An Improved Multiplex IC-RT-PCR Assay Distinguishes Nine Strains of Potato virus Y

Dynamics of Potato Virus Y Infection Pressure and Strain Composition in the San Luis Valley, Colorado

The San Luis Valley (SLV), Colorado, is the second-largest fresh-potato-growing region in the United States, which accounts for about 95% of the total production in Colorado. Potato virus Y (PVY) is the leading cause of seed potato rejection in the SLV, which has caused a constant decline in seed potato production over the past two decades. To help potato growers control PVY, we monitored the dynamics of PVY infection pressure over the growing seasons of 2022 and 2023 (May through August) using tobacco bait plants exposed to field infection weekly. PVY infection dynamics were slightly different between the two seasons, but July and August had the highest infection in both years. The first PVY infection was detected in the second half of June, which coincides with the emergence of potato crops in the valley. PVY infection increased toward the beginning of August and declined toward the end of the season. Three PVY strains were identified in tobacco bait plants and potato fields, namely PVYO, PVYN-Wi, and PVYNTN. Unlike other producing areas of the United States, PVYO is still the major strain infecting potato crops in Colorado, comprising ∼40% of total PVY strain composition. This could be explained by the prevalence of the potato cultivar Russet Norkotah that lacks any identified N genes, including the Nytbr that controls PVYO, which imposes no negative selection against this strain. The current study demonstrated the usefulness of bait plants to understand PVY epidemiology and develop more targeted control practices of PVY.

Genome sequences of six recombinant variants of potato virus Y identified in North American potato cultivars grown in China

Six genome sequences for potato virus Y (PVY) recombinants are reported from two North American potato cultivars grown in China. The coding complete sequences encode a single open reading frame characteristic of potyviruses. The six sequenced PVY isolates represent three distinct recombinants of PVY, namely N-Wi, SYR-I, and SYR-II.

Prevalence and Strain Composition of Potato virus Y Circulating in Potato Fields in China's North-Central Province of Shanxi

Potato is an important crop in Shanxi province, located in north-central China. In 2019 to 2020, 319 potato leaf samples were collected from eight locations distributed in three major potato production areas in Shanxi. BioChip testing revealed the presence of several potato viruses, of which Potato virus Y (PVY) was the most common, reaching an incidence of 87.8% of all symptomatic samples. Immunocaptured 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 PVY^N-Wi (33, 13.6%), PVY-SYR-I (28, 11.6%), 261-4 (22, 9.1%), PVY^NTNa (20, 8.3%), PVY^NTNb (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 to 1,902 nt in SXKL-12 shared the highest sequence identity of 82.2% with an uncharacterized PVY isolate, JL-23, from China. Interestingly, PVY^N-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 PVY^N-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 symptom expression, and three cultivars, 'Jinshu 16', 'Qingshu 9', and 'Xisen 6', were fully resistant.

Prevalence of Recombinant Strains of Potato Virus Y in Seed Potato Planted in Idaho and Washington States Between 2011 and 2021

Potato virus Y (PVY) has emerged as the main reason for potato seed lot rejections, seriously affecting seed potato production in the United States throughout the past 20 years. The dynamics of PVY strain abundance and composition in various potato growing areas of the United States has not been well documented or understood up to now. The objective of this study was to find out the prevalence of PVY strains in potato fields in the Pacific Northwest (PNW), including seed potato production systems in the State of Idaho and commercial potato fields in the Columbia Basin of Washington State between 2011 and 2021. Based on the testing of >10,000 foliar samples during Idaho seed certification winter grow-out evaluations of seed potato lots and seed lot trials in Washington State, a dramatic shift in the PVY strain composition was revealed in the PNW between 2011 and 2016. During this time period, the prevalence of the ordinary, PVY^O strain in seed potato dropped 8- to 10-fold, concomitantly with the rise of recombinant strains PVY^N-Wi and PVY^NTNa, which together accounted for 98% of all PVY positives by 2021. In Idaho seed potato, PVY^NTNa strain associated with the potato tuber necrotic ringspot disease (PTNRD) was found to increase threefold between 2011 and 2019, accounting for 24% of all PVY positives in 2019. Mild foliar symptoms induced by recombinant PVY strains may be partially responsible for the proliferation of PVY^N-Wi and PVY^NTNa in potato crops. A spike of another PTNRD-associated recombinant, PVY-NE11, was recorded in the PNW between 2012 and 2016, but after reaching a 7 to 10% level in 2012 to 2013 this recombinant disappeared from the PNW potato by 2019. Whole genome sequence analysis of the PVY-NE11 suggested this recombinant was introduced in the United States at least three times. The data on PVY strain abundance in the PNW potato crops suggest that virus management strategies must consider the current dominance of the two recombinant PVY strains, PVY^N-Wi and PVY^NTNa.

