Simultaneous detection and typing of plum pox potyvirus (PPV) isolates by heminested-PCR and PCR-ELISA

New Cherry-Adapted Plum Pox Virus Phylogroups Discovered in Russia

Plum pox virus (PPV) is the most pathogenic virus of stone fruit crops worldwide. Unusual PPV isolates were discovered on sour cherry (Prunus cerasus L.) and steppe cherry (P. fruticosa Pall.) in the Republic of Tatarstan and the Middle Ural region, Russia. They induced typical sharka symptoms and tested positive for PPV by ELISA and RT-PCR, but were not detected by PCR using known strain-specific primers. Their complete genomes were determined using high-throughput sequencing. Phylogenetic analysis allocated new isolates to four clearly distinguished lineages (SC, TAT, Y, Tat-26) within a cluster of PPV cherry-adapted strains. The phylogroups SC and TAT had 84.5 to 86.9% average nucleotide identity to each other and strain CR, with which they comprised a common subcluster. Isolates from the Middle Ural region (group Y) were closer to strain C, sharing 96.9% identity. The fourth lineage is represented by the isolate Tat-26, which was a recombinant of strain CR and C isolates as major and minor parents, respectively. These results show that the genetic diversity of PPV is higher than thought and may contribute to a better understanding of the origin and evolution of cherry-adapted strains of the virus. P. fruticosa was reported as a new natural PPV host for the first time.

Plum Pox Virus Strain C Isolates Can Reduce Sour Cherry Productivity

The impact of plum pox virus (PPV) on sour cherry (Prunus cerasus L.) productivity has been studied by comparing the yield of PPV-infected and PPV-free fruit-bearing trees. A total of 152 16- to 17-year-old trees of nine cultivars and hybrids were surveyed in the production orchards (cultivar collection and hybrid testing plots) in the Republic of Tatarstan, Russia. Sixty trees tested positive for PPV using ELISA and RT-PCR. Among them, 58 PPV isolates belonged to the strain C and the other 2 isolates to the strain CV. For the cultivars Sevastyanovskaya, Shakirovskaya, hybrids 88-2 and 80-8, the average (2012 to 2019) productivity of infected trees was 38% to 45% lower than for PPV-free trees of the same cultivar or hybrid. No ilarviruses (prunus necrotic ringspot virus, prune dwarf virus, apple mosaic virus, American plum line pattern virus) were detected in PPV-infected trees, suggesting that reduced cherry productivity was attributed to the PPV infection. Thus, it was shown for the first time that PPV can reduce the productivity of at least some sour cherry cultivars and hybrids, and strain C isolates are responsible for crop losses.

Applications of Proteomic Tools to Study Insect Vector-Plant Virus Interactions

Proteins are crucial players of biological interactions within and between the organisms and thus it is important to understand the role of proteins in successful partnerships, such as insect vectors and their plant viruses. Proteomic approaches have identified several proteins at the interface of virus acquisition and transmission by their insect vectors which could be potential molecular targets for sustainable pest and viral disease management strategies. Here we review the proteomic techniques used to study the interactions of insect vector and plant virus. Our review will focus on the techniques available to identify the infection, global changes at the proteome level in insect vectors, and protein-protein interactions of insect vectors and plant viruses. Furthermore, we also review the integration of other techniques with proteomics and the available bioinformatic tools to analyze the proteomic data.

Sequence Analysis of Plum pox virus Strain C Isolates from Russia Revealed Prevalence of the D96E Mutation in the Universal Epitope and Interstrain Recombination Events

The understanding of genetic diversity, geographic distribution, and antigenic properties of Plum pox virus (PPV) is a prerequisite to improve control of sharka, the most detrimental viral disease of stone fruit crops worldwide. Forty new PPV strain C isolates were detected in sour cherry (Prunus cerasus) from three geographically distant (700⁻1100 km) regions of European Russia. Analysis of their 3'-terminal genomic sequences showed that nineteen isolates (47.5%) bear the D96E mutation in the universal epitope of the coat protein. Almost all of them cannot be detected by the monoclonal antibody 5B in triple antibody sandwich enzyme-linked immunosorbent assayand Western blot analysis that may potentially compromise serological PPV detection in cherries. Full-length genomes of seven PPV-C isolates were determined employing next-generation sequencing. Using the Recombination Detection Program (RDP4), the recombination event covering the region from (Cter)P1 to the middle of the HcPro gene was predicted in all the available PPV-C complete genomes. The isolates Tat-4, belonging to the strain CV, and RU-17sc (PPV-CR) were inferred as major and minor parents, respectively, suggesting possible pathways of evolution of the cherry-adapted strains. Downy cherry (P. tomentosa) was identified as the natural PPV-C host for the first time.

Analysis of Genetic Diversity of Russian Sour Cherry Plum pox virus Isolates Provides Evidence of a New Strain

Plum pox virus (PPV) exists as a complex of nine strains adapted to different Prunus hosts. Unusual PPV isolates that do not belong to the known cherry-adapted strains were discovered on sour cherry in Russia. Here, two complete genomes of isolates Tat-2 and Tat-4 were determined by sequencing on the Illumina HiSeq 2500 platform. Both were composed of 9,792 nucleotides, excluding the poly(A) tail, with the organization typical of PPV and had 99.4 and 99.7% identity between each other at the nucleotide and amino acid levels. The sequence identities between Tat-2/Tat-4 and known PPV strains ranged from 77.6 to 83.3% for genomic RNA and from 80.0 to 93.8% for polyprotein. Phylogenetic analysis placed Tat-2 and Tat-4 in a separate clade, distinct from the C and CR strains. Three more Tat-2/Tat-4-like isolates were detected in local cherry plantings using the newly developed, specific RT-PCR assay. Based on the phylogenetic analysis, sequence identities, and environmental distribution, Tat-2, Tat-4, and related isolates represent a new cherry-adapted PPV strain for which the name PPV-CV (Cherry Volga) is proposed.

