Molecular analysis of prune dwarf virus reveals divergence within non-Turkish and Turkish viral populations

Prune dwarf virus (PDV) infection affects the production of stone fruits (Prunus spp.) around the world, including in Turkey. In this study, we analyzed the available nucleotide (nt) and amino acid (aa) sequences of P1, P2, movement protein (MP), and coat protein (CP) genes to assess the molecular variability and structure of non-Turkish and Turkish PDV populations. Global isolates were clustered into three major groups in nt-based phylogenetic trees of MP and CP. Comparison of geographically different isolates showed that the MP aa sequences were more conserved than the CP aa sequences. The major aa changes in MP and CP showed the most effect on group 3 isolates. MP and CP-based analyses revealed the lowest number of variable sites (S), total number of mutations (η), average number of nt differences between sequences (k), and nt diversity (per site) (π) values in group 3 isolates, indicating high genomic similarities. The Turkish isolates manifested the highest S and η, and the second highest k and π values were observed in the comparison with CP, confirmed the high intra-group divergence of the Turkish isolates belonging to the three phylogroups. A stronger purifying selection pressure was observed in the MP region than in the CP region. Neutrality tests deduced negative values for all the MP and CP phylogroups and positive values for the P1, P2, Bulgarian, and Polish populations. MP and CP comparisons showed the divergence of the three phylogroups, as revealed by the results of the K S*, K ST*, Z*, and S nn permutation statistical tests. The fixation index (F ST) values suggested that non-Turkish PDV isolates had a higher genetic distance compared with Turkish isolates from group 3 and the Turkish isolates from the other two groups.