RT-PCR Detection and Molecular Characterization of Prunus necrotic ringspot virus Isolates Occurring in Turkey

Sour cherry (Prunus cerasus L.), sweet cherry (P. avium L.), peach [P. persica (L.) Batsch], nectarine [P. persica (L.) Batsch var. nucipersica (Suckow) C.K. Schneid], apricot (P. armeniaca L.) and plum (P. domestica L.) trees either known to be infected, or shown to be so during a survey of different stone fruit growing regions of Turkey, were tested for the occurrence of Prunus necrotic ringspot virus (PNRSV) using double antibody sandwich (DAS)–enzyme-linked immunosorbent assay (ELISA) and reverse transcription polymerase chain reaction (RT-PCR). DAS–ELISA detected virus in only 31 of 486 samples; an additional 20 samples (total infection 51) were found to be infected by PNRSV when RT-PCR was used. The highest virus incidence occurred in nectarine followed by that in peach. In order to identify specific virus strains, the PCR products amplified from the capsid protein (CP) gene of the 20 isolates selected from different provinces were subjected to restriction fragment length polymorphic (RFLP) analysis. The PCR products were digested by eight different restriction endonucleases. Most of the PNRSV isolates were identified as members of group PV96, but a single isolate was a member of group PV32; none of the isolates belonged to group PE5. Phylogenetic analysis divided the virus isolates into three additional major and three minor groups. No relation was found between the geographic distribution and the grouping of the PNRSV isolates based on RFLP