Molecular characterization of Plum pox virus Rec isolates from Russia suggests a new insight into evolution of the strain

Field isolates of Plum pox virus (PPV), belonging to the strain Rec, have been found for the first time in Russia. Full-size genomes of the isolates K28 and Kisl-1pl from myrobalan and plum, respectively, were sequenced on the 454 platform. Analysis of all known PPV-Rec complete genomes using the Recombination Detection Program (RDP4) revealed yet another recombination event in the 5'-terminal region. This event was detected by seven algorithms, implemented in the RDP4, with statistically significant P values and supported by a phylogenetic analysis with the bootstrap value of 87%. A putative PPV-M-derived segment, encompassing the C-terminus of the P1 gene and approximately two-thirds of the HcPro gene, is bordered by breakpoints at positions 760-940 and 1838-1964, depending on the recombinant isolate. The predicted 5'-distal breakpoint for the isolate Valjevka is located at position 2804. The Dideron (strain D) and SK68 (strain M) isolates were inferred as major and minor parents, respectively. Finding of another recombination event suggests more complex evolutionary history of PPV-Rec than previously assumed. Perhaps the first recombination event led to the formation of a PPV-D variant harboring the PPV-M-derived fragment within the 5'-proximal part of the genome. Subsequent recombination of its descendant with PPV-M in the 3'-proximal genomic region resulted in the emergence of the evolutionary successful strain Rec.

New highly divergent Plum pox virus isolates infecting sour cherry in Russia

Unusual Plum pox virus (PPV) isolates (named Tat isolates) were discovered on sour cherry (Prunus cerasus) in Russia. They failed to be recognized by RT-PCR using commonly employed primers specific to the strains C or CR (the only ones that proved able to infect sour cherry) as well as to the strains M and W. Some of them can be detected by RT-PCR using the PPV-D-specific primers P1/PD or by TAS-ELISA with the PPV-C-specific monoclonal antibody AC. Phylogenetic analysis of the 3'-terminal genomic region assigned the Tat isolates into the cluster of cherry-adapted strains. However, they grouped separately from the C and CR strains and from each other as well. The sequence divergence of the Tat isolates is comparable to the differences between the known PPV strains. They may represent new group(s) of cherry-adapted isolates which do not seem to belong to any known strain of the virus.

Occurrence and characterization of plum pox virus strain D isolates from European Russia and Crimea

Numerous plum pox virus (PPV) strain D isolates have been found in geographically distant regions of European Russia and the Crimean peninsula on different stone fruit hosts. Phylogenetic analysis of their partial and complete genomes suggests multiple introductions of PPV-D into Russia. Distinct natural isolates from Prunus tomentosa were found to bear unique amino acid substitutions in the N-terminus of the coat protein (CP) that may contribute to the adaptation of PPV-D to this host. Serological analysis using the PPV-D-specific monoclonal antibody 4DG5 provided further evidence that mutations at positions 58 and 59 of the CP are crucial for antibody binding.

Plum pox virus and sharka: a model potyvirus and a major disease

TAXONOMIC RELATIONSHIPS

Plum pox virus (PPV) is a member of the genus Potyvirus in the family Potyviridae. PPV diversity is structured into at least eight monophyletic strains.

GEOGRAPHICAL DISTRIBUTION

First discovered in Bulgaria, PPV is nowadays present in most of continental Europe (with an endemic status in many central and southern European countries) and has progressively spread to many countries on other continents.

GENOMIC STRUCTURE

Typical of potyviruses, the PPV genome is a positive-sense single-stranded RNA (ssRNA), with a protein linked to its 5' end and a 3'-terminal poly A tail. It is encapsidated by a single type of capsid protein (CP) in flexuous rod particles and is translated into a large polyprotein which is proteolytically processed in at least 10 final products: P1, HCPro, P3, 6K1, CI, 6K2, VPg, NIapro, NIb and CP. In addition, P3N-PIPO is predicted to be produced by a translational frameshift.

PATHOGENICITY FEATURES

PPV causes sharka, the most damaging viral disease of stone fruit trees. It also infects wild and ornamental Prunus trees and has a large experimental host range in herbaceous species. PPV spreads over long distances by uncontrolled movement of plant material, and many species of aphid transmit the virus locally in a nonpersistent manner.

SOURCES OF RESISTANCE

A few natural sources of resistance to PPV have been found so far in Prunus species, which are being used in classical breeding programmes. Different genetic engineering approaches are being used to generate resistance to PPV, and a transgenic plum, 'HoneySweet', transformed with the viral CP gene, has demonstrated high resistance to PPV in field tests in several countries and has obtained regulatory approval in the USA.

Detection and partial molecular characterization of atypical plum pox virus isolates from naturally infected sour cherry

Atypical isolates of plum pox virus (PPV) were discovered in naturally infected sour cherry in urban ornamental plantings in Moscow, Russia. The isolates were detected by polyclonal double antibody sandwich ELISA and RT-PCR using universal primers specific for the 3'-non-coding and coat protein (CP) regions of the genome but failed to be recognized by triple antibody sandwich ELISA with the universal monoclonal antibody 5B and by RT-PCR using primers specific to for PPV strains D, M, C and W. Sequence analysis of the CP genes of nine isolates revealed 99.2-100 % within-group identity and 62-85 % identity to conventional PPV strains. Phylogenetic analysis showed that the atypical isolates represent a group that is distinct from the known PPV strains. Alignment of the N-terminal amino acid sequences of CP demonstrated their close similarity to those of a new tentative PPV strain, CR.

Sharka: the past, the present and the future

Members the Potyviridae family belong to a group of plant viruses that are causing devastating plant diseases with a significant impact on agronomy and economics. Plum pox virus (PPV), as a causative agent of sharka disease, is widely discussed. The understanding of the molecular biology of potyviruses including PPV and the function of individual proteins as products of genome expression are quite necessary for the proposal the new antiviral strategies. This review brings to view the members of Potyviridae family with respect to plum pox virus. The genome of potyviruses is discussed with respect to protein products of its expression and their function. Plum pox virus distribution, genome organization, transmission and biochemical changes in infected plants are introduced. In addition, techniques used in PPV detection are accentuated and discussed, especially with respect to new modern techniques of nucleic acids isolation, based on the nanotechnological approach. Finally, perspectives on the future of possibilities for nanotechnology application in PPV determination/identification are outlined.

