While rdrp or other gene are absolutely mandatory for viral multiplication in the host, I find that these type of gene are not frequently used for diagnostic RT PCR kit. Rather genes like N, H, E and S are more frequently used. Is there any specific reason for that?
Hello.
The genes that are commonly used for the design of RT-PCR diagnostic kits for viruses are typically chosen based on their level of conservation across different strains and species of the virus, as well as the availability of specific and sensitive primers and probes.
For many RNA viruses, the genes encoding the nucleoprotein (N), the hemagglutinin (H), or the spike protein (S) are well conserved across different strains and species. This means that the primers and probes designed to target these genes will be able to detect a wide range of viral strains, which is useful for diagnostic purposes. These genes are also known to be important for the pathogenesis of the virus, as well as the viral replication and transmission.
While the replication-dependent RNA polymerase (RdRp) gene or other genes that code for a particular enzyme are also important for viral replication, they are often less conserved across different viral strains and species. This means that the primers and probes designed to target these genes will be less likely to detect a wide range of viral strains, making them less useful for diagnostic purposes.
Another reason is that RdRp genes are more complex and may be harder to design primers for because of the large variable regions and conserved regions are relatively shorter compared to the N,H and S genes. Additionally, these genes tend to be smaller and more difficult to amplify with RT-PCR.
It's worth noting that RT-PCR assays are often multiplexed, meaning they can detect multiple different regions of a viral genome simultaneously. So, targeting multiple genes is a good strategy to increase the diagnostic sensitivity and specificity, and also make the diagnostic more reliable.
In short, N, H, and S genes are commonly used in RT-PCR diagnostic kits because they are well conserved across different viral strains, making it more likely that primers and probes designed to target these genes will detect a wide range of viral strains, and also their association with pathogenesis, replication and transmission make them a logical choice.
Regards.
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