Chemiluminescent and colorigenic detection of cherry leaf roll virus with digoxigenin-labeled RNA probes

Polyvalent Detection of Members of the Genus Potyvirus by Molecular Hybridization Using a Genus-Probe

The use of a unique riboprobe named polyprobe, carrying partial sequences of different plant viruses or viroids fused in tandem, has permitted the polyvalent detection of up to 10 different pathogens by using a nonradioactive molecular hybridization procedure. In the present analysis, we have developed a unique polyprobe with the capacity to detect all members of the genus Potyvirus, which we have named genus-probe. To do this, we have exploited the capacity of the molecular hybridization assay to cross-hybridize with related sequences by reducing the hybridization temperature. We observed that sequences showing a percentage similarity of 68% or higher could be detected with the same probe by hybridizing at 50 to 55°C, with a detection limit of picograms of viral RNA comparable to the specific individual probes. According to this, we developed several polyvalent polyprobes, containing three, five, or seven different 500-nucleotide fragments of a conserved region of the NIb gene. The polyprobe carrying seven different conserved regions was able to detect all the 32 potyviruses assayed in the present work with no signal in the healthy tissue, indicating the potential capacity of the polyprobe to detect all described, and probably uncharacterized, potyviruses being then considered as a genus-probe. The use of this technology in routine diagnosis not only for Potyvirus but also to other viral genera is discussed.

Simultaneous detection of six stone fruit viruses by non-isotopic molecular hybridization using a unique riboprobe or 'polyprobe'

A new strategy for the simultaneous detection of plant viruses by molecular hybridization has been developed. Two, four or six viral sequences were fused in tandem and transcribed to render unique riboprobes and designated as 'polyprobes'. The 'polyprobe four' (poly 4) covered the four ilarviruses affecting stone fruit trees including apple mosaic virus (ApMV), prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), and American plum line pattern virus (APLPV) whereas the 'polyprobe two' (poly 2) was designed to detect simultaneously, plum pox virus (PPV) and apple chlorotic leaf spot virus (ACLSV), the two more important viruses affecting these trees. Finally, a 'polyprobe six' (poly 6) was generated to detect any of the six viruses. The three polyprobes were comparable to the individual riboprobes in terms of end-point dilution limit and specificity. The validation of the new simultaneous detection strategy was confirmed by the analysis of 46 field samples from up to seven different hosts collected from 10 different geographical areas.

Comparative Infection Progress Analysis of Lettuce big-vein virus and Mirafiori lettuce virus in Lettuce Crops by Developed Molecular Diagnosis Techniques

ABSTRACT Nonisotopic molecular dot blot hybridization technique and multiplex reverse transcription-polymerase chain reaction assay for the specific detection of Lettuce big-vein virus (LBVV) and Mirafiori lettuce virus (MiLV) in lettuce tissue were developed. Both procedures were suitable for the specific detection of both viruses in a range of naturally infected lettuce plants from various Spanish production areas and seven different cultivars. The study of the distribution of both viruses in the plant revealed that the highest concentration of LBVV and MiLV occurred in roots and old leaves, respectively. LBVV infection progress in a lettuce production area was faster than that observed for MiLV. In spite of different rates of virus infection progress, most lettuce plants became infected with both viruses about 100 days posttransplant. The appearance of both viruses in lettuce crops was preceded by a peak in the concentration of resting spores and zoosporangia of the fungus vector Olpidium brassicae in lettuce roots.

Detection of Melon necrotic spot virus in water samples and melon plants by molecular methods

Melon necrotic spot virus (MNSV) is a water and soil-borne pathogen affecting species of the Cucurbitaceae family both in hydroponic and soil crops. Molecular methods for detecting MNSV in water samples, nutrient solutions and melon plants were developed. For this purpose, water samples from a water source pool of a hydroponic culture or from the recirculating nutrient solution were concentrated by ultracentrifugation or PEG precipitation followed by RT-PCR analysis. Both concentration methods were suitable to allow the detection of MNSV and represent, as far as we know, the first time that this virus has been detected in water samples. A non-isotopic riboprobe specific for MNSV was obtained and used to detect the virus in plant tissue. Different parts of mechanically infected plants were examined including the roots, stems, inoculated cotyledons and young leaves. Excluding the inoculated cotyledons, the tissues showing the highest accumulation levels of the virus were the roots. The potential inclusion of such tools in management programs is discussed.