Occurrence and Genetic Diversity of Winona-Like Plum pox virus Isolates in Russia

In studying the distribution and genetic diversity of Plum pox virus (PPV) in Russia, over a dozen new PPV isolates belonging to the strain Winona (PPV-W) were identified by immunocapture reverse-transcription polymerase chain reaction with the PPV-W-specific primers 3174-SP-F3/3174-SP-R1. Isolates were detected in two geographically distant regions of European Russia (Northern Caucasus and Moscow regions) in naturally infected plum (Prunus domestica), blackthorn (P. spinosa), Canadian plum (P. nigra), and downy cherry (P. tomentosa). The new PPV-W isolates were shown to be serologically related but not identical by triple-antibody sandwich enzyme-linked immunosorbent assay and Western blotting analysis using the monoclonal antibody (MAb) 5B-IVIA and MAbs specific to the N-terminal epitopes of PPV-W isolate 3174. Analysis of nucleotide and deduced amino acid sequences of the (C-ter)NIb-(N-ter)CP genome region indicate great genetic diversity among isolates, with phylogenetic analysis revealing seven clades. Isolates P1 and P3 found in plum in the south of Russia clustered closely with the putative ancestral PPV-W isolate LV-145bt from Latvia, while isolate 1410-7 found in P. nigra in Moscow appears to be closely related to the Canadian isolate W3174. The data obtained indicate wide dissemination of PPV-W isolate in stone fruit in the European part of the former USSR.

Analysis of the epitope structure of Plum pox virus coat protein

Typing of the particular Plum pox virus (PPV) strain responsible in an outbreak has important practical implications and is frequently performed using strain-specific monoclonal antibodies (MAbs). Analysis in Western blots of the reactivity of 24 MAbs to a 112-amino-acid N-terminal fragment of the PPV coat protein (CP) expressed in Escherichia coli showed that 21 of the 24 MAbs recognized linear or denaturation-insensitive epitopes. A series of eight C-truncated CP fragments allowed the mapping of the epitopes recognized by the MAbs. In all, 14 of them reacted to the N-terminal hypervariable region, defining a minimum of six epitopes, while 7 reacted to the beginning of the core region, defining a minimum of three epitopes. Sequence comparisons allowed the more precise positioning of regions recognized by several MAbs, including those recognized by the 5B-IVIA universal MAb (amino acids 94 to 100) and by the 4DG5 and 4DG11 D serogroup-specific MAbs (amino acids 43 to 64). A similar approach coupled with infectious cDNA clone mutagenesis showed that a V74T mutation in the N-terminus of the CP abolished the binding of the M serogroup-specific AL MAb. Taken together, these results provide a detailed positioning of the epitopes recognized by the most widely used PPV detection and typing MAbs.

Role of the 25-26 nt siRNA in the resistance of transgenic Prunus domestica graft inoculated with plum pox virus

The reaction of a genetically engineered plum clone (C5) resistant to plum pox virus (PPV) by graft inoculation with the virus was evaluated. The resistance in this clone has been demonstrated to be mediated through post-transcriptional gene silencing (PTGS). A single C5 plant out of 30 plants inoculated with PPV M strain by double chip-budding showed mild diffuse mosaic 'Sharka' symptom at the bottom section of the scion. The upper leaves of this PPV-infected C5 plant remained symptomless and the virus was not detected in them by either DAS-ELISA or RT-PCR. An RNA silencing associated small interfering RNA duplex, siRNA (21-26 nt), was detected in non-inoculated C5 plants and in the portions of inoculated C5 plant in which PPV could not be detected. In the PPV-infected portion of the C5 plant and in C6 PPV susceptible plants only the approximately 21-22 nt siRNAs was detected. Cytosine-methylation was confirmed in C5 plants both uninfected and showing PPV symptoms. The 25-26 nt siRNA normally present in C5 was absent in PPV-infected C5 tissues confirming the critical role of this siRNA in the resistance of clone C5 to PPV infection. We also show that this PPV infection was limited and transient. It was only detected in one plant at one of four post-dormancy sampling dates and did not appear to affect the overall PPV resistance of the C5 clone.

Cytochrome c oxidase mRNA as an internal control for detection of Potato virus Y and Potato leafroll virus from single aphids by a co-amplification RT-PCR assay

Using cytochrome c oxidase subunit 1 (COX1) mRNA as the internal control, a triplex reverse transcription-polymerase chain reaction (RT-PCR) for detection of Potato virus Y (PVY) and Potato leafroll virus (PLRV) with co-amplification of COX1 from single specimens of various aphid species has been developed. Partial length cDNA of COX1 from green peach aphid, Myzus persicae (Sulzer), potato aphid, Macrosiphum euphorbiae (Thomas), buckthorn aphid, Aphis nasturtii (Kaltenbach), and pea aphid, Acyrthosiphom pisum (Harris), was cloned and sequenced. These sequences, together with existing COX1 sequences from other aphid species capable or suspected to be capable of transmitting PVY and/or PLRV, were analyzed. The sequence identity between any two aphid species ranged from 97 to 100% at the putative protein level, and 89 to 94% at the nucleic acid level. Two highly conserved COX1 nucleotide sequence stretches were selected to design universal primers Aph F and Aph R. This primer pair, together with two existing universal primer pairs (C1-J-2183 and C1-N-2329; Favret F and Favret R), were evaluated at the optimal annealing temperature using RNA from M. persicase, M. euphorbiae, and A. nasturtii. The Aph primer pair performed well in the monoplex RT-PCR but poorly in the triplex RT-PCR in the presence of the PVY- and PLRV-specific primers. On the other hand, the Favret and C1 primer pairs performed well in both monoplex and triplex RT-PCR formats using single aphids of M. persicase, M. euphorbiae and A. nasturtii, demonstrating their suitability to indicate the successfulness of RT-PCR assays for PVY and PLRV. Using the Favret, PVY and PLRV primer sets, single aphids of M. persicase, M. euphorbiae and A. nasturtii that had been exposed to PLRV-infected and/or PVY-infected potato plants were assessed for their acquisition of the viruses by the triplex RT-PCR assay. Although majority (175/180) of the aphid samples produced the COX1 fragment, five aphid samples failed to produce either the COX1- or the virus-specific band, indicating failed RT-PCR in these samples. This method offers a sensitive tool for detection of viruliferous aphids combined to an effective quality control measure.