Molecular and Biological Characterization of Recombinant Isolates of Potato virus Y Circulating in Potato Fields in Mexico

Potato virus Y (PVY) is a significant threat to potato (Solanum tuberosum) production in Mexico. The presence of recombinant strains of PVY circulating in potato has been reported in the country, but no systematic study on the genetic diversity of PVY in potato and prevalence of PVY strains has been conducted yet. We report on a series of surveys in seed potato production areas in two states in Mexico, namely, Chihuahua and Jalisco, between 2011 and 2019. PVY was detected through the period of nine years in multiple potato cultivars in both states, often remaining asymptomatic in the most popular cultivars, such as 'Fianna' and 'Agata'. When typed to strain, all PVY samples studied were found to have N-serotype, and were all identified molecularly as isolates of the same recombinant strain, PVY^NTN. Five of these PVY isolates were tested on tobacco (Nicotiana tabacum), where they induced vein necrosis supporting the molecular typing. This identification was also confirmed biologically on differential potato cultivars, where one PVY^NTN isolate from the 2013 survey triggered the hypersensitive resistance conferred by the Nz_tbr gene in the cv. Maris Bard. Seven of these Mexican PVY^NTN isolates, collected between 2013 and 2019, including two PVY isolates from potato tubers exhibiting potato tuber necrotic ringspot disease, were subjected to whole genome sequencing and found to show a typical PVY^NTNa recombinant structure. When subjected to phylogenetic analysis, Mexican PVY^NTN sequences clustered in more than three separate clades, suggesting multiple introductions of PVY^NTN in the country. The wide circulation of the PVY^NTN strain in Mexican potato should be considered by potato producers, to develop mitigation strategies for this PVY strain associated with tuber necrotic symptoms.

Occurrence and distribution of viruses infecting potato in Russia

Potato viral disease has been a major problem in potato production worldwide including Russia. Here, we detected Potato Virus M (PVM), P (PVP), S (PVS), Y (PVY), and X (PVX) and Potato Leaf Roll Virus (PLRV) by RT-PCR on potato leaves and tubers from the Northwestern (NW), Volga (VF), and Far Eastern (FE) federal districts of Russia. Each sample was co-infected with up to five viruses. RT-PCR disclosed all six viruses in NW, three in VF, and five in FE. Phylogenetic analyses of PVM and PVS strains resolved all PVM isolates in Group O (ordinary) and all PVS isolates in Group O. Seven PVY strains were detected, and they included only recombinants. PVY recombinants were thus the dominant potato virus strains in Russia, although they widely varied among the regions. Our research provides insights into the geographical distribution and genetic variability of potato viruses in Russia.

Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains

In recent years, high throughput sequencing (HTS) has brought new possibilities to the study of the diversity and complexity of plant viromes. Mixed infection of a single plant with several viruses is frequently observed in such studies. We analyzed the virome of 10 tomato and sweet pepper samples from Slovakia, all showing the presence of potato virus Y (PVY) infection. Most datasets allow the determination of the nearly complete sequence of a single-variant PVY genome, belonging to one of the PVY recombinant strains (N-Wi, NTNa, or NTNb). However, in three to-mato samples (T1, T40, and T62) the presence of N-type and O-type sequences spanning the same genome region was documented, indicative of mixed infections involving different PVY strains variants, hampering the automated assembly of PVY genomes present in the sample. The N- and O-type in silico data were further confirmed by specific RT-PCR assays targeting UTR-P1 and NIa genomic parts. Although full genomes could not be de novo assembled directly in this situation, their deep coverage by relatively long paired reads allowed their manual re-assembly using very stringent mapping parameters. These results highlight the complexity of PVY infection of some host plants and the challenges that can be met when trying to precisely identify the PVY isolates involved in mixed infection.

