Analysis of the P1 gene sequences and the 3'-terminal sequences and secondary structures of the single-stranded RNA genome of Potato virus V.

The immunocapture reverse transcriptase PCR method (IC-RT-PCR) was used to selectively amplify specific genome sequences of an isolate of Potato virus V (PVV, genus Potyvirus) from a potato plant infected by multiple viruses in the field in Finland. The sequences of the 5'- and 3'-non-translated regions (NTR) and the P1-and coat protein (CP)-encoding sequences were determined because they are the most variable genomic regions in potyviruses. The sequences of the new Finnish PVV isolate obtained in this study were compared to the sequences of eight PVV isolates characterized from other European countries. The results indicated little genetic variability among the European PVV isolates (nt identity values > 96% for all regions examined). Most PVV isolates were grouped according to their geographical origin using P1-sequences for a phylogenetic analysis. The nucleotide substitution patterns for P1 and the CP genes revealed that variability is due to a random genetic drift. Comparison of the secondary structure predictions for the unusually long 3'-non-translated region (3'-NTR) of PVV to the 3'-NTR of Tobacco etch virus (TEV) and other potyviruses revealed that some of the structures defining regions crucial for viral genome replication in TEV are present in PVV and other potyviruses.