The Incidence and Genetic Analysis of Two Betaflexiviruses Capillovirus alphavii and Tepovirus tafpruni in Iran.

Viral diseases have emerged as a serious threat to cherry trees production in Iran. To determine which virus(es) are present, three leaves from a sweet cherry tree (Qz5) with diffuse white blotch spots and deformation were subjected to high-throughput sequencing. After de novo assembly, blast analysis revealed that 12 contigs ranging from 360 to 7,433 nucleotides (nts) shared 78-96% nt identities with Capillovirus alphavii (cherry virus A, CVA) and seven contigs, ranging from 350 to 6,844 nts, shared 79-88% nt identities with Tepovirus tafpruni (prunus virus T, PrVT). During a survey, CVA, PrVT, and CVA + PrVT infections were detected in 12.6%, 5.1%, and 7.9% of 724 sour and sweet cherry samples. Phylogenetic analysis revealed that Iranian CVA was grouped into GIIIB, whereas PrVT fell into a distinct branch, which was confirmed by diversity plots. The within-population diversity was lower than the between-population diversity suggesting the contribution of a founder effect on diversification of CVA isolates. Host-specific codon adaptation analysis revealed the highest adaptation of CVA to sour cherry. This could suggest that sour cherry may be one of the closest Prunus species to wild progenitors. It raises the possibility that viruses such as CVA may have exerted evolutionary pressures influencing domestication processes. Additionally, the similarity index indicated that the common plum (Prunus domestica) may have exerted significant evolutionary pressure on CVA and PrVT. The association of CVA and PrVT was reported for the first time in the mid-Eurasian region, specifically in Iran, which represents an issue in phytosanitary certification of cherry plants.