Simultaneous detection of the three ilarviruses affecting stone fruit trees by nonisotopic molecular hybridization and multiplex reverse-transcription polymerase chain reaction

ABSTRACT The three most economically damaging ilarviruses affecting stone fruit trees on a worldwide scale are the related Prunus necrotic ringspot virus (PNRSV), Prune dwarf virus (PDV), and Apple mosaic virus (ApMV). Nonisotopic molecular hybridization and multiplex reverse-transcription polymerase chain reaction (RT-PCR) methodologies were developed that could detect all these viruses simultaneously. The latter technique was advantageous because it was discriminatory. For RT-PCR, a degenerate antisense primer was designed which was used in conjunction with three virus-specific sense primers. The amplification efficiencies for the detection of the three viruses in the multiplex RT-PCR reaction were identical to those obtained in the single RT-PCR reactions for individual viruses. This cocktail of primers was able to amplify sequences from all of the PNRSV, ApMV, and PDV isolates tested in five Prunus spp. hosts (almond, apricot, cherry, peach, and plum) occurring naturally in single or multiple infections. For ApMV isolates, differences in the electrophoretic mobilities of the PCR products were observed. The nucleotide sequence of the amplified products of two representative ApMV isolates was determined, and comparative analysis revealed the existence of a 28-nucleotide deletion in the sequence of isolates showing the faster electrophoretic mobility. To our knowledge, this is the first report on the simultaneous detection of three plant viruses by multiplex RT-PCR in woody hosts. This multiplex RT-PCR could be a useful time and cost saving method for indexing these three ilarviruses, which damage stone fruit tree yields, and for the analysis of mother plants in certification programs.

Subcellular localisation of cherry leaf roll virus coat protein and genomic RNAs in tobacco leaves

The in vivo subcellular location of the coat protein and RNAs of cherry leaf roll nepovirus (CLRV) was studied in infected tobacco plants by two different approaches and it was correlated with the cytopathic structures induced by the virus. Subcellular fractions were obtained by differential centrifugation, visualised by electron microscopy and analysed for their viral RNA and coat protein content by Northern blot and Western blot analysis, respectively. Results indicate that viral RNAs accumulated preferentially at the microsomal fraction. Immunocytochemical studies revealed a clear association of the coat protein of CLRV with the virus-induced cytopathological structures. In situ hybridisation studies confirmed the cytoplasmic location of the virus and allowed one to elucidate the distribution of the CLRV genomic RNAs in the different cell types of infected tissue.

A new procedure to differentiate citrus tristeza virus isolates by hybridisation with digoxigenin-labelled cDNA probes

A non-isotopic hybridisation procedure was developed to differentiate isolates of citrus tristeza virus (CTV) using digoxigenin (DIG)-labelled cDNA probes and different kinds of target RNA. Hybridisation of DIG-probes with purified double-stranded RNA (dsRNA) or concentrated total RNA extracts spotted on nylon membranes allowed detection of CTV nucleic acid equivalent to as little as 0.1-1 mg infected tissue, when the reaction was developed with a chemiluminiscent substrate. This sensitivity was similar to or slightly better than that obtained by hybridisation with a 32P-labelled probe. CTV was also detectable by hybridisation of DIG-probes with tissue prints from freshly cut young citrus shoots. Hybridisation of tissue prints with DIG-probes under stringent conditions (60 degrees C and 50% formamide) could differentiate CTV isolates in citrus, whether grown in the greenhouse or in the field. This rapid and sensitive procedure can easily be applied to many samples, even under field conditions, and opens the way to monitoring spatio-temporal movement of specific CTV strains (or groups of strains) in epidemiological studies.

Simultaneous detection of five carnation viruses by non-isotopic molecular hybridization

Several viruses, which in some cases can cause severe losses, affect carnation plants. These viruses include carnation mottle virus, carnation etched ring virus (CERV), carnation vein mottle virus, carnation ringspot virus, carnation Italian ringspot virus and carnation latent virus. A non-isotopic molecular hybridization was developed for the detection of these viruses in host plants and the sensitivity of the technique has been compared with enzyme-linked immunosorbent assay and bioassay methods. A procedure was developed to test simultaneously for the five RNA viruses (except CERV). The conditions established for this simultaneous detection did not include the DNA virus CERV due to the necessity of incorporating an additional step of RNase A treatment in the procedure to eliminate background signals. The sensitivity limits obtained for each virus using this multiple detection assay were identical to those obtained with the individual assays. The relative benefits of using this detection procedure for routine diagnosis of carnation viruses are discussed.

