Whole genome characterization of Potato virus Y isolates collected in the western USA and their comparison to isolates from Europe and Canada

Abstract

Potato virus Y (PVY) is a serious potato pathogen that affects potato seed and commercial production crops. In recent decades, novel PVY strains have been described that cause necrotic symptoms on tobacco foliage and/or potato tubers. The major PVY strains that affect potato include PVY(O) and PVY(N), which have distinct serotypes that can be differentiated by immunoassay. Other economically important strain variants are derived from recombination events, including variants that cause tuber necrotic symptoms (PVY(NTN)) and PVY(O) serotypes that cause tobacco veinal necrosis (PVY(N)-W, PVY(N:O)). Although the PVY(NTN) and PVY(N)-W variants were first reported in Europe, apparently similar strains have been appearing in North America. Confirmation of the existence of these recombinant strains in North America is important, as is whether they spread from a common source or were derived by independent recombination. Whole genome sequencing can be used to positively identify strain variants and begin to address the issue of origins. Symptomology, serology, RT-PCR, and partial sequencing of the coat protein region were used to identify isolates of the PVY(NTN), PVY(N), PVY(NA-N), and PVY(N:O) for whole-genome sequencing. Sequencing confirmed the presence of PVY(NTN) and PVY(N) isolates that were >99% identical to European sequences deposited in GenBank in the 1990's. Sequences of the PVY(NA-N) and PVY(N:O) types were 99.0% and 99.5% identical to known sequences, respectively. There was no indication that recombinant strains PVY(NTN) or PVY(N:O) had different parental origins than recombinant strains previously sequenced. This is the first confirmation by whole-genome sequencing that "European"-type strain variants of PVY(N) and PVY(NTN) are present in North America, and the first reported full-length sequence of a tuber necrotic isolate of PVY(N:O).

Potato virus Y: An Evolving Concern for Potato Crops in the United States and Canada

“…N found, giving additional evidence that PVY N strains are a recent introduction into the seed potato system in North America (24 (50,59,60,84) showed that some strains were molecular recombinants, while others were not.…”

Detection and molecular characterization of Slovak tomato isolates belonging to two recombinant strains of potato virus Y

“…Also, recombination amongst PVY genome sequences is likely to have significant evolutionary implications for the virus, as a dramatic incidence of new recombinant strains occurred in recent years (Lorenzen et al, 2006a;Ka- The analysed sequences are identified by their nt position (numbered based on the reference JF927760 full length sequence), length and genome part targeted. Primer sequences were removed prior to the analysis.…”

“…Recombination between PVY strain groups has given rise to new strain groups, e.g. PVY-NTN, PVY-N-Wi, PVY-N:O, having the tendency to increase worldwide (Glais et al, 2002;Lorenzen et al, 2006a;Karasev and Gray, 2013). Further molecular approaches have made it possible to characterize and classify PVY strains based on genome characteristics (Lorenzen et al, 2006b;Chikh et al, 2010), however, sometimes without a clear-cut linking to their biological traits (Karasev and Gray, 2013).…”

Potato virus Y (PVY) strains in Belgian seed potatoes and first molecular detection of the N-Wi strain

“…in North America and Europe, resulting in a very complex situation of strains, strain groups and variants (Karasev & Gray 2013). However, these variations are mainly introduced by recombination in different parts of the genome (Glais et al 2002, Nie & Singh 2003a, Lorenzen et al 2006a, Chikh Ali et al 2007a, b, 2010b. Three to four recombinant junctions in NTN strains and only one or two recombinant junctions in PVY N-Wi and PVY N:O have been reported (Glais et al 2002, Nie & Singh 2003a, Lorenzen et al 2006a, b, Schubert et al 2007, Visser et al 2012, Karasev & Gray 2013.…”