The detection of tuber necrotic isolates of Potato virus Y, and the accurate discrimination of PVY(O), PVY(N) and PVY(C) strains using RT-PCR

Genome characterization of citrus yellow vein-clearing virus: limited heterogeneity of viral genomes in Mandarivirus-infecting different citrus species

Citrus yellow vein-clearing virus (CYVCV) is a mandarivirus infecting citrus producing yellow vein-clearing symptoms. The leaf samples collected during surveys of different citrus-growing areas in India exhibited diverse symptoms and 40% of the plants were positive for CYVCV in RT-PCR, indicating the wide distribution of the virus in India. It was reported for first time that CYVCV infects kinnow mandarin and sweet oranges and produces chlorotic ringspots symptoms identical to Indian citrus ringspot virus (ICRSV). The complete genome sequences of CYVCV infecting four citrus cultivars have been deciphered through overlapping primers. All the four genomes comprise of 7531 nucleotides excluding the 3' poly (A) tail. The sequence identity of genomes of four CYVCV isolates in the present study ranged from 95.2 to 99.8% with genome sequences of 31 CYVCV isolates available in public domain and the mean genomic diversity was 0.017, indicating low level of heterogeneity. The phylogenetic analysis revealed that CYVCV isolates from India, Pakistan, and Turkey were clustered in the same clad apart from China isolates. The least normalized dN/dS mean value (0.092) indicated that RdRP region evolved under relatively stronger selection constraints than the other five coding regions of CYVCV. The four intragenic putative recombination events detected in RDP4 program occurred naturally in CYVCV genome, indicating the evolutionary progress of the virus. Tajima's and Fu and Li's D parameters were performed using genomic sequences in DnaSP v5 program and the retrieved negative values indicated the presence of limited genetic variability in CYVCV genomes. To the best of our knowledge, this is the first comprehensive report on molecular characterization of CYVCV from India. It will be helpful in understanding the evolutionary relationship of CYVCV and ICRSV.

Detection and Quantification of Potato virus Y Genomes in Single Aphid Stylets

Typically, the detection of a plant virus within its vector is carried out on the entire insect body. This process can be a possible source of confusion in the quantification of transmissible virus particles for styletborne viruses such as Potato virus Y (PVY), since the transmissible virus fraction is the one only retained in the aphid vector's mouthparts. The objective of this study was to develop and validate the quantitative PCR method for the detection and quantification of PVY in the vector's stylet. Using a specific method based on TaqMan chemistry with higher sensitivity than conventional reverse transcription PCR, this study reveals that a significant amount of the virus is enclosed within the dissected stylets of Myzus persicae. Because this quantification only concerns the portion of the virus attached to the stylets, uniformity was observed in the recorded numbers of virus targets. This novel assay is applicable to several PVY strains as a rapid and sensitive detection method for use in PVY research and offers a convenient tool for deciphering the mechanism of Potyvirus acquisition.

Contribution of Noncolonizing Aphids to Potato Virus Y Prevalence in Potato in Idaho

Potato virus Y (PVY) is a major concern for potato production in the United States given its impact on both crop quality and yield. Although green peach aphid, Myzus persicae (Sulzer), is the most efficient PVY vector, it may be less abundant in potato-growing areas of Idaho relative to non-potato-colonizing aphid vectors of PVY that may disperse from nearby cereal fields and other crops. A field study was conducted during 2012-2013 to examine if noncolonizing aphids disperse to nearby potato fields as cereal crops dry down before harvest. The aphid fauna was sampled weekly in four different potato fields in south-central and southeastern Idaho using yellow sticky traps and yellow pan traps. Potato fields were chosen with an adjacent cereal field such that the prevailing westerly wind would facilitate aphid dispersal from cereal fields to potato. Non-potato-colonizing aphids sampled included 10 cereal aphid species, the most abundant of which were Rhopalosiphum padi L. and Metopolophium dirhodum (Walker). More than 35 species from noncereal hosts also were found. Overall, green peach aphid abundance was relatively low, ranging from 0.5-2.5% of the total aphid capture between years and among fields. In both years and all locations, cereal aphid abundance peaked in mid- to late July (cereal ripening stage) and decreased thereafter as cereal crops dried. PVY prevalence in the potato fields increased following these increases in aphid abundance. This study suggests that cereal aphids and other noncolonizing aphids are important contributors to PVY prevalence in potato in southern Idaho.

