Prediction of single nucleotide polymorphisms of RNA dependent RNA polymerase for the potato leafroll virus using computational and experimental approaches

Potato leafroll disease, caused by potato leafroll virus (PLRV), is one of the most devastating diseases, resulting in significant losses to the potato crop. Research on comprehensive studies examining the prediction of mutations in PLRV genes for this viral disease is limited. This study aims to quantify and characterize the accumulation of these genetic mutations by predicting SNPs for PLRV RNA-dependent RNA polymerase (RdRP) using computational approaches. We utilized advanced online protein prediction tools to explore the impact of DNA mutations on protein function and structure. These tools enabled us to assess the potential level and location of disorder within proteins, providing crucial insights into their behavior. In our study, the polymerase chain reaction (PCR) yielded a product corresponding to the PLRV-RdRp gene, measuring 450 base pairs (bp). This sequence has been documented in GenBank under the access number MT576073 and is cataloged in the UniProt database with the ID A0A8E6I3S8. The phylogenetic analysis of the PLRV-RdRp sequence involved a comparative study with reference sequences in the NCBI database. We focused on two notable predicted inversion mutations located at positions 93 (A93T) and 117 (K117G). Remarkably, the (Lys/Gly) mutation at position 117 exhibited a substantial disorder percentage of 61%, significantly higher than the reference sequence's 13.4%. These single nucleotide polymorphisms (SNPs) are not just statistical anomalies; they have real implications. They alter RdRp protein stability and physicochemical properties, altering pocket residues and influencing the protein's interaction with natural compounds. In conclusion, our findings provide a solid foundation for future research and development efforts focused at the rapid diagnosis and sustainable management of PLRV.