Interference Between D and M Types of Plum pox virus in Japanese Plum Assessed by Specific Monoclonal Antibodies and Quantitative Real-Time Reverse Transcription-Polymerase Chain Reaction

ABSTRACT The dynamics of virus interference between two isolates of Plum pox virus (PPV) belonging to the main PPV types, D and M, were analyzed in Japanese plum (Prunus salicina) by challenge inoculations. To assess the consequences of a PPV-M infection on plum already infected with PPV-D, and vice versa (predominance of one of the strains, recombination, synergism, symptoms aggravation, and so on), 30 Japanese plum trees were graft inoculated with PPV-D or PPV-M isolates in quarantine conditions. One year postinoculation, in the event that the inoculated isolates were detected in the whole plant, a second challenge inoculation (PPV-M or PPV-D, respectively) was performed by grafting. The presence of PPV-D, PPV-M, or both was monitored for 7 years by double-antibody sandwich indirect enzyme-linked immunosorbent assay using specific monoclonal antibodies. Reverse transcription-polymerase chain reaction (RT-PCR) with D- and M-specific primers confirmed the serological typing. Real-time RT-PCR assays were performed using D- and M-specific fluorescent 3' minor groove binder-DNA probes, which were able to detect and quantify PPV populations in the inoculated plants with greater precision. The presence of PPV-D in Japanese plum did not cross-protect the trees against PPV-M infection. In PPV-D-infected plants, the PPV-M strain used as challenge inoculum behaved differently depending on the plum cultivar assayed. In cv. Black Diamond, PPV-M invaded the plant progressively, displacing the previous PPV-D population; whereas, in cv. Sun Gold, both PPV isolates coexisted in the plant. In contrast, the PPV-D isolate used was unable to infect plants of both cultivars in which a PPV-M population already was established. After 7 years, no synergism was observed and no recombination event between PPV-D and PPV-M genomes was detected.

A simple wax-embedding method for isolation of aphid hemolymph for detection of luteoviruses in the hemocoel

A protocol for isolating hemolymph from viruliferous aphids has been developed. This method uses warm melted wax to immobilize the aphid. Following removal of a hind leg, the hemolymph can be collected readily. Flushing with RNase-free water allows for collection of sufficient hemolymph for RNA extraction from individual aphids. The extracted RNA was successfully used for detection of barley yellow dwarf virus (BYDV) and pea enation mosaic virus (PEMV) from individual viruliferous Rhopalosiphum padi and Acyrthosiphon pisum aphids, respectively. A TaqMan real-time RT-PCR protocol for quantitation of PEMV in the hemolymph of individual aphids was developed. The wax-embedding hemolymph collection technique provides a useful tool for studying molecular interactions between persistent and circulative plant viruses and their insect vectors.

The complete genome sequence of an El Amar isolate of plum pox virus (PPV) and its phylogenetic relationship to other PPV strains

The genomic sequence of an El Amar isolate of plum pox virus (PPV) from Egypt was determined by sequencing overlapping cDNA fragments. This is the first complete sequence of a member of the El Amar (EA) strain of PPV. The genome consists of 9791 nt, excluding a poly(A) tail at the 3' terminus. The complete nt sequence of PPV EA is 79-80%, 80%, 77%, and 77% homologous with isolates of strains D/M, Rec (BOR3), C, and W, respectively. The polyprotein identity ranged from 87-91%. Phylogenetic analysis using the complete genome sequence of PPV EA confirmed its strain status. No significant recombination signals were identified using PhylPro and SimPlot scans of the PPV EA sequence, however an interesting recombination signal was identified in the P1/HC-Pro region of PPV W3174.

Real-time assay for quantitative detection of non-persistently transmitted Plum pox virus RNA targets in single aphids

A TaqMan real-time RT-PCR was developed to detect and quantify RNA-targets from the non-circulative, non-persistently transmitted Plum pox virus (PPV) in individual fresh or aphids captured previously and squashed on paper. Reliable quantitation ranged from 40 up to 4 x 10(8) copies of control transcripts. This technique was applied successfully to plant material and to individual PPV vector (Myzus persicae) and non-vector of PPV (Aphis nerii) aphid species demonstrating acquisition of viral targets by both vector and non-vector aphids. The number of viruliferous aphids detected by real-time RT-PCR and nested RT-PCR in a single closed tube was similar in parallel assays, nevertheless the sensitivity provided by real-time RT-PCR was 100 times higher than nested RT-PCR and 1000 times higher than DASI-ELISA and conventional RT-PCR. The quantities of PPV-RNA targets detected in a single aphid ranged from 40 to more than 2 x 10(3) units. The combined system (immobilization of targets on paper by squash capture and real-time RT-PCR) allows, for the first time, reliable quantitation of PPV targets acquired by individual aphid species and constitute an excellent tool for understanding better PPV epidemiology.

Distribution of Plum pox virus in Residential Sites, Commercial Nurseries, and Native Plant Species in the Niagara Region, Ontario, Canada

Extensive surveys of native weed populations in peach orchards heavily infected with Plum pox virus strain D (PPV-D) in the Niagara Region quarantine area, Ontario, Canada, failed to identify natural infection in any of the species examined. Surveys of rural and urban residential properties within areas of high PPV incidence did not detect widespread infection of susceptible hosts, with infected Prunus glandulosa (dwarf flowering almond) being found only at one site. The prominent color-breaking observed in blossoms of PPV-infected P. glandulosa would make this an excellent sentinel species for early detection of virus in Prunus orchards. Surveys of susceptible ornamental Prunus spp. in Niagara nurseries failed to demonstrate PPV infection in any of the nursery field plantings.

Stability of gene silencing-based resistance to Plum pox virus in transgenic plum (Prunus domestica L.) under field conditions

Plum pox virus (PPV) is one of the most devastating diseases of Prunus species. Since few sources of resistance to PPV have been identified, transgene-based resistance offers a complementary approach to developing PPV-resistant stone fruit cultivars. C5, a transgenic clone of Prunus domestica L., containing the PPV coat protein (CP) gene, has been described as highly resistant to PPV in greenhouse tests, displaying characteristics typical of post-transcriptional gene silencing (PTGS). We show in this report that C5 trees exposed to natural aphid vectors in the field remained uninfected after 4 years while susceptible transgenic and untransformed trees developed severe symptoms within the first year. C5 trees inoculated by chip budding showed only very mild symptoms and PPV could be detected in these trees by IC-RT-PCR. The PPV-CP transgene in C5 was specifically hyper-methylated with no detectable expression. These results indicate both stability and efficiency of PTGS-based PPV resistance in plum under field conditions.