Assessment of SNaPshot and single step RT-qPCR methods for discriminating Potato virus Y (PVY) subgroups

Potato virus Y (PVY) is the most important virus infecting potato (Solanum tuberosum), causing potato tuber necrotic ringspot disease (PTNRD), with a great impact on seed potato production. Numerous PVY strain groups with different pathogenicity and economical impact are distributed worldwide. Tools for accurate and reliable detection and discrimination of PVY strain groups are therefore essential for successful disease management. Two state of the art characterization tools based on detecting molecular markers - RT-qPCR (Kogovsek et al., 2008) and SNaPshot (Rolland et al., 2008) - were assessed for their ability to assign PVY accurately to the correct group. The results were validated by bioassay, ELISA and in silico sequence analysis. The spectrum of PVY strain groups distinguished by SNaPshot is broader than that by RT-qPCR. However, the latter was more reliable in discriminating the PVY(NTN) group members, known for their ability to induce PTNRD on selected potato cultivars. The difference in discrimination precision was due to different molecular markers being targeted by RT-qPCR and SNaPshot. Both tools use genotypic markers for detecting PVY(NTN) strain groups. Future development, however, should be focused on identifying the genomic determinants of the tuber necrosis property. Until then, the RT-qPCR and SNaPshot methods remain the most powerful diagnostic tools for detecting the PVY subgroup isolates found in Europe.

Molecular and Serological Typing of Potato virus Y Isolates from Brazil Reveals a Diverse Set of Recombinant Strains

In Brazil, Potato virus Y (PVY) currently presents a significant problem for potato production, reducing tuber yield and quality. Recombinant tuber necrotic isolates of PVY had been reported to occur in the country but no systematic study of the PVY isolate diversity was conducted thus far. Here, a panel of 36 PVY isolates, randomly collected in Brazil from potato between 1985 and 2009, was subjected to a systematic molecular and serological typing using reverse-transcription polymerase chain reaction and a series of PVY^O- and PVY^N-specific monoclonal antibodies. The data collected were combined with biological characterization of the same isolates in tobacco. Of the 36 isolates tested, 3 were typed as PVY^O, 10 as PVY^N:O/N-Wi, 21 as PVY^NTN, and 2 as "unusual" or inconclusive. Of the 10 isolates from the recombinant PVY^N:O/N-Wi strain group, 1 isolate, MAF-VOY, was found to have an unusual serological profile identical to the nonrecombinant PVY^O-O5 strain group. The 21 tested PVY^NTN isolates included 1 isolate that did not induce vein necrosis in tobacco and 2 isolates with an unusual serological profile (i.e., displaying negative reactivity to one commercial PVY^N-specific monoclonal antibody). Whole genome sequences were determined for four PVY isolates from Brazil, representing PVY^O, PVY^NTN, and PVY^N-Wi strains. The genome of the MAF-VOY isolate was found to be recombinant, having characteristic N-Wi structure with two recombinant junctions and carrying a single mutation in the capsid protein at position 98, which led to an unusual O5 serological reactivity. Taken together, the data obtained suggest that the two recombinant strains, PVY^NTN and PVY^N:O/N-Wi, now are apparently dominant in the Brazilian potato crop. The data also suggest that recombinant isolates in Brazil often have unusual serological reactivity which may hamper their correct identification by conventional typing based on enzyme-linked immunosorbent assay.

Optimization and improvement of oligonucleotide microarray-based detection of tomato viruses and pospiviroids

Tomato (Solanum lycopersicum L.) is a vegetable crop which is affected by many viruses and several viroids, causing significant economic loss. Their detection and identification is of critical importance for plant protection and quarantine and certification programs. The potential was examined of an array based on the Combimatrix platform for the detection of 37 viruses belonging to 13 families, one of which is unassigned, together with six pospiviroid species, genus Pospiviroid, family Pospiviroidae. More than 470 oligonucleotide probes (40-mer) were selected for the microarray diagnostic technique developed in this investigation. Most of the virus probes were highly specific and were able to identify tomato viruses. Most pospiviroid probes, however, were non-specific in terms of species, but were specific at the genus level as they hybridized to members of the genus Pospiviroid. Only one probe of the Tomato apical stem viroid was species specific. The repeatability and specificity of the Combimatrix method showed that it can be considered for routine diagnostic use in suspected tomato germplasm since it detected 37 viruses and one pospiviroid at the species level and 5-6 pospiviroids at the genus level. The estimated cost for testing of a single tomato virus is similar to or less than the cost of using ELISA.

