Development and Validation of a Duplex RT-qPCR for Detection of Peach Latent Mosaic Viroid and Comparison of Different Nucleic-Acid-Extraction Protocols

Peach latent mosaic viroid (PLMVd) is an important pathogen that causes disease in peaches. Control of this viroid remains problematic because most PLMVd variants are symptomless, and although there are many detection tests in use, the reliability of PCR-based methods is compromised by the complex, branched secondary RNA structure of the viroid and its genetic diversity. In this study, a duplex RT-qPCR method was developed and validated against two previously published single RT-qPCRs, which were potentially able to detect all known PLMVd variants when used in tandem. In addition, in order to simplify the sample preparation, rapid-extraction protocols based on the use of crude sap or tissue printing were compared with commercially available RNA purification kits. The performance of the new procedure was evaluated in a test performance study involving five participant laboratories. The new method, in combination with rapid-sample-preparation approaches, was demonstrated to be feasible and reliable, with the advantage of detecting all different PLMVd isolates/variants assayed in a single reaction, reducing costs for routine diagnosis.

Detection of Viroids by RT-PCR

Reverse transcription-polymerase chain reaction (RT-PCR) is an effective method for detecting the presence of viroids in plant tissue. Viroid RNA is converted to cDNA and amplified to detectable levels, making it a fast and useful detection tool, even when the viroid is present at low levels. Methods of viroid detection using conventional RT-PCR are described in this chapter.

Development of a reverse transcription droplet digital PCR assay for sensitive detection of peach latent mosaic viroid

Peach latent mosaic viroid (PLMVd) represents a continuing threat to peach tree production worldwide. In this study, a sensitive and accurate quantification of PLMVd in peach leaves was established using a reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) assay. The quantitative linearity, accuracy, and sensitivity of RT-ddPCR for the detection of PLMVd were comparatively assessed to those of reverse-transcription real-time quantitative polymerase chain reaction (RT-qPCR) assay. The specificity assay shows no amplification in major peach viruses, apple chlorotic leaf spot virus and prunus necrotic ring spot virus and negative control. Furthermore, the levels of PLMVd transcripts determined using RT-ddPCR and RT-qPCR showed a high degree of linearity and quantitative correlation. Our results also indicated that the RT-ddPCR assay is at least two-fold more sensitive than qPCR and could therefore, be used to detect PLMVd in field samples. Moreover, optimization of RT-ddPCR was found to enhance the sensitivity of PLMVd detection in the peach leaf samples with low viral loads. In summary, the established RT-ddPCR assay represents a promising alternative method for the precise quantitative detection of PLMVd; it would be particularly applicable for diagnosing PLMVd infections in plant quarantine inspection and PLMVd-free certification program.

Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches

Next generation sequencing (NGS) technologies are becoming routinely employed in different fields of virus research. Different sequencing platforms and sample preparation approaches, in the laboratories worldwide, contributed to a revolution in detection and discovery of plant viruses and viroids. In this work, we are presenting the comparison of two RNA sequence inputs (small RNAs vs. ribosomal RNA depleted total RNA) for the detection of plant viruses by Illumina sequencing. This comparison includes several viruses, which differ in genome organization and viroids from both known families. The results demonstrate the ability for detection and identification of a wide array of known plant viruses/viroids in the tested samples by both approaches. In general, yield of viral sequences was dependent on viral genome organization and the amount of viral reads in the data. A putative novel Cytorhabdovirus, discovered in this study, was only detected by analysing the data generated from ribosomal RNA depleted total RNA and not from the small RNA dataset, due to the low number of short reads in the latter. On the other hand, for the viruses/viroids under study, the results showed higher yields of viral sequences in small RNA pool for viroids and viruses with no RNA replicative intermediates (single stranded DNA viruses).

New Iranian and Australian peach latent mosaic viroid variants and evidence for rapid sequence evolution

Peach latent mosaic viroid isolates from peach and plum in Iran have been compared with an Australian isolate from nectarine. Thirteen sequence variants 336-338 nt in size were obtained. All variants clustered phylogenetically with variants reported from several hosts and countries. A total nucleic acid extract, a slightly longer than full-length RT-PCR amplicon, and a recombinant plasmid clone from the Australian isolate were all infectious to, and symptomatic in, mechanically inoculated peach seedlings. The infectious clone generated two progeny viroid molecules, which each showed 10 different mutations compared with the parent clone inoculated 30 days previously.

