genome sequencing efforts of the country,” said Balram Bhargava, director-general, Indian Council of Medical Research (ICMR).

"The kit has not gone into production yet as we got the DCGI approval only on Wednesday. The spike protein is where maximum mutations of Omicron are seen. We have exploited a region where conventional spike protein primers don't pick up Omicron because it is mutated. This is called S-gene target failure.

"We have also identified a unique region in Omicron where there are mutations not found in all other variants and developed a probe for it. So, it combines S-gene dropout and Omicron-specific detection, along with RDRP, which is the polymerase gene to detect all other variants," Dr Ravi said.

It takes about two-and-a-half hours to test the samples with this kit like with any other RT-PCR test.

Dr Vishal Rao, another member of the state genomic surveillance committee said this kit reduces the dependence on genomic surveillance for Omicron detection. However, this will continue to miss 'stealth' Omicron (BA.2), a newer variant. He also said published scientific, peer-reviewed literature in the public domain was required to validate that this is a confirmatory test and not a screening/proxy marker.

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