Genetic diversity and population structure of plum pox virus in Russia

Plum pox virus (PPV) is the causal agent of Sharka that is considered the most detrimental viral disease of stone fruit crops. Regular monitoring of stone fruit plantings using enzyme-linked immunosorbent assay and reverse-transcription polymerase chain reaction for PPV detection and identification resulted in the findings of numerous focuses of the disease in European Russia. The virus was found in collections, variety test plots, nurseries, fructiferous and abandoned orchards, decorative plantings, private gardens, wild stone fruit trees growing in urban and rural areas. PPV was detected in naturally infected plum ( Prunus domestica ), peach ( P. persica ), nectarine ( P. persica var. nectarina ), myrobalan ( P. cerasifera ), blackthorn ( P. spinosa ), downy cherry ( P. tomentosa ), sour cherry ( P. cerasus ), sweet cherry ( P. avium ), apricot ( P. armeniaca ) and Canadian plum ( P. nigra ). PPV has been reported from Petersburg, Novgorod, Tver, Moscow, Tula, Voronezh, Tambov, Lipetsk, Belgorod, Rostov, Samara, Saratov, Volgograd, Astrakhan, Stavropol, Krasnodar, Karachay-Cherkessia, Dagestan, and Crimea regions. Six of the nine known PPV strains (D, M, Rec, W, C, CR) have been revealed in European Russia. Most isolates belong to the strains D (38 %), W (25 %), CR (23 %), M (7 %) and C (7 %). Two distinct PPV-Rec isolates have been found on myrobalan and plum in Crimea and Stavropol regions. Population of PPV in European Russia and, probably, all over the European part of the former USSR seems to be the most diverse in the world due to wide spread of PPV isolates belonging to the strains W, C, and CR that were never detected or only sporadically identified in other countries until now. Phylogenetic analysis of their genomes shows that these three strains constitute the supercluster divergent from other PPV strains. This evolutionary branch originated from a common ancestor and apparently developed mainly in Russia. The wide dissemination of PPV in Russia is a potential threat for newly bred stone fruit cultivars and further selection and biotechnological works.