Detection and differentiation of Plum pox virus using real-time multiplex PCR with SYBR Green and melting curve analysis: a rapid method for strain typing

A real-time multiplex PCR procedure with melting curve analysis, using the green fluorescence dye SYBR Green I, was developed for rapid and reliable identification of Plum pox virus (PPV) isolates of strains D and M. Members of the different strains were identified by their distinctive melting temperatures (T(m)s); 84.3-84.43 degrees C for D isolates, and 85.34-86.11 degrees C for M isolates. The associated amplicon sizes were 114 and 380 bp, respectively. The procedure was used for detection and identification of PPV in both herbaceous and woody hosts. The Tm for members of a particular strain was very similar, with a host effect that did not hinder strain identification. Universal primers included in the study detected all isolates of PPV tested, amplifying a 74 bp fragment. The Tm of this fragment varied from 80.12 to 81.52 degrees C and may have supplementary value for PPV identification. SYBR Green-based detection was compared to detection using a hybridization LUX fluorogenic primer. Better resolution of the melting peaks was observed with SYBR Green I, than with the LUX primers, hence strain identification with SYBR Green I was more reliable. This is a simple approach to PPV strain identification with the relatively inexpensive dye SYBR Green I, and eliminates any need for electrophoretic analysis of amplicons or RFLP patterns using ethidium bromide.

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.

Specific detection and quantification of Plum pox virus by real-time fluorescent reverse transcription-PCR

Plum pox virus (PPV), a destructive and economically devastating pathogen of Prunus species, was recently discovered in Pennsylvania and Canada. Current containment efforts involve eradication of infected trees based on ELISA surveys, which are laborious and less sensitive than PCR-based techniques. A real-time, fluorescent, reverse transcription-polymerase chain reaction (RT-PCR) assay was developed for the detection of PPV in the Smart Cycler (Cepheid). The methods developed are reproducible, specific to PPV, and sensitive enough to consistently detect PPV transcripts at the 10-20 fg level. The assay is more sensitive than either ELISA or traditional PCR followed by visualization with ethidium-bromide. PPV was detected from multiple hosts and from multiple Prunus tissues (leaf, stem, bud, and root). A dilution series using an in vitro synthesized transcript containing the target sequence as a standard demonstrated that the assay was effective for quantitation of viral template. The real-time PCR assay is a valuable tool for PPV detection and liter quantification in field or laboratory settings.

Estimation of the number of aphids carrying Citrus tristeza virus that visit adult citrus trees

Aphid species were counted on citrus trees in orchards in Valencia, Spain, in the spring and autumn of 1997, 1998 and 1999. Moericke yellow water traps, the 'sticky shoot' method and counts of established colonies were used in extensive surveys in which 29,502 aphids were recorded and identified. Aphis spiraecola and Aphis gossypii were the most abundant aphid species. The numbers of aphid species landing on mature trees of grapefruit, sweet orange, lemon and clementine and satsuma mandarins, were estimated by counting the numbers of young shoots/tree and aphids trapped on sticky shoots. The proportions of the different aphid species captured were: A. gossypii (53%), A. spiraecola (32%), Toxoptera aurantii (11%), Myzus persicae (1%), Aphis craccivora (1%) and other species (2%). Clementine was the most visited species with 266,700 aphids landing/tree in spring 2000, followed by lemon (147,000), sweet orange (129,150), grapefruit (103,200), and satsuma (92,400). The numbers and relative percentages of aphids carrying Citrus tristeza virus (CTV) were assessed by nested RT-PCR in single closed tubes and analysed by extraction of RNA-CTV targets from trapped aphids. An average of 37,190 CTV-carrying aphids visited each tree in spring 2000 (29 per shoot). The percentage detection of viral RNA in the aphid species that landed were 27% for A. gossypii, 23% for A. spiraecola and 19% for T. aurantii. This high incidence of aphids carrying CTV is consistent with the high prevalence and rapid spread of CTV in sweet orange, clementine, and satsuma mandarins in recent years in the region. The infection rate was proportional to the number of aphids landing/tree.

Innovative tools for detection of plant pathogenic viruses and bacteria

Detection of harmful viruses and bacteria in plant material, vectors or natural reservoirs is essential to ensure safe and sustainable agriculture. The techniques available have evolved significantly in the last few years to achieve rapid and reliable detection of pathogens, extraction of the target from the sample being important for optimising detection. For viruses, sample preparation has been simplified by imprinting or squashing plant material or insect vectors onto membranes. To improve the sensitivity of techniques for bacterial detection, a prior enrichment step in liquid or solid medium is advised. Serological and molecular techniques are currently the most appropriate when high numbers of samples need to be analysed. Specific monoclonal and/or recombinant antibodies are available for many plant pathogens and have contributed to the specificity of serological detection. Molecular detection can be optimised through the automatic purification of nucleic acids from pathogens by columns or robotics. New variants of PCR, such as simple or multiplex nested PCR in a single closed tube, co-operative-PCR and real-time monitoring of amplicons or quantitative PCR, allow high sensitivity in the detection of one or several pathogens in a single assay. The latest development in the analysis of nucleic acids is micro-array technology, but it requires generic DNA/RNA extraction and pre-amplification methods to increase detection sensitivity. The advances in research that will result from the sequencing of many plant pathogen genomes, especially now in the era of proteomics, represent a new source of information for the future development of sensitive and specific detection techniques for these microorganisms.

Detection of a New and Unusual Isolate of Plum pox virus in Plum (Prunus domestica)

Plum pox virus (PPV) isolate 3174-01 was detected by triple-antibody sandwich enzyme-linked immunosorbent assay using the universal PPV monoclonal antibody (MAb) 5B as the secondary antibody, and by reverse-transcription polymerase chain reaction (RT-PCR) using primers that amplify a 243-bp fragment in the C-terminus of the coat protein coding region. The restriction sites RsaI and AluI were absent from this fragment, which is a feature unique to PPV-C isolates. The restriction sites in 3174-01 were replaced by GTAA/GTGA and GGCA, respectively. There was 95 to 99, 94, 91, and 92 to 94% identity of the 243-bp fragment of 3174-01 with the corresponding region of the strains C, D, EA, and M, respectively. Attempts to detect the virus by RT-PCR using strain C-specific primers in three different approaches were unsuccessful. All molecular techniques assessed in attempting to strain type isolate 3174-01 gave negative results, or results inconsistent for D or M in the case of P3-6K₁ restriction fragment length polymorphism analysis. Isolate 3174-01 reacted in Western blot assay with MAb 5B, with an estimated molecular mass of 32 kDa. No reaction was observed with D-, M-, EA-, or C-specific monoclonal antibodies in Western blot or enzyme-linked immunosorbent assay. The molecular and serological data seem to indicate that PPV isolate 3174-01 does not belong to any of the recognized strains of PPV.

