Molecular variability among isolates of Prunus necrotic ringspot virus from different Prunus spp.

Viral sequences amplified by polymerase chain reaction from 25 isolates of Prunus necrotic ringspot virus (PNRSV), varying in the symptomatology they cause in six different Prunus spp., were analyzed for restriction fragment polymorphisms. Most of the isolates could be discriminated by using a combi nation of three different restriction enzymes. The nucleotide sequences of the RNA 4 of 15 of these isolates were determined. Sequence comparisons and phylogenetic analyses of the RNA 4 and coat proteins (CPs) revealed that a ll of the isolates clustered into three different groups, represented by th ree previously sequenced PNRSV isolates: PV32, PE5, and PV96. The PES-type group was characterized by a 5' untranslated region that was clearly differ ent from that of the other two groups. The PV32-type group was characterize d by an extra hexanucleotide consisting of a duplication of the six immedia tely preceding nucleotides. Although most of the variability was observed i n the first third of the CP, the amino acid residues in this region, which were previously thought to be functionally important in the replication cyc le of the virus, were strictly conserved. No clear correlation with the typ e of symptom or host specificity could be observed. The validity of this gr ouping was confirmed when other isolates recently characterized by other au thors were included in these analyses.