Differentiation of closely related but biologically distinct cherry isolates of Prunus necrotic ringspot virus by polymerase chain reaction

Prunus necrotic ringspot ilarvirus (PNRSV) exists as a number of biological ly distinct variants which differ in host specificity, serology, and pathol ogy. Previous nucleotide sequence alignment and phylogenetic analysis of cl oned reverse transcription-polymerase chain reaction (RT-PCR) products of s everal biologically distinct sweet cherry isolates revealed correlations be tween symptom type and the nucleotide and amino acid sequences of the 3a (p utative movement protein) and 3b (coat protein) open reading frames. Based upon this analysis, RT-PCR assays have been developed that can identify iso lates displaying different symptoms and serotypes. The incorporation of pri mers in a multiplex PCR protocol permits rapid detection and discrimination among the strains. The results of PCR amplification using type-specific pr imers that amplify a portion of the coat protein gene demonstrate that the primer-selection procedure developed for PNRSV constitutes a reliable metho d of viral strain discrimination in cherry for disease control and will als o be useful for examining biological diversity within the PNRSV virus group . Published by Elsevier Science B.V.