Covid-19: Can RT-PCR tests detect Omicron variant infection?


Timely detection of the variant is, as a result, key to checking its spread. (File)

The coronavirus’ Omicron variant has emerged as a big threat with the World Health Organization (WHO) on Sunday assessing a “very high” global risk. Preliminary data suggests that the variant could have higher transmissibility, and also a greater ability to evade immune response generated through prior infection or vaccines.

Timely detection of the variant is, as a result, key to checking its spread. The WHO said one positive about the variant is that it could be detected by some RT-PCR tests being used across the world, unlike other variants whose presence can only be determined after genetic sequencing. This can speed up detection and help control the spread.

However, this is not straightforward, scientists told The Indian Express. Most RT-PCR tests used in India might not be able to distinguish between the Omicron and other variants.

How a ‘miss’ by RT-PCR helps
RT-PCR tests can only confirm infections and are not designed to determine the variant causing the infection. To determine that, a genome sequencing study needs to be done.

However, not all infected samples undergo genome sequencing as it is a slow, complicated, and expensive process. Only a small subset of positive samples — about 2-5% — is sent for gene analysis.

Also Read | Covid-19: Random testing at airports among revised rules for foreign travellers amid Omicron scare

RT-PCR tests look for specific identifiers in the genetic material (not the entire gene sequence) of the virus in humans. Usually, the test looks for two or more identifiers to increase the probability of finding a match. If one identifier has mutated, the other can still return a positive result.

Many RT-PCR tests look for an identifier in the virus’ spike protein, the protruded area that enables its entry into the human body. If the spike protein mutates, as it has with the Omicron variant, then it is possible that such RT-PCR tests looking for identifiers in this region would not recognise the mutation as an identifier and would return a negative result.

Since RT-PCR tests look for more than one identifier, if it finds the identifier in the other region (meaning the person has the infection) but cannot find the identifier in the spike protein, it could indicate infection caused by the Omicron variant.

However, the Omicron is not the only variant to have mutations in the spike protein. A few others, especially the Alpha variant, also have mutations in the region and could show similar behaviour in RT-PCR tests.

Nonetheless, such a result can screen the Omicron variant, especially since the Alpha variant’s prevalence among Indians has significantly gone down. Such diagnostic screening can be vital in identifying and isolating potential Omicron variant infections.

Gene sequencing
Institute of Genomics and Integrative Biology (IGIB) Director Anurag Agarwal told The Indian Express that such a result would indicate presence of Omicron variant but would need to be confirmed through gene sequencing. But it is an important head start.

The WHO said the RT-PCR kits developed by Thermo Fisher Scientific, one of the most widely used, can detect the Omicron variant. Some of the kits used in India can also detect the variant. IGIB Scientist Vinod Scaria told The Indian Express that the kit’s ability to detect the variant depended on the primers (chemicals that pick up the identifiers) being used.

Also Read | Covid-19: Maharashtra on alert after passenger from South Africa tests positive

However, the primer details of a majority of kits being used in India are not available publicly. As a result, one cannot say if a particular kit being used will detect the variant, Scaria said.

If the diagnostic tests do not indicate the presence of the Omicron or any other variant, the detection would have to await the result of gene sequencing that takes between 24 and 96 hours. However, since all samples are not sent for sequencing, it is likely that the Omicron variant will have started circulating without being picked up. A way to counter this is by sending more samples for sequencing.

RR Gangakhedkar, former head of epidemiology at the Indian Council of Medical Research, said a smart strategy was needed since it was impossible to send all samples for gene sequencing. He said the Delta variant was still the most prevalent variant in India. As a result, diagnostic laboratories should look for the missing identifier in the spike protein region and mark these for gene sequencing.

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