Potato virus Y (PVY) strain groups are based on host response and resistance gene interactions. The strain groups PVY(O), PVY(C) and PVY(N) are well established for the isolates infecting potato in the field. A switch in the emphasis from host response to nucleotide sequence differences in the virus genomes, detection of isolates recombining sequences of different strains, and the need to recognize isolates that cause necrotic symptoms in potato tubers have led to the assignment of new acronyms, especially to isolates of the PVY(N) strain group. This discussion paper proposes that any newly found isolates should be described within the context of the original strain groups based on the original methods of distinguishing strains (i.e., tobacco and potato assays involving use of 'differential' potato cultivars). Additionally, sequence characterization of the complete genomes of isolates is highly recommended. However, it is acceptable to amend the names of PVY isolates with additional, specific codes to show that the isolate differs at the molecular, serological or phenotypic level from the typical strains within a strain group. The new isolates should preferably not be named using geographical, cultivar, or place-association designations. Since many new variants of PVY are being discovered, any new static classification system will be meaningless for the time being. A more systematic investigation and characterization of PVY from potato at the biological and molecular levels should eventually result in a biologically meaningful genetic strain concept.

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.

A range of selected PVY isolates that induce superficial necrosis on potato tubers, originating from several countries, were compared with standard strains of PVA, PVV and PVY. Biological properties (e.g., host range, aphid transmissibility and relationships based on cross‐protection between virus isolates) were studied. PVYNN isolates differ from the normal PVYC, PVYN and PVO strains by their ability to infect Capsicum annuum but not Chenopodium amaranticolor and C. quinoa. All PVYNN isolates are transmissible by Myzus persicae, without any significant differences from one standard strain. These additional data confirm that these tuber‐necrosing isolates belong to PVY. However, they could be ranged in a homogeneous and distinct group inside the PVYN group, based on the differences revealed in the host range, in addition to the specific ability naturally to induce necrosis on tubers.

Viral molecular determinant(s) involved in the tobacco vein necrosis (TVN) symptom induced by necrotic isolates of Potato virus Y (PVY) on Nicotiana tabacum cv. Xanthi leaves remain undetermined. Reference isolates belonging to PVYN (infectious PVYN-605 clone) and PVYO (PVYO-139) were used to produce PVY chimeric genomes by using reverse-genetic techniques. These chimeric clones were inoculated biolistically onto Nicotiana clevelandii plants to establish the clone, prior to being tested on N. tabacum for their ability to induce TVN symptoms. Comparison between sequence data and symptoms observed for each mutated PVY construct shows that the C-terminal part of the multifunctional HC-Pro protein includes two residues (K400 and E419) that are involved in TVN induced by PVYN isolates. Site-directed mutagenesis was used to confirm that these two HC-Pro residues are involved in the TVN phenotype.

A collection of 332 PVY isolates, originating from potato crops, was characterized in order to seek the newly described PVY variants, PVYNW and PVYZ. Serologically, 284 samples were found to contain only PVYO, 36 samples to contain only PVYN, whereas 12 samples were doubly infected by both PVYO and PVYN. All 36 isolates, serologically PVYN‐typed and 16 isolates serologically PVYO‐typed, induced vein necrosis on tobacco. The latter 16 isolates reacted like a Polish standard PVYNW isolate and are probably new members of that PVY subgroup; in the panel of samples, they originated from potato cultivars never previously reported as infected by PVYNW and their high incidence probably indicates that they are more widespread than commonly accepted. Indexing of 108 PVYO isolates on three potato cultivars (Desiree, Eersteling and Maris Bard) carrying hypersensitivity resistance genes to PVYO, PVYC and PVYZ, respectively, revealed the presence of various pathotypes. Two isolates reacted as two standard isolates, designated PVYZE, originating from Spain and previously suspected to be PVYZ members; these isolates were able to overcome the hypersensitivity genes in the three potato cultivars and consequently were members of a newly recognized pathotype. Another isolate evoked the reactions expected after infection with PVYZ. Surprisingly, PVYC was only found in one sample that was doubly infected by PVYO.