Interspecific interactions within a vector-borne complex are influenced by a co-occurring pathosystem

Potato virus Y (PVY) and zebra chip (ZC) disease are major threats to solanaceous crop production in North America. PVY can be spread by aphid vectors and through vegetative propagation in potatoes. ZC is associated with "Candidatus Liberibacter solanacearum" (Lso), which is transmitted by the tomato/potato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae). As these two pathosystems may co-occur, we studied whether the presence of one virus strain, PVY°, affected the host preference, oviposition, and egg hatch rate of Lso-free or Lso-carrying psyllids in tomato plants. We also examined whether PVY infection influenced Lso transmission success by psyllids, Lso titer and plant chemistry (amino acids, sugars, and phytohormones). Lso-carrying psyllids showed a preference toward healthy hosts, whereas the Lso-free psyllids preferentially settled on the PVY-infected tomatoes. Oviposition of the Lso-carrying psyllids was lower on PVY-infected than healthy tomatoes, but Lso transmission, titer, and psyllid egg hatch were not significantly affected by PVY. The induction of salicylic acid and its related responses, and not nutritional losses, may explain the reduced attractiveness of the PVY-infected host to the Lso-carrying psyllids. Although our study demonstrated that pre-existing PVY infection can reduce oviposition by the Lso-carrying vector, the preference of the Lso-carrying psyllids to settle on healthy hosts could contribute to Lso spread to healthy plants in the presence of PVY infection in a field.

Small RNA profiling analysis of two recombinant strains of potato virus Y in infected tobacco plants

Plant viral infections lead to accumulation of virus-derived small interfering RNAs (vsiRNAs) as a result of host defense mechanisms. High-throughput sequencing technology enables vsiRNA profiling analyses from virus infected plants, which provide important insights into virus-host interactions. Potato virus Y (PVY) is a detrimental plant pathogen that can infect a variety of solanaceous crops, e.g., potato, tobacco, tomato, and pepper. We analyzed and characterized vsiRNAs derived from Nicotiana tabacum cv. Samsun infected with two recombinant PVY strains, N-Wi and NTN. We observed that the average percentage of vsiRNAs derived from plants infected with N-Wi was higher than from plants infected with NTN, indicating that N-Wi invokes a stronger host response than NTN in tobacco. The size distribution pattern and polarity of vsiRNAs were similar between both virus strains with the 21 and 22 nucleotide (nt) vsiRNA classes as most predominant and the sense/antisense vsiRNAs ratio nearly equal in the 20-24 nt class. However, the percentage of sense vsiRNAs was significantly higher in the 25-26 nt long vsiRNAs. Distinct vsiRNA hotspots, identifying highly abundant reads of different unique vsiRNA sequences, were observed in both viral genomes. Previous studies found an A or U bias at the 5' terminal nucleotide position of 21 nt vsiRNAs; in contrast, our analysis revealed a C and U nucleotide bias. This study provides insights that will help further elucidate differential processing of vsiRNAs in plant antiviral defense.

Potato Virus Y (PVY) Isolates from Solanum betaceum Represent Three Novel Recombinants Within the PVYN Strain Group and Are Unable to Systemically Spread in Potato

Tamarillo, or tree tomato (Solanum betaceum), is a perennial small tree or shrub species cultivated in subtropical areas for fresh fruit and juice production. In Ecuador, tamarillo orchards are affected by several viruses, with one previously identified as potato virus Y (PVY); however, the specific strain composition of PVY in tamarillo was not determined. In 2015 and 2016, eight tamarillo plants exhibiting symptoms of leaf drop, mosaic, and mottled fruit were sampled near Tumbaco and Quito, Ecuador. These tamarillo PVY isolates were able to systemically infect tobacco, Nicotiana benthamiana, naranjilla, and tamarillo. Seven of the eight PVY isolates from tamarillo exhibited N-serotype, while one of the PVY isolates studied, Tam15, had no identifiable serotype. One isolate, Tam17, had N-serotype but produced asymptomatic systemic infection in tobacco. In tamarillo, four tamarillo isolates induced mosaic and slight growth retardation and were unable to systemically infect pepper or potato. Tamarillo, on the other hand, was unable to support systemic infection of PVY isolates belonging to the PVY^O and PVY^Eu-N strains. The whole genomes of eight PVY isolates were sequenced from a series of overlapping RT-PCR fragments. Phylogenetically, tamarillo PVY isolates were found to belong to the large PVY^N lineage, in a new tamarillo clade. Recombination analysis revealed that these tamarillo PVY isolates represent at least three novel recombinant types not reported before. The combination of the biological and molecular properties found in these eight PVY isolates suggested the existence of a new tamarillo strain of PVY that may have coevolved with S. betaceum.

