Polymerase chain reaction detection and assessment of genetic variation in New South Wales isolates of passionfruit woodiness potyvirus

A reverse transcription polymerase chain reaction system was developed to detect passionfruit woodiness potyvirus (PWV) in leaves of Passflora species. PWV coat protein (CP) sequences which were amplified from New South Wales isolates and PWV strain K had identical Hinf I, Hae III, Rsa I and Cfo I restriction profiles. Some polymorphism was revealed by digestion with Alu I. PWV CP sequences from 20 out of 21 plants had identical Alu I patterns which differed from that of PWV-K. The remaining isolate produced Alu I restriction fragments characteristic of both the common New South Wales isolates and of PWV-K, suggesting that the original plant contained a mixed infection. Three CP cDNA clones, each from an individual plant sample, and six clones from the sample which showed a mixed infection were sequenced. Analysis of the sequence data showed that these isolates from New South Wales had over 97% nucleotide sequence similarity and were closely related to PWV-K. There was 82-85% similarity in the deduced amino acid sequence to the previously described tip blight, severe and mild strains.