Characterization of Pepper Veinal Mottle Virus Isolates Based on Coat Protein and Movement Protein Gene Sequences

Abstract

Pepper veinal mottle virus (PVMV) is an economically important potyvirus affecting pepper production, causing mosaic, vein mottling, leaf distortion, and significant yield reduction in infected plants. The present study aimed to characterize PVMV isolates based on coat protein (CP) and movement protein (MP) gene sequences to understand their molecular diversity and evolutionary relationships. Symptomatic pepper leaf samples were collected from major cultivation areas, and total RNA was extracted for RT-PCR amplification of CP and MP gene regions. The amplified products were sequenced and analyzed for nucleotide and amino acid variability among isolates. Sequence comparisons revealed moderate genetic diversity within and between PVMV populations, indicating ongoing evolutionary divergence. Phylogenetic analysis based on CP and MP genes grouped isolates into distinct clusters, partially correlated with geographic origin, suggesting localized diversification and limited long-distance gene flow. The coat protein gene exhibited relatively higher conservation compared to the movement protein gene, which showed greater sequence variability, reflecting differential selective pressures on viral functional regions. Recombination analysis suggested possible genetic exchange events contributing to viral evolution. Field observations indicated that disease severity was influenced by environmental conditions and aphid vector abundance, particularly Aphis spp., which facilitate virus transmission in pepper fields. Mixed infections with other potyviruses were occasionally detected, potentially exacerbating symptom severity. The study highlights the importance of molecular characterization for understanding PVMV variability and epidemiology. Overall, the findings provide valuable insights into the genetic structure, evolutionary dynamics, and molecular diversity of PVMV isolates, supporting the development of improved diagnostic tools and integrated disease management strategies for sustainable pepper production systems.