Genetic Diversity of Nine Non-Recombinant Potato virus Y Isolates From Three Biological Strain Groups: Historical and Geographical Insights

Potato virus Y (PVY) isolates from potato currently exist as a complex of six biologically defined strain groups all containing nonrecombinant isolates and at least 14 recombinant minor phylogroups. Recent studies on eight historical UK potato PVY isolates preserved since 1984 found only nonrecombinants. Here, four of five PVY isolates from cultivated potato or wild Solanum spp. collected recently in Australia, Mexico, and the U.S.A. were typed by inoculation to tobacco plants and/or serological testing using monoclonal antibodies. Next, these five modern isolates and four additional historical UK isolates belonging to biological strain groups PVY^C, PVY^Z, or PVY^N obtained from cultivated potato in 1943 to 1984 were sequenced. None of the nine complete PVY genomes obtained were recombinants. Phylogenetic analysis revealed that the four historical UK isolates were in minor phylogroups PVY^C1 (Y^C-R), PVY^O-O (Y^Z-CM1), PVY^NA-N (Y^N-M), or PVY^Eu-N (Y^N-RM), Australian isolate Y^O-BL2 was in minor phylogroup PVY^O-O5, and both Mexican isolate Y^N-Mex43 and U.S.A. isolates Y^N-MT12_Oth288, Y^N-MT12_Oth295, and Y^N-WWAA150131G42 were in minor phylogroup PVY^Eu-N. When combined, these new findings and those from the eight historical UK isolates sequenced earlier provide important historical insights concerning the diversity of early PVY populations in Europe and the appearance of recombinants in that part of the world. They and four recent Australian isolates sequenced earlier also provide geographical insights about the geographical distribution and diversity of PVY populations in Australia and North America.

Effects of the Age-Related Resistance to Potato virus Y in Potato on the Systemic Spread of the Virus, Incidence of the Potato Tuber Necrotic Ringspot Disease, Tuber Yield, and Translocation Rates Into Progeny Tubers

The recombinant strain of potato virus Y (PVY), PVY^NTN, is the main cause of the potato tuber necrotic ringspot disease (PTNRD) in susceptible potato cultivars, which reduces the quality of potato tubers, in addition to the yield loss. Control of PVY has been the main challenge in most potato-producing areas. Here, the effects of the age-related resistance (ARR) were investigated in transplants of a potato cultivar Yukon Gold to the infection with PVY^NTN strain in greenhouse experiments. Within the first 3 weeks after transplanting into soil (week 1 [W1] to W3), Yukon Gold plants developed ARR that impaired the systemic movement of PVY^NTN into upper noninoculated leaves and concomitant translocation into progeny tubers starting from W4 after transplanting. The yield and quality of tubers from PVY-infected plants with the established ARR (W5 to W8) were comparable with the healthy controls, suggesting that late PVY infection would not significantly affect commercial potato production. Plants inoculated early (W1 to W2), before the establishment of the ARR, exhibited a 100% primary systemic infection with PVY^NTN and produced fewer tubers of smaller sizes, exhibiting PTNRD; this resulted ≤70% yield reduction compared with plants inoculated later in the season (W5 to W8). This ARR greatly restricted the systemic movement of PVY^NTN in the foliage and resulted in very limited translocation rates of the virus into tested progeny tubers: 7.8 and 4.1% in 2017 and 2018, respectively, of all plants inoculated later in the season (W5 to W8). This study suggests that PVY^NTN management programs in Yukon Gold seed potato should focus more on the early stages of the potato development before the onset of the ARR.

