Molecular Characterization and Phylogenetic Analysis of Melon Necrotic Spot Virus Isolates in Cucurbit Fields

Abstract

Melon necrotic spot virus (MNSV) is an important seed- and soil-borne pathogen affecting cucurbit crops, leading to significant yield losses and quality deterioration in melon and related species. The present study aimed to investigate the molecular characterization and phylogenetic relationships of MNSV isolates collected from cucurbit fields showing characteristic necrotic lesions, chlorotic spotting, and plant stunting. Leaf samples from symptomatic plants were collected, and total RNA was extracted for RT-PCR amplification targeting the coat protein gene of MNSV. Amplified products were sequenced and analyzed to assess genetic variability among isolates. Sequence comparisons revealed high nucleotide similarity among field isolates, indicating a relatively conserved viral population, while minor variations suggested local adaptation and genetic drift. Phylogenetic analysis grouped the isolates into distinct clusters closely related to previously reported MNSV strains from different cucurbit-growing regions, confirming their taxonomic identity and evolutionary relationships. Molecular data further supported the presence of a single predominant viral lineage with limited diversification within the sampled population. Epidemiological observations indicated that disease incidence was favored by warm temperatures, high soil moisture, and continuous cucurbit cultivation practices, which facilitate virus persistence and spread. The study highlights the importance of molecular tools in accurate virus detection and characterization, enabling better understanding of MNSV population structure. These findings contribute to improved knowledge of the genetic diversity and phylogeny of MNSV in cucurbit ecosystems. Overall, the results emphasize the need for integrated disease management strategies, including the use of virus-free seed material, crop rotation, and vector/soilborne pathogen control to reduce the impact of MNSV in cucurbit production systems.