Characterisation of potato virus Y isolates from Iran

A survey of Potato virus Y (PVY) was conducted in cultivated fields in six Iranian provinces between January 2005 to July 2007. Two hundred samples from potato and tomato were collected and analyzed by enzyme-linked immunosorbent assay (ELISA) for potyviruses. Almost one fourth of the samples were found to be infected by PVY. Analysis of these PVY-positive samples using three monoclonal antibodies (MAbs) facilitating the simultaneous detection of three main strains namely the ordinary (PVY(O)), strain (PVY(N)) and C (PVY(C)) strains. However, the fourth strain (PVY(NTN)) and some others recombinant isolates were also identified by molecular methods. Host range and symptoms analysis using sap inoculation of four different strains of PVY onto a range of plants revealed that the four strains showed biological properties that seemed to be consistent with their molecular grouping. Fourteen isolates of PVY were chosen based on the host and geographical location, primer specificity and serology for further biological and molecular characterisation. The coat protein (CP) and P1 genes and 3'-non-translated region (3'NTR) from 14 representative isolates were sequenced and analysed with the sequences available in GenBank. Composite analysis of the P1, CP and 3'-UTR sequences with all full genome sequences of PVY revealed that there are three potential strains of PVY in Iran, PVY(O), PVY(N)-W and PVY(NTN). Isolate KER.SA(N) was the most divergent of all the 14 isolates reacted with PVY(N) specific MAbs but grouped with PVY(O) strains in maximum likelihood phylogentic analysis. The PVY(NTN) isolates from Iran more closely related to the European than North American PVY(NTN) isolates.

Expression of G-Ry derived from the potato (Solanum tuberosum L.) increases PVY(O) resistance

In Solanaceae, potato virus Y(O) (PVY(O)) is a widespread virus leading to severe damages such as necrosis, molting, and yield reduction. The resistance Y gene (Ry gene) of potato specifically confers resistance to PVY infection. Previously, potatoes resistant to PVY(O) infection were screened among the 32 Korean cultivars. 'Golden Valley' displayed the most resistance to PVY(O) infection. 'Golden Valley''s Ry gene (G-Ry) was cloned from 'Golden Valley', and the function was investigated. G-Ry protein contains 1134 amino acid residues and is structurally similar to the Y-1, which confers resistance to PVY infection in Solanum tuberosum subsp. andigena. To generate a PVY(O)-resistant potato, the G-Ry gene has been introduced into 'Winter Valley', the cultivar most susceptible to PVY(O) infection among the 32 Korean cultivars. Transgenic 'Winter Valley' ('Winter Valley'-G) showed an increased resistance to PVY infection. This approach may ultimately lead to the development of a virus-resistant plant.

Genomic variability in potato virus M and the development of RT-PCR and RFLP procedures for the detection of this virus in seed potatoes

Potato virus M (PVM, Carlavirus) is considered to be one of the most common potato viruses distributed worldwide. Sequences of the coat protein (CP) gene of several Canadian PVM isolates were determined. Phylogenetic analysis indicated that all known PVM isolates fell into two distinct groups and the isolates from Canada and the US clustered in the same group. The Canadian PVM isolates could be further divided into two sub-groups. Two molecular procedures, reverse transcription - polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP) were developed in this study for the detection and identification of PVM in potato tubers. RT-PCR was highly specific and only amplified PVM RNA from potato samples. PVM RNAs were easily detected in composite samples of 400 to 800 potato leaves or 200 to 400 dormant tubers. Restriction analysis of PCR amplicons with MscI was a simple method for the confirmation of PCR tests. Thus, RT-PCR followed by RFLP analysis may be a useful approach for screening potato samples on a large scale for the presence of PVM.

The simultaneous differentiation of Potato virus Y strains including the newly described strain PVY(NTN-NW) by multiplex PCR assay

New recombinant strain and genotype of PVY, designated as PVY(NTN-NW) and SYR-III, respectively, shared properties with PVY(NTN) and PVY(N)W has been reported recently. PVY(NTN-NW) predominated in potato fields in Syria and was able to induce potato tuber necrotic ringspot disease (PTNRD). Due to the rapid spread of the recombinant strains of PVY which might be the case of PVY(NTN-NW), a specific and reliable detection method is an essential step to control this strain and minimize its spread. The shared properties of PVY(NTN-NW) and SYR-III with PVY(NTN) and PVY(N)W, however, complicate their identification involving multiple detection methods. Therefore, a multiplex polymerase chain reaction (PCR), that relies on a combination of previously published and newly designed primers was developed for the detection and identification of PVY(NTN-NW) and SYR-III in single or mixed infections with the main PVY strains, PVY(O), PVY(N), PVY(NTN) and PVY(N)W. In addition, the present PCR assay was able to detect the recombination points in the P1 region enabling the differentiation of the variable genotypes of the recombinant strains PVY(NTN-NW), PVY(NTN) and PVY(N)W. The reliability of this PCR assay was confirmed using a significant number of well characterized PVY isolates collected from Syria and Japan including those of PVY(NTN-NW), SYR-III, PVY(O), NA-PVY(N), PVY(N)W and PVY(NTN).