Proliferation of Recombinant PVY Strains in Two Potato-Producing Regions of Canada, and Symptom Expression in 30 Important Potato Varieties with Different PVY Strains

Potato virus Y (PVY) exists as several strains with distinct symptomology and tuber yield effects in different potato varieties. Recently, new recombinant strains have proliferated and dominated local populations around the world. In this study, PVY^O, PVY^N:O, PVY^N-Wi, and PVY^NTN strains were tracked across Canada from 2014 to 2017, showing rapid evolution of populations away from the traditionally dominant PVY^O to recombinants PVY^N-Wi (western Canada) and PVY^NTN (eastern Canada). Simultaneously, 30 potato varieties were inoculated with PVY^O, PVY^N:O, and PVY^NTN in controlled greenhouse experiments. Foliar symptoms of primary (mechanical inoculation mimicking aphid infection) and secondary (tuber seedborne) infection were cataloged, and tuber yield measured. On average, and generally similar in primary and secondary infection, symptom expression and yield reduction were most severe with PVY^O, followed by PVY^N:O and PVY^NTN. Strong mosaic symptoms were most commonly expressed with PVY^O infection, and only seen with PVY^N:O or PVY^NTN in 15 and 3 varieties, respectively. Across variety-strain combinations, yield reduction was correlated with symptom severity, most strongly in PVY^O-infected plants (e.g., AC Chaleur, Beljade, Envol, Norland, and Pacific Russet), and four varieties exhibited tuber necrotic ringspot disease with PVY^NTN (AC Chaleur, Envol, Pacific Russet, and Yukon Gold).

A New Tymovirus Isolated From Solanum quitoense: Characterization and Prevalence in Two Solanaceous Crops in Ecuador

Naranjilla (Solanum quitoense Lam.) and tamarillo (S. betaceum Cav.) are two important perennial solanaceous crops grown in Ecuador for the fresh market and juice production. Viruses infecting tamarillo and naranjilla are currently poorly studied, and no clean stock program exists in Ecuador. Here, we report a new virus, provisionally named as naranjilla mild mosaic virus (NarMMV) (genus Tymovirus, family Tymoviridae), isolated from naranjilla grown in an orchard in Pichincha Province, Ecuador. The complete genome of the virus consists of 6,348 nucleotides and encodes three open reading frames typical for members of the genus Tymovirus. Phylogenetically, Chiltepin yellow mosaic virus, Eggplant mosaic virus, and the recently characterized naranjilla chlorotic mosaic virus (NarCMV) were found to be the closest relatives of NarMMV. Unlike NarCMV, the new virus induced mild mosaic in naranjilla and more severe symptoms in tamarillo. Similar to NarCMV, NarMMV was unable to systemically infect potato. Virus surveys found NarMMV prevalent in naranjilla production areas of two provinces of Ecuador, especially where hybrid cultivars of naranjilla were cultivated. NarMMV was also found in field-grown tamarillo. The new virus cross-reacted with antibodies developed against NarCMV. Hence, this antibody will be useful for its field diagnosis using enzyme-linked immunosorbent assay or immunocapture reverse transcription polymerase chain reaction in future virus-free certification programs.

Molecular Evolutionary Analysis of Potato Virus Y Infecting Potato Based on the VPg Gene

Potato virus Y (PVY) is an important plant pathogen infecting solanaceous crops, causing significant losses to global potato and tobacco production. Some aspects of the plant pathology and molecular biology of PVY have been studied intensively, but the evolutionary dynamics of this virus are poorly understood. Here, we performed a comprehensive set of rigorous evolutionary analyses using 177 nucleotide sequences of the viral genome linked protein (VPg) gene, which interacts with the plant eukaryotic translation initiation factor 4E (eIF4E). Our Bayesian analysis reveals that the VPg gene of PVY has been evolving at a rate of 5.60 × 10^–4 subs/site/year (95% credibility interval 3.35 × 10^–4–8.17 × 10^–4), which is equivalent to those of other plant-infecting RNA viruses. We identified different evolutionary constraints on the two clades of PVY, clade N and clade O, whose diverge time were estimated at the year 1861 CE (95% credibility interval 1750–1948 CE). We also found that genetic variations were correlated with geographic regions, suggesting that the evolution of this pathogen is strongly affected by geographical associated factors. Taken together, the results of our study have potential implications for the control strategies of PVY.

Characterization of potato virus Y populations in potato in Israel

Potato virus Y (PVY) is the most common virus infecting potato worldwide. We analysed potato tuber PVY infections from the major Israeli growing region in 2014-2017. Isolates were characterized by multiplex PCR according to Chikh-Ali et al. (Plant Disease 97, 1370, 2013), whose primers were not fully compatible with the Israeli isolates. New primers were designed for a multiplex PCR assay to differentiate the Israeli isolates. Three recombinant strains were observed: PVY^NTNa (72% of the isolates), PVY^NWi (24%) and PVY^Syr-III (found only in 2015). The archetypal PVY^O strain was found only once. The classical PVY strains have recently been displaced by recombinant forms, with PVY^NTNa dominating. The Israeli isolates appear very similar to those of Europe (the seed tuber source), except for PVY^Syr-III.

