Molecular Epidemiology and Sequence Diversity of Pepper Veinal Yellows Virus in Sweet and Hot Pepper Fields

Abstract

Pepper veinal yellows virus (PeVYV) is an economically important polerovirus associated with severe yellowing, vein clearing, stunting, and yield reduction in sweet and hot pepper production systems. Field surveys were conducted in major pepper-growing regions to investigate the molecular epidemiology and sequence diversity of PeVYV infecting both cultivated pepper types. Symptomatic leaf samples were collected from infected plants and subjected to molecular detection using reverse transcription polymerase chain reaction (RT-PCR) with virus-specific primers targeting conserved genomic regions. Amplification of expected fragments confirmed widespread presence of PeVYV in both sweet and hot pepper fields, while asymptomatic samples tested negative. Sequence analysis of amplified products revealed high nucleotide similarity with previously reported PeVYV isolates, confirming virus identity across diverse agroecological zones. Phylogenetic reconstruction grouped local isolates within established PeVYV clades, while also indicating measurable genetic variation among isolates from different geographic locations and host types. Comparative analysis suggested the occurrence of distinct viral subpopulations possibly influenced by host adaptation and vector-mediated transmission dynamics. Disease incidence was strongly associated with high whitefly populations and warm environmental conditions that favored vector activity and virus spread. Infected plants exhibited reduced vigor, leaf deformation, and significant decline in fruit yield and quality. Molecular epidemiological findings indicate active movement and diversification of PeVYV within pepper production systems, emphasizing the need for continuous monitoring and genetic characterization. The integration of RT-PCR detection and sequence analysis provides a reliable framework for early diagnosis and epidemiological tracking of PeVYV outbreaks.