Insights into the virome of the Andean blackberry (Rubus glaucus) in Ecuador

The commercial cultivation of Andean blackberry (Rubus glaucus Benth) in Ecuador has expanded significantly over the past decade. No certification program exists to ensure the production of planting material free of pathogens of concern. This multi-year study explored the virome of R. glaucus as a first step toward a hazard analysis to identify viruses of concern and to establish targeted testing practices. Four viruses were detected: raspberry bushy dwarf virus (RBDV), strawberry necrotic shock virus (SNSV), rose ilarvirus-2 (RIV-2), and a new reovirus-like virus. Genomic analyses revealed that Ecuadorian RBDV isolates show substantial genetic diversity, suggesting a long-term presence, whereas SNSV and RIV-2 isolates showed low variability, indicating recent introductions. Phylogenetic analysis placed the novel reovirus close to arthropod-associated Hubei reo-like virus 6 and plant viruses such as rice ragged stunt virus and raspberry latent virus. RBDV, SNSV and RIV-2 were prevalent amongst tested material reaching as high as 100% infection. These findings highlight the urgent need for virus management in Ecuadorian blackberry production.