Genetic diversity of Prunus necrotic ringspot virus infecting stone fruit trees grown at seven regions in China and differentiation of three phylogroups by multiplex RT-PCR

• Prunus necrotic ringspot virus was identified from seven Prunus species in China by RT-PCR.
• The CP gene of 28 isolates and MP gene of 15 isolates were sequenced.
• A multiplex RT-PCR assay based on CP gene sequences was developed to differentiate isolates in the three phylogroups.

Prunus necrotic ringspot virus (PNRSV) is an important pathogen of stone fruit trees (Prunus sp.) worldwide. In this study, 35 out of 166 (21.1%) samples of Prunus sp. randomly collected from seven regions in China were tested to be positive for PNRSV by reverse transcription-polymerase chain reaction (RT-PCR). The coat protein (CP) gene of 28 isolates and movement protein (MP) gene of 15 isolates shared 87.1–100% and 82.9–99.9% nucleotide sequence identity, respectively. Phylogenetic analyses of CP and MP gene sequences revealed three well-defined phylogroups represented by isolates PV96, PV32 and PE5, with distribution frequencies of 37.5%, 56.3% and 6.3%, respectively. Sequence variations around a hexanucleotide insertion at sites 124–129 in the CP gene in six PV32-type isolates from Prunus avium resulted in an alteration of secondary structure. A multiplex RT-PCR assay based on CP gene sequences was developed to differentiate isolates in three phylogroups.