The Omicron variant of SARS-CoV2 is being seen as a big trouble, with the World Health Organization (WHO) on Sunday assessing the global threat as “ veritably high”. Primary data has indicated that Omicron could have advanced transmissibility, and also a lesser capability to shirk the vulnerable response generated either through previous infection or through vaccines.
Timely discovery of this variant is, thus, crucial to containing its spread. The WHO has said one positive thing about this variant is that it could be detected in some of the RT-PCR individual tests being used across the world, unlike other variants whose presence can be determined only after inheritable sequencing. This can speed up discovery and help in controlling the spread But as scientists told The Indian Express, this isn’t straightforward; most RT-PCR tests in India might not be suitable to distinguish between Omicron and other variants.
Omicron variant How a‘ miss’by RT-PCR helps
RT-PCR tests can only confirm whether the person has an infection or not. They aren’t designed to determine which particular variant has infected the person. For that, a genome sequencing study has to be done Not all infected samples are transferred for genome sequencing, because it’s a slow, complicated and expensive process. Typically, only a veritably small subset of all positive samples — about 2 to 5 per cent — is transferred for gene analysis RT-PCR tests look for the presence of some specific identifiers in the inheritable material (not the entire gene sequence) of the contagion in the mortal body. Generally, two or further identifiers are searched to increase the probability of chancing amatch.However, the other bone can still return a positive result, If one of the identifiers has shifted.
Numerous of the RT-PCR tests look for an identifier in the coronavirus shaft protein, the protruded area that allows the contagion to enter the mortalbody.However, as is the case with the Omicron variant, also there’s a possibility that similar RT-PCR tests, If there are mutations in the shaft protein But as mentioned over, RT-PCR tests look for further than one identifier. So, if the test finds the identifier in the other region (which would mean the person has coronavirus infection) but doesn’t find the identifier in the shaft protein, also it could be an suggestion that the infection is with the Omicron variant.
The problem is that Omicron isn’t the only variant that has mutations in the shaft protein. A many others, specially the Nascence variant, also have mutations in this region, and thus could show analogous geste in RT-PCR tests Nevertheless, such a result can be seen as a webbing medium for the Omicron variant, especially since the frequence of the Nascence variant in the Indian population has gone down significantly. Similar webbing at the individual test stage can be vital in relating and segregating the implicit infections with the Omicron variant.
Gene sequencing for certainty
As Anurag Agarwal, director of Delhi grounded Institute of Genomics and Integrative Biology (IGIB) explained, such a result would only be reflective of the presence of Omicron variant, and would need to be verified through gene sequencing. But it’s still an important head launch The WHO said one of the extensively- used RT-PCR accoutrements, developed by Thermo Fisher Scientific, can descry the presence of Omicron variant. Some of the accoutrements being used in India can also potentially descry the variant. As Vinod Scaria, a scientist at IGIB, said, the capability of tackle to descry the variant depended on the manuals (chemicals that will pick up the identifiers) being used.
“ Unfortunately, the manual details for a maturity of accoutrements used in India aren’t intimately available. So, one can not say whether a particular tackle being used will be suitable to descry this variant or not,” Scaria said.
From the NYT| Will the vaccines stop Omicron? Scientists are contending to find out Still, the discovery of Omicron, or any other variant, If the individual tests don’t offer any suggestion. But since all samples aren’t transferred for sequencing, it’s possible that the Omicron variant will have started circulating but not been picked up. One way to fight this is by adding the number of samples transferred for sequencing.
R R Gangakhedkar, former head of epidemiology at ICMR, said a smart strategy demanded to be worked out since it wasn’t possible to shoot all samples for gene sequencing. He said that in India, it was still the Delta variant that was most current and, thus, wherever applicable, the individual test laboratories should look out for the missing identifier in the shaft protein region, and incontinently mark these for gene sequencing.
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