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EXPLAINED: OmiSure, The Made-In-India Test Kit That Can Detect Omicron Variant

The Indian Medical Research Council approved OmiSure on December 30 and it's said to be priced at Rs 250 for laboratories. (Reuters File)

The Indian Medical Research Council approved OmiSure on December 30 and it's said to be priced at Rs 250 for laboratories. (Reuters File)

The first-of-its-kind RT-PCR test kit can capture both the gene dropout and specific mutation to sniff out the newest VoC, its makers are reported to have said

A new test kit has been approved in India that can pick up the Omicron variant of the novel coronavirus amid a fresh surge in cases that is liable to put pressure on testing facilities. The kit created by Tata Medical and Diagnostics (TMD) is called ‘OmiSure’ and has been described as being the first of its kind in the world. Here’s what you need to know.

What Is The OmiSure Test Kit?

Reports quoted Ravi Vasanthapuram, the head of the research and development of TMD, as saying that OmiSure “can help eliminate" the need for genome sequencing to detect Omicron, the newest WHO-designated variant of concern (VOC) of the novel coronavirus.

Like the existing RT-PCR tests, the TMD kit, too, relies on nasal and oral swab samples and is compatible with all standard PCR machines being used in India.

Vasanthapuram said the OmiSure test has a run time of a little over two hours and that it is able to sniff out Omicron by combining S-gene target failure (SGTF) and S-gene mutation amplification (SGMA). He was quoted by the New Indian Express as saying that while test kits globally are designed to catch either the gene dropout or a specific mutation, “Omisure is the first test kit combining both".

During its assessment by the Indian Council of Medical Research (ICMR), it showed 100 per cent accuracy, he added. TMD is said to have priced the OmiSure test at Rs 250 per unit for laboratories with reports saying the company has a daily production capacity of 2 lakh kits that it will be ramping up to 5 lakh shortly.

How Can An RT-PCR Test Identify A Sars-CoV-2 Variant?

The RT-PCR test is considered to be the ‘gold standard’ for detecting Covid-19. Amid the emergence of Omicron, it has been found that in certain cases, a positive RT-PCR test can also give a good idea if the infection was caused by this variant. But not all RT-PCR tests can identify Omicron which, further, is not the only variant thus susceptible to detection.

The Reverse Transcription-Polymerase Chain Reaction, or RT-PCR, test works by detecting the presence of specific genetic material in a pathogen. In case of the novel coronavirus, most RT-PCR tests seek out genes in its spike protein, which the virus uses to invade human cells.

Now, to ensure that the test is accurate, more than one spike gene is targeted so that even if a mutation may have changed one of the genes, the other would still get captured in the test. That has proved to be an advantage of sorts when it comes to detecting an infection with Omicron since one of its specific mutations is not captured by certain RT-PCR tests.

The World Health Organisation (WHO) said that this phenomenon, called the S gene dropout or S gene target failure, means that specific RT-PCR tests can “therefore be used as marker for this variant, pending sequencing confirmation". The WHO added that “using this approach, this variant has been detected at faster rates than previous surges in infection".

Does This Mean Omicron Can Evade The RT-PCR Test?

No. As already pointed out, there is only one mutation that escapes detection by the RT-PCR test, which uses two or three target genes to track an infection. The WHO has clarified that “most diagnostic tests continue to work and can detect" Omicron, although it is being assessed whether rapid antigen tests (RAT) continue to be effective in confirming positive cases.

Nonetheless, amid apprehensions over whether tests can detect Omicron, the Centre said that this variant cannot escape the RT-PCR or RAT test even as states were asked to ramp up testing.

Do Other RT-PCR Tests In India Also Detect Omicron?

It depends on which RT-PCR test is being used. Further, as WHO has underlined, “confirmation of Omicron by sequencing is recommended".

Vinod Scaria, a scientist at the Institute of Genomics and Integrative Biology (IGIB) in Delhi, pointed out that RT-PCR tests “typically… target the virus nucleic acid at two or more genes/sites in the genome". He further noted that “unfortunately, the primer details for the majority of kits used in India is not publicly disclosed/available, which limits the possibility to ascertain which ones can detect specific variants or which ones are likely to fail for a given variant or mutations".

The Times Of India had reported that a member of the Maharashtra state task-force on Covid-19 had called for laboratories to ensure that RT-PCR tests targeted all the three genes so as to be able to detect the absence of the ‘S’ gene. “Unfortunately, not all laboratories conducting RT-PCR tests are checking for the ‘S’ gene," it quoted Dr Shashank Joshi as saying.

Is The ‘S-Drop Out’ Mutation Only Present In Omicron?

No, the Alpha, another WHO-designated VoC, too, displays the same S-dropout mutation. But the WHO points out that since the prevalence of Alpha is actually “very low in the vast majority of countries", a positive RT-PCR test where the S-gene is not detected “may be indicative of circulation of the Omicron".

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first published:January 06, 2022, 12:53 IST