Fungal pathogens pose a major threat to grapevine cultivation, leading to substantial economic losses, reduced yields, and consequently a decline in wine quality. Currently, the development of alternative control methods is necessary to reduce dependence on synthetic fungicides. In this regard, mycoviruses appear as a promising strategy for the biological control of fungal pathogens, as they can induce hypovirulence in targeted fungal species. This approach would ultimately result in a reduction of disease severity without any negative effects on grapevines or beneficial organisms. For this reason, we are analyzing fungal communities to identify viruses that show the capacity for horizontal transmission between isolates collected from the same vine stock. These include viruses with RNA-based genomes, which are widespread in fungi, and DNA viruses, which are rarer but have a greater potential for horizontal transmission. Moreover, we are analyzing the dynamic fungal collection maintained at Agroscope Changins (www.mycoscope.ch) to identify novel and/or known DNA and RNA mycoviruses that can induce hypovirulence in fungi that are most problematic in grapevines. We are particularly interested in understanding the viral diversity of lesser studied emerging fungal pathogens, such as Phyllosticta ampelicida (Engelm.) Aa, or major endophytes, such as Cladosporium sp. and Alternaria sp., that might represent a reservoir for mycoviruses. Fungal strains displaying viral dsRNA profiles were analyzed using targeted RT-PCR to study the distribution of known polymycoviruses, namely Cladosporium ramotenellum polymycovirus 1 (CrPMV1) and Cladosporium cladosporioides polymycovirus 2 (CcPMV2), and high-throughput sequencing (HTS) for viral discovery. CrPMV1 and CcPMV2 were selected for their transmission potential. They were undetectable in the tested fungal strains, hence pointing towards a reduced and limited prevalence within fungal communities. Further analyses by high-throughput sequencing (HTS) revealed presence of a putative new species within the proposed new Zetapartitivirus genus and the known virus Alternaria alternata chrysovirus 1 (AaCV1).
