Distribution and Genetic Diversity of Viruses Infecting Cultivated Roses in Japan

This study presents a molecular survey of viruses infecting cultivated roses across five botanical sites in Japan, aiming to assess their distribution, prevalence, and genetic diversity. A total of 250 leaf samples, including both symptomatic and asymptomatic tissues, were collected and tested using RT-PCR with genus- and species-specific primers. Five viral pathogens were detected: Prunus necrotic ringspot virus (PNRSV), rose cryptic virus 1 (RCV-1), rose yellow mosaic virus (RoYMV), rose spring dwarf-associated virus (RSDaV), and rose yellow vein virus (RYVV). PNRSV was the most widespread; it was particularly dominant at a park in Hiroshima and was frequently associated with visible symptoms. RCV-1 was detected at all sites, but often manifested as asymptomatic infections. RSDaV, RoYMV, and RYVV were less frequent but consistently correlated with symptomatic expression, indicating their pathogenic nature. Mixed infections occurred in three samples and produced combined symptom profiles. Phylogenetic analysis revealed that most Japanese virus isolates formed geographically structured clades, suggesting localized transmission pathways or shared propagation sources. While some isolates showed close genetic relationships to global reference strains, others exhibited sequence divergence, implying possible regional evolution. RoYMV and RYVV were confined to certain sites, possibly due to early detection and removal prompted by their symptomatic impact, whereas PNRSV’s high incidence may suggest long-standing latent infections spread via vegetative propagation. RSDaV’s variable presence across sites may be due to the influence of vector ecology on virus distribution. This study provides the first multi-site molecular overview of rose-infecting viruses in Japan, underscoring the virological complexity arising from asymptomatic carriers, mixed infections, and regional variation. The findings serve as foundational data for future epidemiological surveillance and support the development of integrated management strategies to protect Japan’s economically and culturally valuable rose cultivation systems.