Genomic characterization and host range study of pepper veinal mottle virus (Potyvirus capsivenae) (PVMV) infecting tomato

Pepper veinal mottle virus (PVMV), a member of the Potyvirus genus, is primarily a pathogen of pepper, but its emerging impact on tomato poses a growing concern due to its broad host range, aphid transmission and potential for significant yield losses. Despite its economic importance, studies on the genomic characterization and host range of PVMV isolates are limited. This study characterizes, through host range analysis, complete genome sequencing and comparative analysis of two PVMV isolates Tom1 (from tomato) (PV476910) and EP1 (from eggplant) (PV476911) in Taiwan. Mechanical inoculation onto 20 plant species revealed distinct host responses: Tom1 induced severe mosaic and necrotic symptoms in tomato (PDI 100%), while EP1 caused milder symptoms in tomato (PDI 60%) but higher virulence in Capsicum species (PDI 100%). Full-length genomes (9,796 nt each) comprised a single open reading frame encoding a 3,073 amino acid polyprotein processed into ten characteristic potyviral proteins. Sequence Demarcation Tool (SDT) and sequence identity matrix analyses showed Tom1 and EP1 share 94.3% nucleotide identity, with highest identities (96%) to Japanese (Tom1) and Taiwanese (EP1) isolates. Both clustered with East/Southeast Asian isolates, sharing only 74–84% identity with African isolates and < 61% with non-PVMV potyviruses. Phylogenetic reconstruction revealed four major clades, placing Tom1 with East Asian isolates and EP1 with Taiwanese isolates, indicating regional diversification. Gene-wise comparison showed high conservation in the coat protein (99.3% nt, 100% aa) and greater variability in non-structural proteins (P1, HC-Pro, CI, VPg), suggesting roles in host adaptation. These findings enhance understanding of PVMV genetic diversity, phylogenetic relationships, and host specificity, providing a basis for targeted resistance breeding and regional disease management strategies.