Hi

The RNA-dependent RNA polymerase (RdRp) enzyme, encoded by the rdrp gene, plays a critical role in the replication of SARS-CoV-2, the virus that causes COVID-19. RdRp is responsible for synthesizing the viral RNA genome, which is essential for the virus to replicate and produce more virions. Therefore, the rdrp gene is a key target for antiviral drugs and vaccines.

It is not uncommon for different RT-PCR kits to target different genes for the detection of SARS-CoV-2. This is because different kits are designed for different purposes, such as detecting the presence of the virus, quantifying the viral load, or identifying the genetic variation of the virus. Some kits may be more sensitive or specific for certain genes than others, depending on the design of the primers and probes used in the assay.

Using the rdrp gene as a target for RT-PCR may not necessarily be more complicated than targeting other genes. However, it is important to consider the specific characteristics of the gene and the assay when selecting a kit. For example, the rdrp gene may be more conserved across different strains of SARS-CoV-2, which could make it a more reliable target for detecting the virus. On the other hand, the rdrp gene may be more prone to mutations, which could affect the sensitivity or specificity of the assay.

It is generally recommended to carefully evaluate the performance of different RT-PCR kits, including their sensitivity, specificity, and reproducibility, before using them for diagnostic or research purposes. This can help ensure that the results of the assay are reliable and accurate.

Regards

Hello Zabed B. Ahmed

An optimal COVID-19 RT-PCR test should detect targets that are highly specific for SARS-CoV-2 and therefore do not exhibit cross-reactivity with other organisms (including other viruses and coronaviruses). This will minimize the chance of false positive results. Target regions should also have a low rate of mutation to maintain the assay sensitivity as new strains of the virus emerge over time. The target region should also be suitable for designing efficient primers and probes.

If you consider the N gene which is the nucleocapsid (N) protein of SARS-CoV-2, has 90% amino acid homology with SARS-CoV (SARS, the illness that swept through Asia in 2003), which indicates that this particular gene is stable and that the sequence has been conserved over time. Primers and probes designed on the divergent regions of the N gene will ensure the specific detection of SARS-CoV-2, making the N gene overall one of the most promising targets for SARS-CoV-2 detection (see ref 1).

The E genes exhibit fewer mutations than the S-protein (see ref 2).

For the S gene, mutations in this gene are more likely to occur because they confer a genetic advantage to the virus in terms of increased transmissibility (see ref 3). Similarly, multiple mutations in the S gene have been identified in three new SARS-CoV-2 variants that had emerged in the UK, South Africa, and Japan (see ref 4).

If you consider the RdRp gene, point mutations in the RdRp gene have been well documented due to the ability of these mutations to interfere with both diagnostic assays as well as anti-viral treatments such as Remdesivir (see ref 5).

References:

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7307180/

2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7980187/

3. https://www.ecdc.europa.eu/sites/default/files/documents/SARS-CoV-2-variant-multiple-spike-protein-mutations-United-Kingdom.pdf

4. https://www.cnbc.com/2021/01/11/japan-covid-variant-how-it-compares-to-strains-in-uk-south-africa.html

5. https://doi.org/10.1093/cid/ciaa1474

Best.