An assessment of molecular variability and recombination patterns in South African isolates of Potato virus Y

The coat protein (CP) gene of 75 South African Potato virus Y (PVY) isolates was amplified using reverse-transcriptase polymerase chain reaction (RT-PCR). The resulting cDNA products were cloned and sequenced. These sequences were used to identify the strains to which the isolates belonged. Some, when compared to reference sequences, belonged to the PVY(N) and PVY(O) strains. A number of isolates were found to demonstrate significant homology to PVY(N) strains from China. A large number of South African isolates possessed CP sequences showing evidence of recombination between PVY(N) and PVY(O) strains, similar to those of PVY(NTN) isolates. Multiplex RT-PCR analysis allowed further differentiation of PVY(O) isolates and revealed that the majority were of the PVY(N)-Wilga strain. It was deduced that the most likely way in which these isolates reached South Africa was via the importation of infected material.

A point mutation changes the serotype of a potato virus Y isolate; genomic determination of the serotype of PVY strains

A Syrian isolate of Potato virus Y (PVY), named PVY-12, reacted to two monoclonal antibodies that are specific to PVY(O,C) and PVY(N) strains, although its coat protein (CP) belongs to the PVY(N) strain. Analysis of the CP of PVY-12 revealed that a point mutation in its N terminus switched it from PVY(N)-like to PVY(O)-like at this position. This mutation changed the second nucleotide of the codon that encodes the 29th amino acid of the CP of PVY-12 from A to G, which resulted in one amino acid substitution from Glu(29 )to Gly(29). The role of Gly(29) in the binding of PVY-12 to PVY(O,C)-specific monoclonal antibody was confirmed by gene expression in Escherichia coli. The N terminus of the CP gene of PVY-12 and another PVY isolate of the N serotype with identical CP to PVY-12 except for one amino acid substitution from Gly(29 )to Glu(29) was cloned and expressed in E. coli using a pUC18 vector. Resulting antigens showed similar reactivity to the relevant antibodies as same as the native CPs of these two isolates. Further analysis of the CP of PVY isolates showed that Gly(29) was conserved in the CP of PVY(O), PVY(C), PVY(N)W, and non-potato isolates of PVY while Gln(17) and Glu(31 )were conserved in the CP of PVY(N/NTN). Therefore, these amino acids are characteristic of the CP for these strain groups and subgroups in agreement with the serotype and phylogenetic relationships previously determined.

No recombination detected in artificial potyvirus mixed infections and between potyvirus derived transgenes and heterologous challenging potyviruses

Risk-assessment studies of virus-resistant transgenic plants (VRTPs) focussing on recombination of a plant virus with a transgenic sequence of a different virus should include a comparison of recombination frequencies between viruses in double-infected non-transgenic plants with those observed in singly infected transgenic plants to estimate recombination incidence in VRTPs. In this study, the occurrence of recombination events was investigated in non-transgenic plants double-infected with two different potyviruses, as well as in potyviral genomes in singly infected transgenic plants expressing potyvirus sequences. Different potyviruses, namely Potato virus A (PVA), Tobacco vein mottling virus (TVMV), two strains of Potato virus Y (PVY-O, PVY-H) and two strains of Plum pox virus (PPV-NAT, PPV-SK68), were used in three combinations for double infection of a common host. Furthermore, transgenic plants expressing either potyviral coat protein (CP), helicase (CI) or polymerase (NIb) coding sequences (PPV-NAT-CP, PVY-CI, PVY-NIb) were singly-infected with a heterologous potyvirus, which was not targeted by the respective transgenic resistance. To identify recombinant potyviral sequences, a sensitive RT-PCR was developed to detect up to one recombinant molecule out of 10(6) parental molecules. In 304 mixed infected non-transgenic plants, 92 mixed and 164 single infected transgenic plants screened for recombinant sequences no recombinant potyviral sequence was found. These results indicate that recombination events between different potyviruses in mixed infections and between a potyvirus infecting a potyvirus-resistant transgenic plant are likely to be very infrequent.