The use of DIG-labelled cRNA probes for the detection of cymbidium mosaic potexvirus (CymMV) and odontoglossum ringspot tobamovirus (ORSV) in orchids

DIG-labelled sense and antisense cRNA probes were synthesized from cDNA clones of CymMV and ORSV for virus detection in infected plants. A slot-blot hybridization assay was developed using either crude leaf extracts or total RNA from infected leaves. The assay could detect 50 and 250 pg of purified CymMV and ORSV RNA, respectively. As little as 30 mg of Nicotiana benthamiana infected leaves was sufficient to provide positive detection. CymMV and ORSV were detected at 3125 and 625 times dilution of leaf extracts, respectively. The DIG-labelled cRNA probes are stable for more than a year. This method is sensitive, reliable and suitable for large-scale routine testing of plant viruses. By using the two DIG-labelled cRNA probes in situ, CymMV and ORSV were localized in systemically infected leaves and stems of N. benthamiana and orchids.

Quantitative determination of tomato yellow leaf curl geminivirus DNA by chemiluminescent assay using digoxigenin-labeled probes

A quantitative dot-blot hybridisation assay was developed for tomato yellow leaf curl geminivirus (TYLCV). The assay is based on chemiluminescent detection of viral and plasmid DNA using digoxigenin-labeled probes on nylon membranes. The response-error relationship was studied and a square root transformation was found to stabilise the variance of the response. An asymmetric sigmoid (gompertz) curve was used to describe the dose-response relationship. The detection limits and the precision profiles of the curves were studied. A method is suggested for setting an upper limit on the maximum DNA amount that can be discriminated from the upper asymptote. With respect to different times of exposure of an X-ray film to a membrane, the shortest times gave better upper limits and the longest times provided better detection limits. Purified virus and plasmid preparations were studied in various dilution media, such as TYLCV-free Bemisia tabaci (the whitefly vector) and tomato extracts, with particular attention to parallelism with standard calibration curves. Plasmid diluted in buffer was found useful for calibration of purified virus and virus in the vector, while extraction of known amounts of virus, in parallel with samples to be examined, was needed to quantify viral DNA in plant hosts.

Non-isotopic tissue-printing hybridization: a new technique to study long-distance plant virus movement

A non-isotopic tissue-print hybridization technique was developed to study long-distance plant virus movement. By using digoxigenin-labeled RNA probes the distribution pattern of the viral RNA was observed in leaf, stem and petiole tissues. In leaf tissue viral RNA was confined preferentially to symptoms and veins, and in stem and petiole sections, the hybridization signal was observed in vascular tissue. Both chemiluminescent and colorigenic detection methods were used. The colorigenic method, though less sensitive, is advantageous in that it gives some anatomical information on the signal distribution. This non-isotopic tissue-print hybridization technique can provide considerable information about the spatial and temporal virus expression with regard to its symptoms.

Improvement in the sensitivity of PVYN detection by increasing the cDNA probe size

Cloned cDNA to a North American isolate of tobacco veinal necrotic strain of potato virus Y (PVYN) RNA was used for the detection of PVYN in diseased samples. Digoxigenin-labelled cDNA probes were prepared from approximately 0.56 kb, approximately 1.2 kb, approximately 2.5 kb, and approximately 3.25 kb overlapping clones representing the 3'-terminus of the PVYN genome. It was shown that the probe sizes, as determined by alkaline gel-electrophoresis, generally corresponded to the size of the template cDNA used. The sensitivity of detection of PVYN was maximum using the largest probe and the sensitivity generally decreased with a decrease in probe size. Five pg of homologous purified PVYN RNA was detected with the approximately 3.25 kb probe, and 1000 pg of PVYN RNA was required for the approximately 0.56 kb probe. The different levels of sensitivity of detection were also apparent when crude nucleic acid extracts from PVYN and PVYO infected plants were used. In comparison with tobacco bioassay, and dot immunobinding assay nucleic acid hybridization was found to be more sensitive.