Molecular characterization of new Crimean Plum pox virus isolates

Abstract

Molecular analysis of new Plum pox virus (PPV) isolates found in peach, apricot, and plum cultivar collections of the Nikita botanical gardens–National scientific center of the Russian Academy of Sciences (NBS), as well as in wild myrobalans growing in the surrounding area was performed. Nineteen new PPV isolates were detected using ELISA and immunocapture reverse transcription-polymerase chain reaction. Most of them belonged to the strain D; one isolate of the strain Rec and another one belonging to the strain M were also found. 3’-terminal genomic sequences of new isolates encompassing the coat protein (CP) gene and flanking sequences of the NIb gene and 3’-untranslated region were sequenced. Phylogenetic analysis of the 3’-terminal sequences assigned PPV-D isolates to several clusters or clades. The average level of divergence of new and previously characterized Crimean PPV-D isolates was 2%. The comparatively high genetic diversity of the strain D isolates from the Crimea suggests a long-standing introduction of their ancestors to the NBS. The H23 isolate found in the apricot cultivar collection belonged to the strain M. This is the first PPV-M detection in the Crimea. The strain Rec Al-Ch isolate was revealed on a wild myrobalan tree. A K59T mutation was found in the СP of the K87 isolate (strain D), which impairs its recognition by PPV-D-specific monoclonal antibody 4DG5. Аmino acid substitutions were found in position 68 of the CP of the Al-Ch as well as previously characterized Russian K28 and Kisl-1pl strain Rec isolates. These substitutions did not affect the recognition of these isolates by PPV-M-specific monoclonal antibody AL suggesting that position 68 seems to be outside the epitope. In all likelihood, PPV entered the NBS as a result of several independent introductions of the infected stone fruit crops from various regions of the world and spread along the plantings by aphids.