Detection and molecular characterization of a badnavirus in an autochthonous grape from Apulia (Italy)

Vegetative propagation of grapevines favours the perpetuation and dissemination in nature, of intracellular pathogens (over than 70 considering viruses, viroids and phytoplasmas). Once in the field, their presence may affect in various ways the plant's yield and its quality. Preventing infection spreading through a prompt identification, characterization and exclusion approach, is still the most effective action of containment. To this aim, in 2014, registered native grapevine cultivars from Apulia were analyzed to determine their "absolute" sanitary status (virome), i.e. the totality of the infectious agents present in any single accession using a high throughput sequencing (HTS) approach. Small RNA libraries were therefore synthesized and analyzed for the presence virus/viroid sequences. Among these, a symptomless accession D205 of cv. "Bombino nero" growing in a foundation block showed the presence of 21 contigs (ranging from 329 to 56 nt in length) identified as badnavirus-like. Using the closest badnavirus found by BLASTX search as a reference sequence, i.e. Fig Badnavirus 1 (FBV-1, accession No. NC017830), a set of specific primers was designed. Amplification with these primers produced the expected amplicon, which has 91% nucleotide similarity identity with a badnavirus recently discovered in Greece and denoted Grapevine Roditis leaf discoloration-associated virus (GRLDaV). For a preliminary assessment of the incidence of this virus in the field, a preliminary survey in the same foundation block was conducted. A total of 11 samples from different autochthonous cultivars were checked by PCR but none of them tested positive