Rapid identification of potato virus Y strains by one-step triplex RT-PCR

A one-step triplex RT-PCR method was characterised that allows rapid, strain-specific detection of potato virus Y (PVY) occurring on potato: PVY(N), PVY(O), PVY(NTN) (recombinant isolates), PVY(N)Wi and PVY(C). Three specific primer pairs were designed on aligned PVY sequences available from genomic data banks. The specificity of the selected primers was first examined by simplex RT-PCR with a large number of PVY reference isolates. Two fragments of 0.44 and 1.11kb were amplified for PVY(N) and non-recombinant PVY(NTN) isolates, two fragments of 0.53 and 0.66kb for PVY(O) isolates, a single fragment of 0.44kb for recombinant PVY(NTN) isolates, a 0.66kb fragment for PVY(C) isolates and a 0.53kb fragment for PVY(N)Wi isolate. The primers were then combined in a one-step triplex RT-PCR reaction, optimised stepwise and validated with the reference isolates. The great similarity between the genomes of PVY(N) and non-recombinant PVY(NTN) prevented their differentiation using this method. No fragments were amplified with samples infected by non-related potato viruses, as well as with samples from healthy tobacco and potato plants. The one-step triplex RT-PCR described here fastens specific detection of PVY strains that are otherwise only distinguishable by combined serological and biological assays.

Differentiation of Potato virus Y strains using improved sets of diagnostic PCR-primers

Potato virus Y (PVY) is one of the most important viruses of potato world-wide, several strain groups are recognized. In the past two decades, novel PVY variants have appeared causing necrotic symptoms on potato tubers. Implicated are two groups of recombinant strains: PVY(N)W and PVY(NTN), and NA-PVY(NTN). While the first two are recombinants between PVY-N- and O-strains the latter is a recombinant between an N-strain and an unknown PVY strain or other Potyvirus. Available biological and molecular data on PVY suggest that classification of PVY strains has to be revised. Some drawbacks have been found with recently published primers used in RT-PCR based differentiation of PVY strains as some defined isolates could not be identified correctly. Consequently we developed new primers using both recently available sequences and newly generated complete sequences of PVY strains. The reliability of these newly developed primers and procedures was successfully demonstrated on nearly 100 biologically and serologically characterised PVY isolates.

The Occurrence of PVYO, PVYN, and PVYN:O Strains of Potato virus Y in Certified Potato Seed Lot Trials in Washington and Oregon

Totals of 960 and 286 certified potato seed lots from locations across North America were planted in trials in Washington and Oregon, respectively, in 2001 to 2003 and tested for strains of Potato virus Y (PVY). The incidence of PVY^O-infected lots averaged 16.4 and 25.9% in the Washington and Oregon trials, respectively. There was a general trend of increasing incidence of the PVY^O, PVY^N:O, and PVY^N strains during this period, as evidenced by more infected cultivars, sites of seed origin, and number of seed growers providing infected seed lots. In particular, there was a dramatic increase in seed lots with the PVY^N:O strain from 2002 to 2003. PVY^N:O, in contrast to PVY^O, which only causes yield reduction, also causes internal and external damage to tubers, making them unmarketable. In 2003, PVY^N:O occurred in seed lots originating in eight states and three Canadian provinces. The increased incidence of PVY^N:O was likely due to the difficulty in differentiating this strain from PVY^O. The prevalence of PVY in potato seed lots documented herein poses a threat to potato production in the United States and suggests that current measures to reduce the incidence of this virus are inadequate.

A Multiplex PCR Assay to Characterize Potato virus Y Isolates and Identify Strain Mixtures

Potato virus Y (PVY) has become a serious problem for the seed potato industry, with increased incidence and rejection of seed lots submitted for certification. New PVY strains and strain variants have emerged in recent decades in Europe and North America, including the PVY^N strain that causes veinal necrosis in tobacco, and strain variants that represent one or three recombination events between the common strain (PVY^O) and PVY^N. Several reverse transcription-polymerase chain reaction (RT-PCR) assays have been described that characterize PVY isolates as to strain type, but they are limited in their ability to detect some combinations of mixed strain infections. We report here the development of a single multiplex RT-PCR assay that can assign PVY strain type and detect mixed infections with respect to the major strain types. Validation of this assay was achieved using 119 archived PVY isolates, which had been previously characterized by serology and bioassay and/or previously published RT-PCR assays. Results for single-strain isolates were comparable to previous results in most cases. Interestingly, 16 mixed infections were distinguished that had previously gone undetected. The new multiplex RT-PCR assay will be useful for researchers and seed production specialists interested in determining PVY infection type using a single assay.

