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Potato virus Y (PVY) the type member of the genus Potyvirus, occurs world-wide as isolates which differ in host range and the type of symptoms caused. The sequences of a 5' segment of viral RNA overlapping the 5' non-translated region (5'NTR) alone (ten isolates) or the 5'NTR and the adjacent P1 coding region (eight isolates) were established. These data were used to quantify the polymorphism in the 5'-terminal part of the PVY genome. Nucleotide sequence identity between isolates ranged from 66-100% in the 5'NTR and from 70-100% in the P1 coding region. The lowest amino acid sequence similarity between PVY P1 was 77%, illustrating the high variability of this protein in the PVY species. Phylogenetic trees based on either 5'NTR or P1 sequence analyses resulted in the same clustering of the studied isolates into three groups. Group I comprises potato isolates all inducing 'tobacco veinal necrosis' symptoms. Group II contains isolates inducing either 'tobacco veinal necrosis' or mosaic symptoms in tobacco. Group III contains mainly pepper or tomato isolates inducing mosaic symptoms in tobacco and shows a geographical clustering of the Tunisian isolates. This clustering into three groups is discussed in comparison with phylogenetic trees previously obtained from capsid gene or 3'NTR sequence analysis in the PVY species. Multiple sequence alignment indicated conserved motifs potentially involved in viral functions.

Sequence polymorphism in the 5'NTR and in the P1 coding region of potato virus Y genomic RNA