An apricot (Prunus armeniaca L.) F2 progeny linkage map based on SSR and AFLP markers, mapping plum pox virus resistance and self-incompatibility traits

A genetic linkage map of apricot ( Prunus armeniaca L.) was constructed using AFLP and SSR markers. The map is based on an F(2) population (76 individuals) derived from self-pollination of an F(1) individual ('Lito') originated from a cross between 'Stark Early Orange' and 'Tyrinthos'. This family, designated as 'Lito' x 'Lito', segregated for two important agronomical traits: plum pox virus resistance (PPV) and self-incompatibility. A total of 211 markers (180 AFLPs, 29 SSRs and two agronomic traits) were assigned to 11 linkage groups covering 602 cM of the apricot genome. The average distance (cM/marker) between adjacent markers is 3.84 cM. The PPV resistance trait was mapped on linkage group G1 and the self-incompatibility trait was mapped on linkage group G6. Twenty two loci held in common with other Prunus maps allowed us to compare and establish homologies among the respective linkage groups.

Expression of self-complementary hairpin RNA under the control of the rolC promoter confers systemic disease resistance to plum pox virus without preventing local infection

BACKGROUND

Homology-dependent selective degradation of RNA, or post-transcriptional gene silencing (PTGS), is involved in several biological phenomena, including adaptative defense mechanisms against plant viruses. Small interfering RNAs mediate the selective degradation of target RNA by guiding a multicomponent RNAse. Expression of self-complementary hairpin RNAs within two complementary regions separated by an intron elicits PTGS with high efficiency. Plum pox virus (PPV) is the etiological agent of sharka disease in Drupaceae, although it can also be transmitted to herbaceous species (e.g. Nicotiana benthamiana). Once inside the plant, PPV is transmitted via plasmodesmata from cell to cell, and at longer distances, via phloem. The rolC promoter drives expression in phloem cells. RolC expression is absent in both epidermal and mesophyll cells. The aim of the present study was to confer systemic disease resistance without preventing local viral infection.

RESULTS

In the ihprolC-PP197 gene (intron hair pin rolC PPV 197), a 197 bp sequence homologous to the PPV RNA genome (from base 134 to 330) was placed as two inverted repeats separated by the DNA sequence of the rolA intron. This hairpin construct is under the control of the rolC promoter.N. benthamiana plants transgenic for the ihprolC-PP197 gene contain siRNAs homologous to the 197 bp sequence. The transgenic progeny of ihprolC-PP197 plants are resistant to PPV systemic infection. Local infection is unaffected. Most (80%) transgenic plants are virus free and symptomless. Some plants (20%) contain virus in uninoculated apical leaves; however they show only mild symptoms of leaf mottling. PPV systemic resistance cosegregates with the ihprolC-PP197 transgene and was observed in progeny plants of all independent transgenic lines analyzed. SiRNAs of 23-25 nt homologous to the PPV sequence used in the ihprolC-PP197 construct were detected in transgenic plants before and after inoculation. Transitivity of siRNAs was observed in transgenic plants 6 weeks after viral inoculation.

CONCLUSIONS

The ihprolC-PP197 transgene confers systemic resistance to PPV disease in N. benthamiana. Local infection is unaffected. This transgene and/or similar constructs could be used to confer PPV resistance to fruit trees where systemic disease causes economic damage.

Detection of hepatopancreatic parvovirus (HPV) infection in Penaeus monodon using PCR-ELISA

A rapid and sensitive PCR-ELISA has been developed for detection of hepatopancreatic parvovirus (HPV) in Penaeus monodon. The specific primer set amplified 156 bp fragment and could detect as a little as 0.01 fg of purified HPV DNA which equivalent to three viral particles. No cross-reactivity was observed when nucleic acid templates from white spot syndrome virus, yellow-head virus, monodon baculovirus and shrimp were tested. The crude DNA simple prepared from hepatopancreas can be used as DNA template and provide a favorable result. Using this technique for detection of HPV infection in 87 carrier shrimps revealed the higher sensitivity and efficiency of detection when compared to histological examination and conventional PCR. Sixty-two percent infection was detected by PCR-ELISA from samples with HPV negative diagnosed by histological examination. Therefore, this sensitive and specific method is promisingly useful for early detection of HPV infection in broodstock, carriers and for ex situ application where large numbers of samples can be analyzed simultaneously.

Simultaneous and co-operational amplification (Co-PCR): a new concept for detection of plant viruses

A new and highly sensitive method for the amplification of viral RNA targets from plant material has been developed and patented. This technique called Co-operational amplification (Co-PCR) can be carried out easily in a simple tetraprimer reaction based on the simultaneous action of four primers. The reaction process consists of the simultaneous reverse transcription of two different fragments from the same target, one containing the other; the production of four amplicons by the combination of the two pair of primers, one pair external to other; and the co-operational action of amplicons for the production of the largest fragment. The technique was used successfully, both in metal block and capillary air thermal cyclers for the detection of plant RNA viruses (Cherry leaf roll virus, Strawberry latent ringspot virus, Cucumber mosaic virus, Plum pox virus and Citrus tristeza virus). The sensitivity observed is at least 100 times higher than that achieved with RT-PCR and similar to nested RT-PCR. Colorimetric detection was coupled with this methodology facilitating its introduction for routine indexing programs and for phytosanitary selection of virus-free plant material.

A novel multiplex RT-PCR probe capture hybridization (RT-PCR-ELISA) for simultaneous detection of six viroids in four genera: Apscaviroid, Hostuviroid, Pelamoviroid, and Pospiviroid

A rapid and sensitive assay was developed for the detection and identification of viroids by standard or multiplex reverse transcription-polymerase chain reaction (RT-PCR)-probe capture hybridization (RT-PCR-ELISA). The assay was applied successfully for the detection and identification of the following six viroid species from infected tissues: Potato spindle tuber viroid (Pospiviroid), Peach latent mosaic viroid (Pelamoviroid), Apple scar skin viroid (Apscaviroid), Apple dimple fruit viroid (Apscaviroid), Pear blister canker viroid (Apscaviroid), and Hop stunt viroid (Hostuviroid). Total RNA was obtained from infected tissue by the Qiagen RNeasy kit and, then viroid cDNA was synthesized using viroid specific complementary DNA primer. To identify and differentiate the amplicons of the six viroids, each amplicon was digoxigenin (DIG)-labelled during the amplification process, and then detected by a colorimetric system using a biotinylated cDNA capture probe specific for each viroid. The results revealed that each capture probe hybridized only to its complementary DIG-labelled amplicon. Thus the six viroids can be detected and differentiated in a multiplex RT-PCR-ELISA assay. In the multiplex assay, cDNAs of six viroids were synthesized simultaneously in one tube, DIG-labelled during amplification, then a portion of the DIG-labelled amplified products was hybridized with selected capture probe. All the six viroid capture probes hybridized to their respective complementary DIG-labelled RT-PCR-amplified product. These findings are important for viroid detection and identification for studying host-viroid interactions and for management and control viroid diseases.

