Improving Potato virus Y strain nomenclature: lessons from comparing isolates obtained over a 73‐year period

Biological and whole genome properties were compared between eight historical European (1943–1984) and five Australian (2003–2012) Potato virus Y (PVY) isolates. Based on eliciting hypersensitivity genes Nc, Ny or Nz, the former belonged to biological strain groups PVY^C (CT, CRM1), PVY^O (CRN, KE, RS) or PVY^Z (CM2, CRM2, DS). The latter were inoculated to differential and other potato cultivars, tobacco and tomato. Two belonged to PVY^O (BL, DEL3), one to PVY^Z (ATL1), and one (KIP1) to suggested strain group (PVY^D) which elicited putative hypersensitivity gene Nd. Tomato isolate CN1 (and unsequenced CN2), which were poorly adapted to infect potato, were not grouped. Next‐generation sequencing (NGS) of samples containing all isolates except CN2, yielded 13 complete sequences of 9592–9700 nucleotides (nt), and one partial sequence of 9002 nt, none being recombinants. Comparing the former with 60 other PVY complete genomes, found one (CRM2) in phylogenetic subgroup Y^O, eight in Y^O5 (CM2, CRN, DS, KE, RS, ATL1, BL, DEL3), three in Y^C2 (CRM1, CT, KIP1) and one in Y^C1 (CN1). Thus, biologically defined PVY^O (5) and PVY^Z (4) isolates were within phylogenetic subgroups Y^O or Y^O5, biological PVY^C isolates (2) within Y^C2, biological PVY^D isolate KIP1 in Y^C2 and tomato isolate CN1 in Y^C1. NGS identified KIP1 and partial sequence KIP from mixed infection. KIP was in Y^O5. Grouping of four PVY^Z isolates within phylogenetic PVY^O, and the PVY^D isolate within phylogenetic PVY^C, reveals disagreement between current biological and phylogenetic PVY nomenclature systems. Using Latinized numerals for phylogenetic group names resolved this.