Genetic variability and population structure of Grapevine virus A coat protein gene from naturally infected Italian vines

Grapevine virus A is considered one of the viruses associated with rugose wood one of the important diseases of grapevine. Thirty-seven GVA isolates collected from grapevine cultivars from Marche, Apulia and Campania, were subjected to molecular characterization. The genetic and population diversities were studied in the coat protein gene by RT-PCR-RFLP analysis with three restriction enzymes, and nucleotide sequencing. A new primer pair allowing to amplify the whole CP gene (621 bp) was developed. RFLP with AciI yielded the highest number of variants in GVA isolates, showing 7 different “simple” profiles “Complex” profiles were also found, and the most common variant combination was A+B in 39% of isolates. The analysis of GVA sequences confirmed the presence of plants infected with more than one GVA variant and suggested that RFLP is suitable to evaluate population diversity of GVA and to carry on a screening of different haplotypes. In the same vineyards under examination, the distribution of RFLP profiles and the phylogenetic analysis were not correlated with the location of infected plants, showing the presence of GVA population with genetic diversity in the average with those of RNA viruses.