New Cherry-Adapted Plum Pox Virus Phylogroups Discovered in Russia

Abstract

Plum pox virus (PPV) is the most pathogenic virus of stone fruit crops worldwide. Unusual PPV isolates were discovered on sour cherry (Prunus cerasus L.) and steppe cherry (P. fruticosa Pall.) in the Republic of Tatarstan and the Middle Ural region, Russia. They induced typical sharka symptoms and tested positive for PPV by ELISA and RT-PCR, but were not detected by PCR using known strain-specific primers. Their complete genomes were determined using high-throughput sequencing. Phylogenetic analysis allocated new isolates to four clearly distinguished lineages (SC, TAT, Y, Tat-26) within a cluster of PPV cherry-adapted strains. The phylogroups SC and TAT had 84.5 to 86.9% average nucleotide identity to each other and strain CR, with which they comprised a common subcluster. Isolates from the Middle Ural region (group Y) were closer to strain C, sharing 96.9% identity. The fourth lineage is represented by the isolate Tat-26, which was a recombinant of strain CR and C isolates as major and minor parents, respectively. These results show that the genetic diversity of PPV is higher than thought and may contribute to a better understanding of the origin and evolution of cherry-adapted strains of the virus. P. fruticosa was reported as a new natural PPV host for the first time.