Phylogeny of Prunus necrotic ringspot virus cherry variants based on RNA 3 coding region

Prunus necrotic ringspot virus (PNRSV) is an important pathogen of stone fruit species (Prunus sp.) including sweet (Prunus avium) and sour cherry (Prunus cerasus). In present study twenty seven cherry variants of PNRSV from three regions of Bulgaria were molecularly studied based on the nucleotide and amino acid sequences of the coat protein (CP) and the movement protein of RNA3 coding region. Fifteen more variants were studied only in the CP genome region. Phylogenetic analyses of the two genome regions revealed the formation of the four well-defined phylogroups PV32-I, PV96-II, PE5-III and CH30. Based on the nucleotide and amino acid sequences of CP genome region twenty-five and sixteen variants belonged to PV96-II and to PV32-I phylogroups, respectively. With one exclusion phylogenetic analyses based on the nucleotide and amino acid sequences of the MP genome region showed the same relationships among studied variants observed in the CP genome region. The comparison of CP and MP amino acid sequences revealed that the studied variants in each of the two groups, PV96-II and PV32-I had phylogroup-conserved amino acid residues. The results obtained showed a correlation between the phylogeny based on the nucleotide and amino acid sequences of RNA3 genomic region and the described for infected with PNRSV cherry trees pathotypes, known as rugose disease and mild mottle virosis. The specific amino acids present both in the CP and MP genome regions of all studied cherry PNRSV variants together with the symptoms on naturally infected cherry trees corresponded to the mild virosis pathotype.