Can an RT-PCR Test Detect Omicron? How Will Genome Sequencing Help?

But is that the case in India? What is genome sequencing and how will it help us detect the variant?

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Edited By :Padmashree Pande

Stating that the global risk from the new coronavirus variant Omicron as "very high," the World Health Organization (WHO), pointed that it could be detected in some RT-PCR tests.

While initial data has detected greater transmissibility, what remains key to stop the spread is the faster detection of the variant itself and the RT-PCR detection can help with it, the WHO has said.

Two cases of COVID-19's Omicron variant have been reported in India so far, said Lav Agarwal, Joint Secretary, Union Health Ministry, on Thursday, 2 December.

But is that the case in India? What is genome sequencing and how will it help us detect the variant? Here's all you need to know.


Can India's RT-PCR test detect Omicron?

Not exactly. RT-PCR test can tell a person if they have been infected with coronavirus but not which variant.

RT-PCR test looks to identify specific genetic material to identify virus in the body. Each test looks for two or more such identifiers – and if they match with what is found in the human body, then a person tests positive.

What is the science behind detection of variant in RT-PCR?

The RT-PCR test looks for three parts of the virus spike (S), nucleocapsid (N2) and envelop (E). Therefore if the N2 and E are detected, but not S, then it means that it COULD BE omicron.

In a statement the WHO said:

"Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout), and this test can therefore be used as a marker for this variant, pending sequencing confirmation," the WHO statement said.

So, why is this not possible in India?

Most ICMR-approved RT-PCR kits do not target the S gene – that is, they do not look for the spike protein.

"Most of the current ICMR approved RT-PCR kits being used in India target the E, Rd Rp and N genes. The mutations in the latest variant have occurred in the S gene. The common RT-PCR kits being used will be able to identify positive or negative, but will not be able to identify if the positive result is due to the mutation in the S gene," Arjun Dang, CEO, Dr Dangs Lab, told IANS.

Veena Menon, Consultant, Clinical Virology, Amrita Hospital told IANS that RT-PCR kit Taqpath kit from Thermofisher could be used to detect the new variant as it detects S gene. Neither the ICMR nor the Health Ministry has said anything about this.

"But mutations in the S gene are more common, which affects not only virus infectivity, but also detection. It was also seen in the case of Alpha and Beta variants. The new variant has a mutation/deletion similar to the Alpha variant and hence S gene drop out test, which is a PCR method, can be used as an initial screening test," Menon told IANS.

Can Rapid Antigen tests detect Omicron?

Not at the moment. An RAT test can tell only if a person has been infected with COVID-19 or not.

What should be done to detect Omicron?

Anurag Agarwal, director of Delhi based Institute of Genomics and Integrative Biology (IGIB) told The Indian Express that diagnostic tests would only be indicative of the presence of Omicron variant. This would still need a genome sequencing to confirm, he added.

According to Centers for Disease Control and Prevention:

"Genomic sequencing allows scientists to identify SARS-CoV-2 and monitor how it changes over time into new variants, understand how these changes affect the characteristics of the virus, and use this information to better understand how it might impact health."

Therefore a genomic sequencing could show the presence/absence of spike protein – which can confirm which variant of virus the person has been infected with.


How long does genomic sequencing take?

The exercise takes between 24 and 96 hours. But in India, not all samples are sent for genomic sequencing.

India has only sequenced 53,562 samples and analysed 46,676 of these between 26 July and 8 November , data from SARS-CoV-2 Consortium on Genomics (INSACOG) revealed. Until 8 November, India has only sequenced 1,15,101 samples – accounting to just 0.21 of the total cases.

(With inputs from IANS, The Indian Express)

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