Prevalence and strain composition of potato virus Y circulating in potato fields in China’s north-central province Shanxi

Potato is an important crop in Shanxi province located in north-central China. During 2019-2020, 319 potato leaf samples were collected from eight locations distributed in three major potato production areas in Shanxi. Bio-chip detection kit revealed the presence of several potato viruses, and among them potato virus Y (PVY) was the most common one, reaching the incidence of 87.8% of all symptomatic samples. The immuno-captured multiplex reverse transcription (RT)-PCR was used to identify strains for all 280 PVY-positive samples, unveiling 242 samples infected with a single strain of PVY (86.4%) and 38 (13.6%) with a mixed infection. Of samples with a single-strain infection, PVY -SYR-II accounted for 102 (42.1%), followed by PVYN-Wi (33, 13.6%) , PVY -SYR-I (28, 11.6%), 261-4 (22, 9.1%), PVYNTNa (20, 8.3%), PVYNTNb (19, 7.9%), and PVY -SYR-III (18, 7.4%). Seven isolates representing different recombinants were selected for whole genome sequencing. Phylogenetic and recombination analyses confirmed the RT-PCR based strain typing for all seven strains of PVY found in Shanxi. SXKL-12 is the first SYR-III strain from potato reported from China. However, unlike that in other known SYR-III isolates, the region positioned from 1,764 to1,902 nt in SXKL-12 shared the highest sequence identity of 82.2% with an uncharacterized PVY isolate, JL-23, from China. Interestingly, the PVYN-Wi isolate SXZY-40 also possessed a more divergent sequence for the region positioned from 6,156 to 6,276 nt than other N-Wi isolates known to date, sharing the highest identity of 86.6% with an uncharacterized Chinese PVY isolate, JL-11. Pathogenicity analysis of dominant strains PVY -SYR-II and PVYN-Wi in six local popular potato cultivars revealed that Kexin 13, Helan 15 and Jizhangshu 12 were susceptible to these two strains with mild mottling or mosaic symptoms expression, while three cultivars, Jinshu 16, Qingshu 9, Xisen 6 were found fully resistant.

Comparison of mineral oil, insecticidal and biopesticide spraying regimes for reducing spread of three potato virus Y (PVY) strains in potato crops

In-field management of potato virus Y (PVY) faces challenges by changing availability and environmental acceptability of chemical agents to control aphid vectors of the virus, and by proliferation of PVY strains with different symptomology and rates of spread. Over 2018-2020, foliar spray treatments were compared in field experiments in New Brunswick, Canada, to measure effectiveness at reducing spread of PVYO, PVYN:O and PVYNTN strains. Mineral oil, insecticide, combined oil and insecticide spray and a biopesticide (i.e., LifeGard® WG) were compared. Insecticide-only and mineral oil-only were not effective, though several combined oil and insecticide, and biopesticide treatments significantly reduced PVY spread. The biopesticide was proportionately more effective with recombinant PVYN:O and PVYNTN strains, possibly from exciting the plant’s hypersensitive resistance response only caused naturally in cv. Goldrush by PVYO. Pesticide residue analysis showed that mineral oil enhanced the retention of pyrethroid insecticide in the potato foliage longer than with insecticide applied alone, which may explain the beneficial synergistic effect of combined sprays for reducing PVY spread. Tuber yields were generally unchanged in chemical insecticide treatments but were slightly lower in biopesticide treatment. The cost per PVY protection was competitive across all effective treatments, including biopesticide, however, there was some revenue loss from lower yield with the biopesticide. This biopesticide is organic-certified, however, thus a small premium on price for organic production could offset this yield deficit.

Phylogenetics and evolution of potato virus V: another potyvirus that originated in the Andes

Potato virus V (PVV) causes a disease of potato (Solanum tubersosum) in South and Central America, Europe and the Middle East. We report here the complete genomic sequences of 42 new PVV isolates from the potato’s Andean domestication centre in Peru, and of eight historical or recent isolates from Europe. When the principal open reading frames (ORFs) of these genomic sequences together with those of nine previously published genomic sequences were analysed, only two from Peru and one from Iran were found to be recombinant. The phylogeny of the 56 non-recombinant ORF sequences showed that the PVV population has two major phylogroups, one of which forms three minor phylogroups (A1-A3) of isolates, all of which are only found in the Andean region of South America (Peru and Colombia), and the other forms two minor phylogroups, a basal one of Andean isolates (A4) that is paraphyletic to a crown cluster containing all the isolates found outside South America (World). This suggests that PVV originated in the Andean region with only one minor phylogroup spreading elsewhere in the world. In minor phylogroups A3 and A4, there were subclades on long branches containing isolates from S. phureja evolving more rapidly than the others, and these interfered with dating calculations. Although no temporal signal was directly detected among the dated non-recombinant sequences, PVV and potato virus Y (PVY) are from the same potyvirus lineage and are ecologically similar, so “sub-tree dating” was done using a single maximum-likelihood phylogeny of PVV and PVY sequences, and PVY’s well-supported 157 CE “time to most common recent ancestor” was extrapolated to date that of PVV as 29 BCE. Thus the independent historical coincidences supporting the datings of the PVV and PVY phylogenies are the same; PVV arose at least 2,000 years ago in the Andes, and was taken to Europe during the Columbian Exchange, where it diversified around 1853 CE soon after the European potato late blight pandemic. PVV is likely to be more widespread than currently realised, and of biosecurity relevance for world regions that have not yet recorded its presence.