Development of a Quick Quantitative Real-Time PCR for the In Vivo Detection and Quantification of Peach latent mosaic viroid

Viroids are plant pathogens infecting a broad range of herbaceous and tree crops. Among them, the Peach latent mosaic viroid (PLMVd) infects mainly peach trees, causing a loss of production with no curative options. Detecting this viroid is thus important for certification procedures aiming to avoid the release of infected material into orchards. Presented here is a complete detection method based on reverse transcription (RT) followed by a quantitative real-time polymerase chain reaction (PCR). New primers were selected and optimal reaction conditions determined for routine application of the method. The technique is 10⁵ times more sensitive than the endpoint RT-PCR used for PLMVd detection, and permits earlier detection of PLMVd in infected plants. The quick, low-cost extraction procedure used and the quality of the results obtained make this method suitable for routine testing.

Probe binding to host proteins: a cause for false positive signals in viroid detection by tissue hybridization

Molecular hybridization assay, especially involving the use of tissues directly, has been developed as a rapid, simple and important technique for plant pathogen detection and/or gene expression analysis on a large scale. In theory, this method relies on the specific binding of a labeled probe to a target nucleotide sequence. However, occasional false positive reactions can pose a problem in its application and the cause is often not well understood. Here, we show that in tissue-printing hybridization to detect Peach latent mosaic viroid (PLMVd) strong signals could arise by interactions between the viroid probe and plant proteins. Such probe-protein interactions made it difficult to show significant correlations between viroid infection and the level of hybridization signals. These results challenge the traditional view that proteins may hamper PCR reactions but have no influence on molecular hybridization. They further demonstrate that such probe-protein interactions in a plant could compromise the quality of molecular hybridization assays for viroid detection. Our results uncovered an important source of false positive reactions in tissue-printing hybridization and suggest that specificity can be improved by removing proteins.

Sensitive and rapid detection of peach latent mosaic viroid by the reverse transcription loop-mediated isothermal amplification

A reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the detection of peach latent mosaic viroid (PLMVd) was developed. Four primer sets (OLD, OLD1, NEW, and Fukuta's) were designed originally. Based on initial experiments the set OLD1 was selected for further evaluation. Simple and accelerated RT-LAMP was preformed using degenerate and no degenerate forward-loop (F-loop) and backward-loop (B-Loop) primers. Degenerate primers were selected, and after determination of their best concentration (0.8microM), the reaction was preformed at different temperatures (60-67.5 degrees C) using three different betaine concentrations (0.8M, 0.4M, and 0.2M). Optimal conditions were found to be 62.5 degrees C and 0.8M betaine. Under these conditions, using tRNA as template, PLMVd was detected within only 32min, compared to 180min of RT-PCR, using the Real Time Turbimeter (LA200, Teramecs) which measures the turbidity caused by the production of insoluble magnesium pyrophosphate. In addition, RT-LAMP was more sensitive than RT-PCR. PLMVd was detected in peach, plum, apricot, pear, wild pear and quince samples.

Development of a one tube-one step RT-PCR protocol for the detection of seven viroids in four genera: Apscaviroid, Hostuviroid, Pelamoviroid and Pospiviroid

A one tube-one step RT-PCR was developed for the detection of seven viroids (Apple scar skin viroid, Apple dimple fruit viroid, Pear blister canker viroid, Hop stunt viroid, Chrysanthemum stunt viroid, Citrus exocortis viroid and Peach latent mosaic viroid) in four genera that infect eight plant species. The efficiency and specificity of this method were optimized by the use of Moloney-murine leukemia virus (M-MLV) reverse-transcriptase and HotStarTaq DNA polymerase which allowed increase sensitivity of viroid detection. The method was assessed with 56 viroid-infected field plants. The multiplex one tube-one step RT-PCR has the advantage of requiring less hands-on time to set up an assay than standard multiplex one, it also reduces the possibility of false positive tests because all steps are performed in the same tube thus, avoiding cross-contamination. The method may be used routinely for viroid detection in sanitary and certification programmes.