Omicron variant: from vaccine to test efficacy, is the RT-PCR enough?

What does an RT-PCR test detect?
RT-PCR tests can only confirm whether the person has an infection or not. Many RT-PCR tests look for an identifier in the coronavirus spike protein, the protruded area that allows the virus to enter the human body.

How do you get to know the variant?
To determine the Covid variant, a genome sequencing study has to be done.

Is an RT-PCR enough?
A complete RT-PCR report for COVID includes a test for ‘N’ , ‘S’ , ‘E’ and ‘ORF’ genes. Absence of the ‘S’ gene and other presence of other genes, is an indirect way of knowing that Omicron is present. However, most of the current ICMR approved RT-PCR test kits being used in India target the E, Rd Rp and N genes and not the S gene which is the target of the Omicron variant.

So, what are the experts saying?
Public health experts want laboratories to conduct RT-PCR tests in whole, for all three genes, particularly on international travelers, to help detect the absence of the ‘S’ gene. But absence of the S gene, doesn’t confirm the presence of the Omicron variant, and sequencing will still need to be done.

What is the current situation?
Genome sequencing is a slow, complicated and expensive exercise. Therefore, not all infected samples are sent for genome sequencing. Normally, only about 2 to 5 per cent of the positive samples are sent for gene analysis.

This is what the WHO is saying on test efficacy!
The widely used PCR tests continue to detect infection, including infection with Omicron, as we have seen with other variants as well. Studies are underway to determine whether there is any impact on other types of tests, including rapid antigen detection tests."

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