Genetic structure and molecular variability of Grapevine fanleaf virus populations

To gain insights into the evolutionary mechanisms of Grapevine fanleaf virus (GFLV) from the genus Nepovirus, family Secoviridae, the sequences of the complete coding region of RNA2, including genes 2AHP, 2BMP and 2CCP, and partial sequence from the RNA1-encoded gene 1EPol of 14 GFLV isolates from three naturally infected California vineyards were characterized. Phylogenetic analyses suggested two to three evolutionarily divergent lineages that did not reflect the vineyard origin of the isolates or an association with rootstock genotype or scion cultivar. Examination of the genetic variability of the California isolates alongside isolates worldwide, for which three RNA1 and 44 RNA2 coding sequences are available, revealed similar patterns of molecular evolution for the different regions within the GFLV genome but distinct selection constraints with the strongest pressure exerted on genes 2CCP and 2BMP, an intermediate level of pressure exerted on gene 1EPol, and the weakest pressure exerted on gene 2AHP. Some of the California isolates resulted from interspecies recombination events between GFLV and Arabis mosaic virus with crossover sites suspected in gene 1EPol and identified in genes 2AHP and 2BMP; and intraspecies recombination events inferred in the four target genes but most frequently observed within gene 2CCP. This study suggested that purifying selection and recombination are important evolutionary mechanisms in the genetic diversification of GFLV.