Single-step multiplex RT-PCR for simultaneous and colourimetric detection of six RNA viruses in olive trees

A single-step multiplex RT-PCR was developed for the simultaneous and colourimetric detection of six RNA viruses (Cucumber mosaic virus, Cherry leaf roll virus, strawberry latent ringspot virus, Arabis mosaic virus, Olive latent-1 virus and Olive latent-2 virus) which infect olive trees. Six compatible primer set for one-step RT-PCR amplification in a single closed-tube and 3' digoxigenin labelled probes were designed in optimal, specific and conserved regions. The method has been assessed with 195 Spanish field olive trees, suggesting that approximately 1.5% of the tested material was infected by Cucumber mosaic virus and 0.5% by Cherry leaf roll virus. This method saves time and reagent costs compared with monospecific RT-PCR which needs several reactions for the same number of tests. Using colourimetric detection, it is possible to analyse many samples, it increases sensitivity 10-fold, and whilst facilitating the interpretation of results, it avoids the use of gels and the toxic ethidium bromide. The method could be used routinely for sanitary and certification programmes.

Highly sensitive one-tube RT-PCR and microplate hybridisation assay for the detection and for the discrimination of classical swine fever virus from other pestiviruses

Rapid, sensitive and specific laboratory diagnostic methods are necessary to confirm outbreaks of classical swine fever. The detection of classical swine fever virus (CSFV) and its discrimination from other pestiviruses can be achieved by virus isolation on cell culture, antigen detection, or molecular methods. To reduce the time and the number of steps in the diagnostic procedure a sensitive and rapid detection method based on specific amplification of the pestiviral RNA by one-step reverse transcription-polymerase chain reaction (RT-PCR) followed by detection and differentiation of the amplification products by pestivirus-, bovine viral diarrhoea virus- (BVDV-) and CSFV-specific capture probe hybridisation and colorimetric assay in microwell plates (enzyme liked immunosorbent assay (ELISA)) was developed. Two different methods using two gene regions for pestivirus RT-PCR amplification were carried out. One pair of primers was selected from the 5'-UTR region and the second one from the gene region coding for N(pro), C and E0 proteins. The designed oligonucleotide primers were used for several pestivirus reference strains as well as for some field isolates detection in cell culture supernatants and in clinical specimens. The specificity and sensitivity of both methods were compared using EZ rTth RNA PCR kit and ACCESS RT-PCR system for combined RT-PCR assay. The use of one-step RT-PCR eliminates the additional manipulations that are generally required for a two reaction system and limits the risk of carry-over contamination. Labelling of PCR products with digoxigenin (DIG) during the amplification reaction enables colorimetric assessment of hybridisation reactions. For solution hybridisation pestivirus-, BVDV- and CSFV-specific biotin-labelled capture probes were used. By serial dilutions of DIG-labelled PCR products the RT-PCR-ELISA was found to be 100-times more sensitive than the conventional agarose gel electrophoresis. Higher sensitivity of RT-PCR-ELISA detection using specific biotin-labelled probes offers the opportunity to eliminate strain specific nested PCR and to overcome the problems with contamination and false positive results.

Integrated RT-PCR/nested PCR diagnosis for differentiating between subgroups of plum pox virus

An RT-PCR/nested PCR technique was developed for the simultaneous detection and typing of plum pox virus (PPV) and its major types--Dideron (D), Marcus (M), El-Amar (EA) and Cherry (C). Degenerated oligonucleotides were synthesized for the general detection of PPV, flanking the coding sequence for the N-terminal portion of the coat protein (CP), within which strain-specific differences were identified. On the basis of these characteristic differences, degenerated primer pairs were designed to differentiate between the four major subgroups of the virus in nested PCR reactions. The validity of the technique was tested on viral strains and cloned cDNAs overlapping the CP region. High specificity was observed with no detectable cross-reactions. The results of general PPV detection with the new primers and those of the PCR-based detection of the 3' non-coding region of the viral genome correlated with complete coincidence. The PCR typing results correlated well with those of the RsaI-RFLP and serological typing and revealed a surprisingly high incidence of PPV-D in Hungary.

Sensitive detection of the Egyptian species of sugarcane streak virus by PCR-probe capture hybridization (PCR-ELISA) and its complete nucleotide sequence

A rapid and sensitive assay for the specific detection of Sugarcane streak virus (SSV) using PCR-probe capture hybridization (PCR-ELISA) was developed. Nucleic acids suitable for PCR were extracted from SSV-infected tissue using organic solvents or Fast DNA kit. SSV cDNA was amplified using viral specific primers and the amplified SSV cDNA (amplicon) was DIG-labelled during the amplification process. The amplicon was then detected in a colorimetric hybridization system by a microtiter plate using a biotinylated cDNA (22 nt), cDNA (789 nt) or cRNA (789 nt) capture probe. This system combines the specificity of molecular hybridization, the ease of the colorimetric protocol, and is 10-100 fold more sensitive than agarose gel electrophoretic analysis in detecting the amplified product. Long cDNA or cRNA capture probe was 2-7 fold more sensitive than the oligo cDNA probe for the detection. Complete nucleotide sequence of SSV from Naga Hammady, Egypt, revealed that SSV-EG is a new species of SSV that shares 66% nucleotide identity with the virus species from Natal, South Africa.

