Genomic variability in Potato potyvirus Y (PVY): evidence that PVY(N)W and PVY(NTN) variants are single to multiple recombinants between PVY(O) and PVY(N) isolates.

Fourteen Potato virus Y (PVY) isolates representative of PVY(O), PVY(N), PVY(NTN) and PVY(N)W groups were characterised at genomic level. Restriction fragment length polymorphism study (RFLP) of each gene of these isolates and sequencing of the first 2700 nucleotides of two PVY(N)W isolates were performed. A mosaic structure was revealed in PVY(N)W and PVY(NTN) genomes, which showed either PVY(O) or PVY(N)-like sequences, depending on the particular gene. Indeed, starting from the 5'-end, these isolates showed a switching, from PVY(N)- to PVY(O)-like sequence, in the HC-Pro C-terminal region. Reversion to PVY(N)-like sequence was also revealed in the NIa N-terminal area of PVY(NTN) isolates, followed by a switching back to a PVY(O)-like sequence in the CP gene. Lastly, some PVY(N)W isolates showed a switching from PVY(O)- to PVY(N)-like sequence in the P1 N-terminal part, thus separating our PVY(N)W isolates into two subgroups. All these apparent recombination events were shown by statistical analysis. Comparison of molecular traits with pathogenic properties of our isolates suggested that the HC-Pro protein is involved in induction of necrosis in tobacco leaves, and the NIa, NIb and/or CP protein in necrosis in potato tubers. Nevertheless, multiple recombination events observed in the PVY(NTN) genome may play a role in the latter phenomenon.