Identification and Molecular Characterization of Recombinant Potato Virus Y (PVY) in Potato from South Korea, PVYNTN Strain

Potato is an important source of food in South Korea, and viruses represent a significant threat to sustainable and profitable potato production. However, information about viruses affecting the potato crop in South Korea is limited. In 2017, potato plants of five cultivars exhibiting foliar mosaic, crinkling, and mottle were collected in two seed potato production areas, in Gangwon-do and Jeollabuk-do Provinces, and subjected to virus testing and characterization. Potato virus Y (PVY) was found associated with mosaic symptoms, and samples were characterized using reverse transcription polymerase chain reaction (RT-PCR) and whole genome sequencing. All analyzed PVY-positive samples were found to represent the same recombinant PVY strain: PVY^NTN. Three PVY isolates were subjected to whole genome sequencing using overlapping RT-PCR fragments and Sanger methodology, and all three were confirmed to represent strain PVY^NTNa after a recombination analysis of the complete genomes. In phylogenetic analysis, the three South Korean isolates were placed most closely to several PVY^NTNa isolates reported from Japan and Vietnam, suggesting a common source of infection. This is the first report and complete molecular characterization of a PVY^NTN strain present in the country, and because this strain induces tuber necrotic ringspot disease in susceptible cultivars of potato, appropriate management tools need to be implemented to mitigate potential tuber quality losses.

Integrating Spectroscopy with Potato Disease Management

Spectral phenotyping is an efficient method for the nondestructive characterization of plant biochemical and physiological status. We examined the ability of a full range (350 to 2,500 nm) of foliar spectral data to (i) detect Potato virus Y (PVY) and physiological effects of the disease in visually asymptomatic leaves, (ii) classify different strains of PVY, and (iii) identify specific potato cultivars. Across cultivars, foliar spectral profiles of PVY-infected leaves were statistically different (F = 96.1, P ≤ 0.001) from noninfected leaves. Partial least-squares discriminate analysis (PLS-DA) accurately classified leaves as PVY infected (validation κ = 0.73) and the shortwave infrared spectral regions displayed the strongest correlations with infection status. Although spectral profiles of different PVY strains were statistically different (F = 6.4, P ≤ 0.001), PLS-DA did not classify different strains well (validation κ = 0.12). Spectroscopic retrievals revealed that PVY infection decreased photosynthetic capacity and increased leaf lignin content. Spectral profiles of potato cultivars also differed (F = 9.2, P ≤ 0.001); whereas average spectral classification was high (validation κ = 0.76), the accuracy of classification varied among cultivars. Our study expands the current knowledge base by (i) identifying disease presence before the onset of visual symptoms, (ii) providing specific biochemical and physiological responses to disease infection, and (iii) discriminating between multiple cultivars within a single plant species.

Potato virus Y (PVY) Isolates from Physalis peruviana are Unable to Systemically Infect Potato or Pepper and Form a Distinct New Lineage Within the PVYC Strain Group

Poha, or cape gooseberry (Physalis peruviana L.), is a plant species cultivated in Hawaii for fresh fruit production. In 2015, an outbreak of virus symptoms occurred on poha farms in the South Kohala District of the island of Hawaii. The plants displayed mosaic, stunting, and leaf deformation, and produced poor fruit. Initial testing found the problem associated with Potato virus Y (PVY) infection. Six individual PVY isolates, named Poha1 to Poha6, were collected from field-grown poha plants and subjected to biological and molecular characterization. All six isolates induced mosaic and vein clearing in tobacco, and three of them exhibited O-serotype while the other three reacted only with polyclonal antibodies and had no identifiable serotype. Until now, PVY isolates have been broadly divided into pepper or potato adapted; however, these six PVY isolates from poha were unable to establish systemic infection in pepper and in four tested potato cultivars. Whole-genome sequences for the six isolates were determined, and no evidence of recombination was found in any of them. Phylogenetic analysis placed poha PVY isolates in a distinct, monophyletic "Poha" clade within the PVYC lineage, suggesting that they represented a novel, biologically and evolutionarily unique group. The genetic diversity within this poha PVYC clade was unusually high, suggesting a long association of PVYC with this solanaceous host or a prolonged geographical separation of PVYC in poha in Hawaii.

