NS omicron With the World Health Organization (WHO) on Sunday citing the version of SARS-CoV2 as a major threat Assessing global risk as “very high”, Preliminary data indicated that omicron There may be higher transmittance, and there may also be a greater ability to survive an immune response generated through prior infection or vaccines.
Therefore, timely detection of this type is the key to control its spread. The WHO has stated that one positive thing about this variant is that it is detectable in some RT-PCR diagnostic tests being used around the world, unlike other variants whose presence can only be determined after genetic sequencing. May go. This can speed up detection and help control the spread.
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But as the scientists told Indian Express, it is not straightforward; Most RT-PCR tests in India may not be able to differentiate between Omicron and other types.
How ‘Miss’ by RT-PCR Helps
It is only through the RT-PCR test that it can be confirmed whether a person has the infection or not. They are not designed to determine which particular type has infected a person. For that genome sequencing study will have to be done.
Not all infected samples are sent for genome sequencing, as it is a slow, complicated and costly process. Typically, only a very small subset of all positive samples — about 2 to 5 percent — are sent for gene analysis.
RT-PCR tests look for the presence of certain unique identifiers in the genetic material (not the entire gene sequence) of the virus in the human body. Typically, two or more identifiers are searched to increase the chances of finding a match. If one of the identifiers has mutated, the other may still return a positive result.
Many RT-PCR tests look for an identifier coronavirus Spike protein, the protruding region that allows the virus to enter the human body. If the spike protein contains mutations, as in the case of the oomicron variant, there is a possibility that such RT-PCR tests looking for identifiers in this region will not detect the mutation as the identifier it is looking for. has been, and thus will give a negative result.
But as mentioned above, RT-PCR tests look for more than one identifier. Therefore, if the test finds an identifier in the second region (which would mean that the person has a coronavirus infection) but does not find an identifier in the spike protein, it may be an indication that the infection is with the omicron variant.
The problem is that Omicron isn’t the only variant that has a mutation in the spike protein. Some others, notably the alpha variant, also have mutations in this region, and may therefore show similar behavior in RT-PCR tests.
Nonetheless, such a result can be seen as a screening mechanism for the omicron variant, especially since the prevalence of the alpha variant in the Indian population has decreased significantly. Such screening at the diagnostic test stage may be important in identifying and isolating potential infections with omicron variants.
Gene sequencing for certainty
As Anurag Aggarwal, director of the Delhi-based Institute of Genomics and Integrative Biology (IGIB), explained, such a result would only indicate the presence of an oomicron variant, and would need to be confirmed through gene sequencing. But it is still an important start.
The WHO said that one of the widely used RT-PCR kits developed by Thermo Fisher Scientific can detect the presence of the omicron variant. Some of the kits being used in India could potentially detect the variant as well. As Vinod Scaria, a scientist at IGIB said, the ability of the kit to be detected depends on the primers (chemicals that will pick up the identifiers).
“Unfortunately, the primer details for most of the kits used in India are not publicly available. Hence, one cannot say whether a particular kit being used will be able to detect this variant or not,” said Scaria.
If diagnostic tests give no indication, detection of omicron, or any other variant, will have to wait for the result of a gene sequencing exercise, which would have taken anywhere between 24 to 96 hours, depending on the technology being used. Is. But since not all samples are sent for sequencing, it is possible that the Omicron variant may have started circulating but not picked up. One way to combat this is to increase the number of samples sent for sequencing.
RR Gangakhedkar, former head of epidemiology at ICMR, said a smart strategy needs to be worked out as it is not possible to send all the samples for gene sequencing. He said that in India still delta version This was most prevalent and therefore, wherever applicable, clinical trial laboratories should look for missing identifiers in the spike protein region, and immediately mark these for gene sequencing.
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