Improvement of Potato virus Y (PVY) detection and quantitation using PVY(N)- and PVY(O)-specific real-time RT-PCR assays

A Potato virus Y (PVY) single nucleotide polymorphism (A/G(2213)), recently identified as a molecular determinant of the tobacco leaf necrosis symptom induced by PVY(N) isolates, has been used as a target to develop two PVY group-specific (PVY(N) and PVY(O)) fluorescent (TaqMan-based) real-time RT-PCR assays. These procedures allow detection, characterisation, and quantitation of a wide range of PVY isolates in samples containing 10(3)-10(8) viral transcripts. Moreover, the high specificity of these two new assays make the simultaneous detection and the reliable quantitation of PVY(N) and PVY(O) isolates in mixed solutions, regardless of the Y(N)/Y(O) ratio, feasible. The high sensitivity (threshold of 10(3) copies per reaction) and the PVY group specificity of these two new PVY detection tools clearly improve previously published PVY detection tests and offer new opportunities for PVY research programs.

Plant pathogen forensics: capabilities, needs, and recommendations

A biological attack on U.S. crops, rangelands, or forests could reduce yield and quality, erode consumer confidence, affect economic health and the environment, and possibly impact human nutrition and international relations. Preparedness for a crop bioterror event requires a strong national security plan that includes steps for microbial forensics and criminal attribution. However, U.S. crop producers, consultants, and agricultural scientists have traditionally focused primarily on strategies for prevention and management of diseases introduced naturally or unintentionally rather than on responding appropriately to an intentional pathogen introduction. We assess currently available information, technologies, and resources that were developed originally to ensure plant health but also could be utilized for postintroduction plant pathogen forensics. Recommendations for prioritization of efforts and resource expenditures needed to enhance our plant pathogen forensics capabilities are presented.

Biological and Serological Properties of Potato virus Y Isolates in Northeastern United States Potato

A survey of six potato viruses, Potato virus A (PVA), Potato virus M (PVM), Potato virus S(PVS), Potato virus X (PVX), Potato virus Y (PVY), and Potato leafroll virus (PLRV), was conducted in New York and Maine during 2002 and 2003. Leaf samples were tested by enzyme-linked immunosorbent assay and PVY-positive samples were further tested to determine whether a necrotic strain of PVY (PVY^N) or a strain able to induce necrosis in tobacco and in potato tubers (PVY^NTN) were present. In both years, PVY and PVS were identified in a majority of the samples, and mixed infections predominated in 83% of the symptomatic leaves in 2002. Of the total 394 PVY-positive samples, 3 reacted with monoclonal antibody (MAb) 1F5 and caused veinal necrosis (VN) in tobacco. Two of these isolates caused tuber necrosis in the potato cv. Yukon Gold. Three PVY isolates reacted with MAb 1F5 but did not cause VN in tobacco, and two caused VN but did not react with MAb 1F5. None of these eight isolates were able to overcome the Ry resistance gene in the potato cultivar Eva, but several were able to overcome the Ny resistance gene found in Allegany. PVY^N isolates were not widespread in the northeastern United States; however, several PVY isolates differed from both PVY^N and the ordinary strain of PVY and may represent strain recombinants.

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

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).

Phylogenetic analysis and real time PCR detection of a presumbably undescribed Peronospora species on sweet basil and sage

Downy mildew of sweet basil (Ocimum basilicum) has become a serious disease issue for the producers of sweet basil in Switzerland since it was first recorded in 2001. Reported in Africa in Uganda as early as 1933, major outbreaks of this disease in Europe were first noted in Italy in 1999 and in the USA from 1993. Previous reports have named the pathogen as Peronospora lamii. Its preferential hosts belong to the Lamiaceae family including basils (Ocimum spp.), mints (Menta spp.), sages (Salvia spp.) and other aromatics. This study investigated the taxonomic status of the downy mildew pathogen, using both morphological characters and molecular analysis of the ITS region of the rDNA. The inherent variability of conidial dimensions made species differentiation difficult. Sequence homology and phylogenetic analysis of nine collections of the Peronospora on sweet basil showed unique ITS sequences distinct from those of P. lamii and any other sequenced Peronospora species. This paper describes and illustrates the morphology of this presumably undescribed species of Peronospora. Its taxonomic position and relationships with other related species in the same genus are presented and discussed. In addition to this work, PCR primers for real time PCR analysis have been developed for the specific detection of this downy mildew pathogen from infected tissues or seeds. It is shown that these primers can also be used in classic PCR.

