NE-11 represents a new strain variant class of Potato virus Y

This report describes the characterization by whole-genome sequencing of four PVY isolates with unique combinations of molecular and symptomatic characteristics. Three of these four isolates were of type PVY^N:O (ID-1, OR-1, PN10A), including one of “type B”, which contains an extra recombination event in the 5′UTR/P1 cistron; the other (NE-11) represents a novel PVY molecular genotype, previously misclassified as a PVY^NA-NTN isolate. The full genome sequence of this latter isolate is unique inasmuch as it is nearly identical to that of PVY^N isolates for the first 2,000 nucleotides (nts), after which it very strongly resembles PVY^NA-NTN isolates for the next 600 nts. For the final 7,000 nts of its genome, NE-11 shares intermediate identity with these other two previously reported classes of PVY^N genomes, except for a portion of the capsid protein region in which it resembles neither. Recombination in each of the four isolates was verified by a suite of recombination detection programs. PN10A represents the first complete sequence of a PVY strain variant of the class reported as PVY^N-W (or PVY^N:O) type B. Specific PCR assays for two unique regions of NE-11 are presented that will allow the identification of this strain variant by other researchers.