Molecular Detection and Sequence Analysis of Pepino Mosaic Virus (PepMV) Strains in Greenhouse Tomato Production

Abstract

Tomato is one of the most widely cultivated vegetable crops in greenhouse production systems, where viral diseases pose a major threat to yield and fruit quality. Pepino Mosaic Virus (PepMV), a member of the genus Potexvirus, has emerged as one of the most economically important pathogens affecting greenhouse tomato cultivation worldwide. Infected plants commonly exhibit symptoms such as mosaic patterns, leaf distortion, fruit discoloration, uneven ripening, and reduced marketability. The present study was conducted to detect and characterize PepMV strains associated with greenhouse tomato production using molecular diagnostic and sequence analysis approaches. Field surveys were carried out in commercial greenhouse facilities, and symptomatic as well as asymptomatic tomato samples were collected for laboratory examination. Total RNA was extracted from plant tissues and subjected to reverse transcription polymerase chain reaction (RT-PCR) using PepMV-specific primers targeting conserved genomic regions. Amplified products were sequenced and analyzed using BLAST and phylogenetic tools to determine strain identity, genetic diversity, and evolutionary relationships among the detected isolates. The results confirmed the presence of PepMV in symptomatic tomato plants, whereas asymptomatic samples showed either weak or no amplification. Sequence analysis revealed high nucleotide similarity between the obtained isolates and previously reported PepMV strains from different geographic regions, indicating the circulation of genetically related strains within greenhouse production systems. Phylogenetic analysis demonstrated the occurrence of multiple PepMV strain groups and suggested possible introduction through infected seed material, contaminated tools, or plant-to-plant mechanical transmission. The study highlights the widespread occurrence and molecular variability of PepMV in greenhouse tomato cultivation. Early detection and accurate molecular characterization are essential for effective disease monitoring and implementation of integrated management strategies.