Genetic Diversity of Potato virus Y in Potato Production Areas in Northeast China

In 2011–2014, ELISA or nucleic acid spot hybridization (NASH) testing for common potato viruses or Potato spindle tuber viroid (PSTVd) was performed on 500 leaf samples collected in potato fields in the northeast provinces Heilongjiang and Inner Mongolia, China. The results revealed that 38.4% (Heilongjiang) and 27.7% (Inner Mongolia) were positive for Potato virus Y (PVY). To unveil the strain composition and population structure of PVY in the region, the multiplex RT-PCR described by Chikh-Ali et al. was performed on all of the ELISA-PVY-positive samples. Of the 158 samples whose PVY strain scenarios could be determined, PVYᴺᵀᴺ⁻ᴺᵂ-SYR-II and PVYᴺ⁻ᵂⁱ were the most abundant strains, occurring in 58.9 and 47.5% samples, followed by PVYᴺᵀᴺ⁻ᴺᵂ-SYR-I (31.0%), PVYᴺ:ᴼ (19.6%), Eu-PVYᴺᵀᴺ (7.6%), NA-PVYᴺ (1.3%), and PVYᴼ (0.6%). In the 84 single-strain-infected samples, PVYᴺ⁻ᵂⁱ accounted for 41.7%, PVYᴺᵀᴺ⁻ᴺᵂ-SYR-II for 40.5%, PVYᴺᵀᴺ⁻ᴺᵂ-SYR-I for 14.3%, and PVYᴺ:ᴼ and Eu-PVYᴺᵀᴺ for 3.6% each. Seven isolates representing PVYᴺᵀᴺ⁻ᴺᵂ-SYR-I (HLJ-6-1 and HLJ-9-4), PVYᴺᵀᴺ⁻ᴺᵂ-SYR-II (INM-W-369-12 and SC-1-1-2), PVYᴺ:ᴼ (HLJ-30-2), and PVYᴺ⁻ᵂⁱ (HLJ-BDH-2 and HLJ-C-429) were sequenced and analyzed molecularly. Whereas the sequence identities for isolates belonging to the same strain group were >98.5%, they fell for isolates belonging to different strain groups to 92.7–98.1% at the genome level and 96.1–98.4% at the polyprotein level. Interestingly, the exact location of the recombination events varied among isolates within a strain group. Phylogenetic analysis of all 42 full length PVY sequences from China indicated that most clustered to various recombinant groups, despite the fact that the PVY isolates were isolated from at least five host species. Pathological analysis of four isolates representing PVYᴺ:ᴼ, PVYᴺ⁻ᵂⁱ, PVYᴺᵀᴺ⁻ᴺᵂ-SYR-I, and PVYᴺᵀᴺ⁻ᴺᵂ-SYR-II revealed that the PVYᴺᵀᴺ⁻ᴺᵂ-SYR-II isolate incited the most severe symptoms on potato cultivar Kexin 13, followed by PVYᴺᵀᴺ⁻ᴺᵂ-SYR-I, PVYᴺ:ᴼ and PVYᴺ⁻ᵂⁱ. The PVYᴺᵀᴺ⁻ᴺᵂ-SYR-I and PVYᴺᵀᴺ⁻ᴺᵂ-SYR-II isolates also caused necrotic ringspots on the tubers of Kexin 13, indicating their ability to induce the potato tuber necrotic ringspot disease in potato.