Occurrence of Diverse Recombinant Strains of Potato virus Y Circulating in Potato Fields in Egypt

Potato is one of the staple crops in Egypt, grown under irrigation almost continuously year-round. Potato virus Y (PVY) has been reported as one of the main viruses affecting potatoes in Egypt, but limited information is available on PVY strains circulating in potato fields in the country. From 2014 to 2016, virus surveys were conducted in several potato-growing governorates of Egypt, and PVY-positive samples were found to represent at least five distinct recombinant PVY strains, including PVY^NTN and PVY^N-Wi. Whole genome sequences were determined for four isolates representing strains PVY-SYR-III (Egypt7), PVY-261-4 (Egypt11), PVY^NTNa (Egypt35), and a novel recombinant named Egypt24 that combined molecular properties of strains PVY-261-4 and PVY-Wilga156var. At least three recombinants found in Egypt in potato were previously found associated with potato tuber necrotic ringspot disease (PTNRD). The identification of multiple recombinant types of PVY in potato in Egypt, including the novel recombinant Egypt24, suggests a wide presence of PTNRD-inducing virus strains in the country.

Strain-Specific Resistance to Potato virus Y (PVY) in Potato and Its Effect on the Relative Abundance of PVY Strains in Commercial Potato Fields

Potato virus Y (PVY) is a serious threat to potato production due to effects on tuber yield and quality, in particular, due to induction of potato tuber necrotic ringspot disease (PTNRD), typically associated with recombinant strains of PVY. These recombinant strains have been spreading in the United States for the past several years, although the reasons for this continuing spread remained unclear. To document and assess this spread between 2011 and 2015, strain composition of PVY isolates circulating in the Columbia Basin potato production area was determined from hundreds of seed lots of various cultivars. The proportion of nonrecombinant PVY^O isolates circulating in Columbia Basin potato dropped ninefold during this period, from 63% of all PVY-positive plants in 2011 to less than 7% in 2015. This drop in PVY^O was concomitant with the rise of the recombinant PVY^N-Wi strain incidence, from less than 27% of all PVY-positive plants in 2011 to 53% in 2015. The proportion of the PVY^NTN recombinant strain, associated with PTNRD symptoms in susceptible cultivars, increased from 7% in 2011 to approximately 24% in 2015. To further address the shift in strain abundance, screenhouse experiments were conducted and revealed that three of the four most popular potato cultivars grown in the Columbia Basin exhibited strain-specific resistance against PVY^O. Reduced levels of systemic movement of PVY^O in such cultivars would favor spread of recombinant strains in the field. The negative selection against the nonrecombinant PVY^O strain is likely caused by the presence of the Ny_tbr gene identified in potato cultivars in laboratory experiments. Presence of strain-specific resistance genes in potato cultivars may represent the driving force changing PVY strain composition to predominantly recombinant strains in potato production areas.

Biological and molecular characterization of a tomato isolate of potato virus Y (PVY) of the PVYC lineage

An isolate of potato virus Y (PVY), PVY-H14, was collected on the island of Oahu, Hawaii, from tomato plants exhibiting stunting and necrotic lesions on leaves. PVY-H14 triggered the hypersensitive resistance response in potato cultivars King Edward and Maris Bard, typical of a PVY^C strain, and was unable to infect systemically the four tested cultivars, Desiree, Maris Bard, King Edward, and Russet Norkotah. Phylogenetic analysis of H14 and the whole genomes of 31 PVY isolates of non-recombinant strains of PVY placed PVY-H14 in the same clade with PVY^C and several unclassified PVY isolates from tomato and tobacco.

Occurrence and Molecular Characterization of Recombinant Potato virus YNTN Isolates from Sulawesi, Indonesia

