Strain identification and sequence variability of plum pox virus in Turkey

Plum pox virus (PPV) is the causal agent of sharka disease of stone fruit trees. Since the late 1960s, PPV infection has been reported in different regions of Turkey. In this study, we aim to discover PPV strains in infected regions and determine its genetic variability in Turkey. For this reason, 612 samples were collected from distant locations, where PPV was previously detected in most cases. First, PPV presence in the samples was tested with serological and molecular methods to confirm the disease. Then 314 positive samples were sequence analyzed at a 664-nucleotide length, including the P3-6K1 gene region, one of the most variable regions among Potyvirus species and quite conserved among different strains of a viral species. PPV-D and PPV-T strains were identified mostly in residential gardens, whereas PPV-M was mostly detected in the orchards, except one isolate that was identified as PPV-Rec in Bursa. PPV-T was found to be dominant in the Turkish PPV pool. Estimates of average evolutionary divergence over sequence pairs of P3-6K1 gene regions revealed that the mean intragroup diversity was 0.049 for W; 0.017 for Rec, T, and M; 0.14 for C; 0.012 for Turkish D; 0.009 for global D; and 0.007 for CR.

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