Specific detection of the PVY(N)-W variant of Potato virus Y

PVY(N)-W is one of the variant populations of Potato virus Y (PVY). This variant is of concern in seed potato production and requires a specific diagnosis since it induces more or less symptomless infections and is not detectable easily in field inspections. Moreover, this variant is serologically indistinguishable from the common strain PVY(O). This study describes a simple and specific molecular detection test for the PVY(N)-W variant using a PCR protocol based on the recombinant point within the HC-Pro/P3 region of PVY(N) variants (PVY(NTN), PVY(N)-W). To avoid both detection of recombinant PVY(NTN) and PVY(N)-W isolates, a forward PVY(N)-like primer located in the HC-Pro region coupled to a reverse PVY(O)-like primer located in the NIa region was designed to amplify a specific PCR product of 4114 nt from PVY(N)-W isolates. This technique was assessed on 41 PVY reference and field isolates. Only isolates referenced as PVY(N)-W were amplified and gave the expected PCR product of 4114 nt, whereas no band was obtained from PVY(N), PVY(NTN) or PVY(O) isolates. In conclusion, this PVY(N)-W diagnosis tool is rapid, easy-to-use and suitable for large-scale testing in laboratories of seed potato certification.

A single nucleotide polymorphism-based technique for specific characterization of YO and YN isolates of Potato virus Y (PVY)

One of the most important properties used to classify Potato virus Y (PVY) isolates is their ability to induce (PVY(N)) or not (PVY(O)) veinal necrosis symptoms on the indicator host plant Nicotiana tabacum cv. Xanthi. As an alternative to biological assays, several serological and molecular detection tools have been developed for PVY detection and characterization and these have evolved as our knowledge of PVY has improved. However, the assays that have been previously published are all based on the use of neutral markers (antigenic determinants, sequence data, recombination sites or restriction enzyme cleavage sites), which are unlinked to the biological property being characterized (e.g. veinal necrosis). Using the recently identified molecular determinants of the tobacco leaf necrosis symptom induced by PVY(N) isolates, a one-step fluorescent [TaqMan] RT-PCR assay, based on a single nucleotide polymorphism (SNP) linked to the necrosis property of PVY isolates, has been designed. This assay reliably detects and distinguishes PVY(N) and PVY(O) isolates. The method is simple (leaf soak extraction process, gel-free, no post-PCR manipulations), rapid (96 tests in less than 3h from plants sampling to diagnostic results), sensitive (threshold in a range of 10(4)-10(5) PVY copies), reliable (correctly assigns 42 PVY isolates in their respective group) and allows co-detection of mixed samples containing close to equivalent PVY(N) and PVY(O) quantities. All these characteristics suggest that the newly developed SNP assay could be used to reliably classify PVY isolates, as a substitute for biological assays performed on N. tabacum cv. Xanthi.

Differentiation of Cucumber mosaic virus isolates by hybridization to oligonucleotides in a microarray format

A system for microarrays was developed to detect and differentiate Cucumber mosaic virus (CMV) serogroups and subgroups. The coat protein genes of 14 different isolates were amplified using cy3-labelled generic but species-specific primers. These amplicons were hybridized against a set of five different serotype and subgroup specific 24-mer oligonucleotides bound to an aldehyde-coated glass slide via an aminolinker. The results of the hybridization revealed that the method allowed a clear differentiation of the 14 different CMV isolates into the serogroupes 1 and 2, and in addition was able to assign 9 out of 10 different serogroup 1 isolates correctly into subgroups 1a and 1b. This differentiation was not possible by RFLP analysis with the restriction enzyme MspI. The use of amplicons larger than 700 base pairs and their successful differentiation by hybridization to specific oligonucleotides opens avenues to highly parallel, yet sensitive assays for plant viruses.

The use of real-time RT-PCR (TaqMan®) and post-ELISA virus release for the detection of Beet necrotic yellow vein virus types containing RNA 5 and its comparison with conventional RT-PCR

Real-time RT-PCR (TaqMan) assays were developed for the specific detection of Beet necrotic yellow vein virus (BNYVV). The two assays designed were a broad-spectrum one that detected RNA 2 from all types and a second designed to detect types containing RNA 5. The assays were validated against a range of different isolates from Europe and the Far East. These real-time assays were compared to a conventional RT-PCR assay for the detection of RNA 5. Sensitivity comparisons showed that for the detection of RNA 5, TaqMan was 10,000 times more sensitive than the conventional RT-PCR assay. Further improvements were made to the test procedure by using post-ELISA virus release (VR), as an alternative to RNA extraction. This significantly increased the speed of processing samples and reduced the staff input required, allowing the TaqMan assay to be used routinely as part of an annual survey of UK field samples.

