Detection and Characterization of Plum Pox Virus (Potyvirus plumpoxi) Marcus Strains in Spanish Apricot and Peach Orchards Through RNA-Seq Analysis

Cultivated species of the Prunus genus are of great economic importance worldwide and can be severely affected by viral diseases that compromise both yield and fruit quality. Among the most significant is Potyvirus plumpoxi (PPV), the causal agent of sharka disease, which has a direct and severe impact on stone fruit production. In this study, high-throughput RNA sequencing was employed to detect and characterize viruses present in commercial peach and apricot orchards located in different regions of Spain. After processing five samples, a total of ten viruses were identified, with PPV being the predominant virus in all analyzed samples, specifically the Marcus strain (PPV-M), which is described as one of the most aggressive PPV strains. In addition, other viruses were detected with high sequencing depth, including Luteovirus nucipersicae (nectarine stem pitting associated virus, NSPaV) and Peach-associated luteovirus (PaLV). Single-nucleotide variation (SNV) analysis of PPV-M populations revealed specific mutations distributed across the viral genome. Furthermore, phylogenetic analyses indicated the presence of multiple infection sources of European origin. These results highlight the presence of PPV-M in Spain, providing evidence of different routes of exchange of infected plant material. These findings underscore the need to strengthen monitoring programs, certification of planting material, and phytosanitary control measures to limit the dissemination of viruses and minimize their impact on stone fruit production.