Incidence and epidemiology of Citrus tristeza virus in the Valencian community of Spain

The first outbreak of citrus tristeza disease in Spain caused by Citrus tristeza virus (CTV) was recorded in 1957 in the Valencian Community (VC). In total c. 40 million trees, mainly of sweet orange and mandarin grafted on sour orange rootstocks, declined due to CTV. Large-scale surveys in different municipalities of the VC indicated that the disease spread very fast. Incidence increased from 11% in 1989 to 53% in 1998. Toxoptera aurantii and Aphis spiraecola (inefficient aphid vectors of CTV) predominated before 1985-87. Since then the relatively efficient vector Aphis gossypii has become dominant and induced an epidemic that has been modelled. The large number of A.gossypii that visited each clementine tree (estimated to exceed 97000 per year) explained the difference between the temporal pattern of spread of CTV in clementine which followed the Gompertz model and that in sweet orange (logistic model). The susceptibility of the different citrus species to CTV infection by aphids seems to depend on the number of young, succulent shoots produced. The epidemiological data allowed specific recommendations to be made to growers in order to facilitate a change to a modern citrus industry based on the use of selected varieties grafted on tristeza-tolerant rootstocks produced within a certification scheme. This has been done already in almost 90% of the VC citrus-growing area. The tristeza problem has been solved unless more aggressive isolates are introduced and become prevalent.

Impacts of Molecular Diagnostic Technologies on Plant Disease Management

Detection and diagnosis of plant viruses has included serological laboratory tests since the 1960s. Relatively little work was done on serological detection of plant pathogenic bacteria and fungi prior to the development of ELISA and monoclonal antibody technologies. Most applications for laboratory-based tests were directed at virus detection with relatively little emphasis on fungal and bacterial pathogens, though there was some good work done with other groups of plant pathogens. With the advent of molecular biology and the ability to compare regions of genomic DNA representing conserved sequences, the development of laboratory tests increased at an amazing rate for all groups of plant pathogens. Comparison of ITS regions of bacteria, fungi, and nematodes has proven useful for taxonomic purposes. Sequencing of conserved genes has been used to develop PCR-based detection with varying levels of specificity for viruses, fungi, and bacteria. Combinations of ELISA and PCR technologies are used to improve sensitivity of detection and to avoid problems with inhibitors or PCR often found in plants. The application of these technologies in plant pathology has greatly improved our ability to detect plant pathogens and is increasing our understanding of, their ecology and epidemiology.

Sensitive detection of potato spindle tuber and temperate fruit tree viroids by reverse transcription-polymerase chain reaction-probe capture hybridization

A rapid and sensitive assay for the specific detection of plant viroids using reverse transcription-polymerase chain reaction (RT-PCR) -probe capture hybridization (RT-PCR-enzyme-linked immunosorbent assay (ELISA)) was developed. The assay was applied successfully for the detection of potato spindle tuber viroid, peach latent mosaic viroid, or apple scar skin viroid from viroid infected leaf tissue. Clarified sap extract from infected leaf tissue was treated first with GeneReleaser polymeric matrix to remove inhibitors of RT-PCR reactions. Viroid cDNA was then synthesized and amplified using viroid specific primers in RT-PCR assays and the amplified viroid cDNA (amplicon) was digoxigenin (DIG) -labelled during the amplification process. The amplicon was then detected in a colorimetric hybridization system in a microtiter plate using a biotinylated cDNA capture probe. This system combines the specificity of molecular hybridization, the ease of the colorimetric protocol, and is at least 100-fold more sensitive than gel electrophoretic analysis in detecting the amplified product. Viroid cRNA may replace viroid cDNA as the capture probe. The cRNA probe was several fold more sensitive than the cDNA probe for viroid detection. Six to seven hours are needed to complete the RT-PCR-ELISA for viroid detection from infected leaf tissue.

Specific Detection of Cherry Mottle Leaf Virus Using Digoxigenin-Labeled cDNA Probes and RT-PCR

Cherry mottle leaf virus (CMLV)-associated double-stranded RNA (dsRNA) was isolated from the propagation host Chenopodium quinoa. The dsRNA band, with a molecular weight estimated at 7.0 × 10⁶ Da, was used to produce cDNA. Two recombinant plasmids from the cloned cDNA library were identified that specifically bound with CMLV-associated RNA in dot blot hybridization studies. The cDNA inserts were sequenced, and oligonucleotide primers were designed that specifically amplify an 848-bp fragment of the CMLV genome by reverse-transcription polymerase chain reaction. Also, a poly(T) primer was reliably used for reverse transcription, with specific amplification using the CMLV primers, suggesting polyadenylation of the virus genome. Search of the database revealed some sequence homology of the partially characterized genome of CMLV with that of apple chlorotic leafspot virus. Additional sequence data are required, however, to establish the taxonomic position of the filamentous CMLV.

Detection of each of the causal agents of groundnut rosette disease in plants and vector aphids by RT-PCR

Detection of the three agents of groundnut rosette disease (groundnut rosette assistor virus, groundnut rosette virus and its satellite RNA) in plants and vector aphids by reverse transcription-polymerase chain reaction (RT-PCR) is reported. Three procedures for extraction of total RNA from groundnut were tested, of which two were found to be useful in giving RNA of sufficient quality for RT-PCR. Of these two, the total RNA extraction kit supplied by Qiagen was found to be the most versatile for extraction of all three agents from individual vector aphids (Aphis craccivora). Both groundnut rosette assistor virus and groundnut rosette virus could be detected from total RNA extracted from a single aphid that had been exposed to either green or chlorotic rosette-infected groundnut plants. They could be detected in aphids stored in 70% ethanol for up to 30 days at room temperature. However, satellite RNA could be amplified only when total RNA extracted from two or more aphids was used. Groundnut rosette assistor virus, groundnut rosette virus and its satellite RNA were detected by RT-PCR in aphids that had been exposed only to groundnut rosette diseased plants containing all three agents. The potential of RT-PCR in studying certain key issues of rosette disease epidemiology is discussed.

Reverse-transcription polymerase chain reaction for the detection of viruses from plants and aphids

A reverse transcription polymerase chain reaction (RT-PCR) protocol used for the detection of potato viruses in dormant tubers and leaves and in an aphid vector is described. Problems in plant sample preparation from different hosts, uneven distribution or low concentration of viruses and the presence of PCR inhibitors in plant extracts are discussed and various ways to eliminate their effect are described. Using Potyviridae viruses, it has been shown that RT-PCR in various modified forms can be used to differentiate viruses at the level of family, genus, species, strains and their subtypes or serotypes. The specificity of primer pairs and PCR modifications has been used to separate closely related potato viruses A and PVY strains (PVY(O), PVY(N) and PVY(NTN)) from a known mixture.