Diversity Among Potato virus Y Isolates Obtained from Potatoes Grown in the United States

ABSTRACT Potato field isolates (Solanum tuberosum) of Potato virus Y (PVY) collected from the midwestern and western United States were characterized using serological, molecular, and biological assays. PVY field isolates were grouped into the previously defined categories: PVY(O), European PVY(NTN), North American PVY(NTN), and PVY(N:O) recombinant and four previously undefined groups. Studies reported here agree with published reports from Europe and elsewhere in North America as PVY isolates capable of causing veinal necrosis in tobacco indicator plants appear in high frequency. In contrast to European experiences, PVY tuber necrosis isolates have a PVY(O) coat protein rather than that of PVY(N). Several PVY(N:O) recombinant isolates induced potato tuber necrotic ringspot disease (PTNRD) in the highly susceptible potato cv. Yukon Gold. The PTNRD symptoms produced by these PVY(N:O) recombinants were atypical compared with lesions found on the same cultivar infected with either the European or North American PVY(NTN) isolates. These PVY(N:O) isolates produced a roughly circular, sunken necrotic lesion on the surface of the tuber instead of the typical external sunken ring pattern displayed by PVY(NTN) isolates. This study establishes the complex nature of PVY populations within the U.S. potato industry and clearly demonstrates the diverse nature of PVY in the United States.

Specific differentiation of recombinant PVY(N:O) and PVY(NTN) isolates by multiplex RT-PCR

The recombinant isolates of tobacco veinal necrotic strain of Potato virus Y (PVYN) and potato tuber necrotic group (PVY(NTN)) contain segments of the PVYO and the PVY(N) genome. Three major recombinant junctions (RJ) are present in the genome of the recombinant PVY(NTN) at sites HC/Pro-P3, 6K2-NIa, and the C-terminal region of CP gene and one RJ at HC/Pro-P3 site in some recombinant PVYN isolates (termed PVY(N:O)). Protocols for specific differentiation of the recombinant PVY(NTN) and PVY(N:O) from the non-recombinant PVYN are described. Specific primer pairs were designed to target the three RJs so that sense and antisense primers completely matched the nucleotide sequences at either side of the RJ. In a uniplex reverse transcription-polymerase chain reaction (RT-PCR), the first primer pair amplified a fragment of 641bp from the recombinant PVY(NTN) and PVY(N:O). The second and third primer pairs exclusively amplified fragments of 448 and 290bp, respectively from the recombinant PVY(NTN). In a multiplex (triplex) RT-PCR, when all three primer pairs were used simultaneously, the three fragments (641, 448 and 290bp) were amplified exclusively from the recombinant PVY(NTN), while only one fragment (641bp) was amplified from the PVY(N:O) isolates, clearly differentiating the two recombinant isolates. No amplification was observed from the non-recombinant PVY, including PVYO and North American (NA)-PVY(N/NTN). For further improvement of the multiplex RT-PCR, effects of cDNA preparation using specific antisense primers, random primers or oligo(dT) plus random primers were investigated. The cDNA prepared by random primer plus oligo(dT) increased the overall band intensity.

The detection of recombinant, tuber necrosing isolates of Potato virus Y (PVY(NTN)) using a three-primer PCR based in the coat protein gene

A simple and reliable procedure for reverse transcription-polymerase chain reaction (RT-PCR) detection and strain differentiation of Potato virus Y (PVY) was developed. Three primers were designed within the coat protein (CP) and nuclear inclusion protein b (NIb) region, exploiting a single base polymorphism identified as being present in all the recombinant PVY(NTN) isolates published. Samples infected with PVY produce a single band of 569 bp, while isolates belonging to PVY(NTN) strain give an additional band of 334 bp. The technique was tested on a collection of well-characterised isolates of PVY from a range of strains and was found to detect all of the isolates reported as belonging to the PVY(NTN) strain. All of the isolates detected possess a recombination event within the coat protein. Further sequence analysis revealed that all the recombinant PVY(NTN) isolates reported thus far would be detected using this assay, whilst isolates thought to be PVY(NTN) that do not possess the coat protein recombination event would not be detected.

Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues

Awareness of crop biosecurity and phytosanitation has been heightened since 9/11 and the unresolved anthrax releases in October 2001. Crops are highly vulnerable to accidental or deliberate introductions of crop pathogens from outside U.S. borders. Strategic thinking about protection against deliberate or accidental release of a plant pathogen is an urgent priority. Rapid detection will be the key to success. This review summarizes recent progress in the development of rapid real-time PCR protocols and evaluates their effectiveness in a proposed nationwide network of diagnostic laboratories that will facilitate rapid diagnostics and improved communication.