Molecular Characterization and Phylogenetic Diversity of Potato Virus Y (PVY) Strains Infecting Potato (Solanum tuberosum L.) in Meerut District, Western Uttar Pradesh, India

Potato virus Y (PVY) is a major constraint to potato production worldwide, with significant implications for seed certification systems, particularly in India, where visual detection is often unreliable. This study aimed to characterize PVY isolates from the Meerut region using high-throughput sequencing (HTS) and RT-PCR-based molecular methods. Analysis of the SRA datasets SRR28328534 and SRR28328536 resulted in the assembly of full-length PVY genomes of 9759 and 9622 nt, respectively. BLASTn analysis revealed a high similarity to known PVY isolates from Russia and Poland, with genome identities exceeding 99%. These sequences were submitted to GenBank under third-party accessions BK070204 and BK068726. RT-PCR using universal coat protein (CP) primers confirmed PVY infection in local potato cultivars (302 and Sangam), and the resulting partial CP sequences were deposited under accession numbers PV031671–PV031675. Phylogenetic analysis based on whole-genome and CP sequences placed the Meerut isolates within the global PVY cluster, showing close relatedness to isolates from Europe and North America. The disease Incidence rate across the fields combined was calculated to be 10.0%. These findings confirm the presence of genetically diverse PVY strains in the region and underscore the importance of molecular surveillance for managing PVY infections in potato seed systems.