The importance of potato has increased dramatically in Indonesia over the last three decades. During this period, 'Granola', a potato cultivar originally from Germany, has become the most common cultivar for fresh consumption in Indonesia. In August 2014, a survey was conducted in Sulawesi, where potato fields cultivated with Granola and its selection, 'Super John', were sampled for Potato virus Y (PVY) presence. PVY was found in Sulawesi for the first time. Samples determined to be positive for PVY were subsequently typed to strain using reverse-transcription polymerase chain reaction assays. All PVY isolates sampled were identified as PVY^NTN recombinants, with three recombination junctions in P3, VPg, and CP regions of the genome. Three local PVY isolates were subjected to whole-genome sequencing and subsequent sequence analysis. The whole genomes of the Indonesian PVY^NTN isolates I-6, I-16, and I-17 were found to be closely related to the European PVY^NTN-A. This recombinant type was shown previously to cause potato tuber necrotic ringspot disease (PTNRD) in susceptible potato cultivars. The dependence of potato farmers on mostly a single cultivar, Granola, may have given a competitive advantage to PVY^NTN over other PVY strains, resulting in the predominance of the PVY^NTN recombinant. The dominance of PVY^NTN in Sulawesi, and possibly in Indonesia as a whole, represents a potential risk to any newly introduced potato cultivar to the country, especially cultivars susceptible to PTNRD.

Molecular Characterization of Recombinant Strains of Potato virus Y From Saudi Arabia

Potato virus Y (PVY) exists as a complex of strains, many of which are recombinants. The practical importance of PVY recombinant strains has increased due to their ability to induce potato tuber necrotic ring spot disease (PTNRD) that seriously affects tuber quality. In Saudi Arabia, potato production has increased fivefold during the last three decades, reaching 460,000 tons per year. Although PVY has been reported as one of the main viruses affecting potatoes, no information is available on PVY strains circulating in the country. In August 2014, a survey was conducted in a seed potato field at Al-Jouf, Saudi Arabia. PVY-positive samples selected based on visual symptoms and serological reactivity were subjected to strain typing using multiplex RT-PCR assays and were determined to represent recombinant PVY strains. Whole genome sequences were determined for two representative isolates, S2 and S9, through direct sequencing of a series of overlapping RT-PCR fragments for each isolate, and found to represent strains PVY-NE11 and PVY^Z (SYR-III), respectively. One of the recombinant types, SYR-III, was previously found in nearby Syria and Jordan, but the second recombinant, PVY-NE11, was found before only in the United States. Both recombinants, PVY-NE11 and SYR-III, were previously found associated with PTNRD and thought to be rare. The current identification of PVY-NE11 and SYR-III in seed potato in a new geographic region suggests that these recombinants may not be as rare as previously believed. This is the first report on the occurrence of recombinant strains of PVY in potato in Saudi Arabia, and the first report on the PVY-NE11 strain of PVY found in potato outside of the United States.

Analysis of potato virus Y coat protein epitopes recognized by three commercial monoclonal antibodies

BACKGROUND

Potato virus Y (PVY, genus Potyvirus) causes substantial economic losses in solanaceous plants. Routine screening for PVY is an essential part of seed potato certification, and serological assays are often used. The commercial, commonly used monoclonal antibodies, MAb1128, MAb1129, and MAb1130, recognize the viral coat protein (CP) of PVY and distinguish PVYN strains from PVYO and PVYC strains, or detect all PVY strains, respectively. However, the minimal epitopes recognized by these antibodies have not been identified.

METHODOLOGY/PRINCIPAL FINDINGS

SPOT peptide array was used to map the epitopes in CP recognized by MAb1128, MAb1129, and MAb1130. Then alanine replacement as well as N- and C-terminal deletion analysis of the identified peptide epitopes was done to determine critical amino acids for antibody recognition and the respective minimal epitopes. The epitopes of all antibodies were located within the 30 N-terminal-most residues. The minimal epitope of MAb1128 was 25NLNKEK30. Replacement of 25N or 27N with alanine weakened the recognition by MAb1128, and replacement of 26L, 29E, or 30K nearly precluded recognition. The minimal epitope for MAb1129 was 16RPEQGSIQSNP26 and the most critical residues for recognition were 22I and 23Q. The epitope of MAb1130 was defined by residues 5IDAGGS10. Mutation of residue 6D abrogated and mutation of 9G strongly reduced recognition of the peptide by MAb1130. Amino acid sequence alignment demonstrated that these epitopes are relatively conserved among PVY strains. Finally, recombinant CPs were produced to demonstrate that mutations in the variable positions of the epitope regions can affect detection with the MAbs.

CONCLUSIONS/SIGNIFICANCE

The epitope data acquired can be compared with data on PVY CP-encoding sequences produced by laboratories worldwide and utilized to monitor how widely the new variants of PVY can be detected with current seed potato certification schemes or during the inspection of imported seed potatoes as conducted with these MAbs.