TASPERT: Target-Specific Reverse Transcript Pools to Improve HTS Plant Virus Diagnostics

High-throughput sequencing (HTS) is becoming the new norm of diagnostics in plant quarantine settings. HTS can be used to detect, in theory, all pathogens present in any given sample. The technique’s success depends on various factors, including methods for sample management/preparation and suitable bioinformatic analysis. The Limit of Detection (LoD) of HTS for plant diagnostic tests can be higher than that of PCR, increasing the risk of false negatives in the case of low titer of the target pathogen. Several solutions have been suggested, particularly for RNA viruses, including rRNA depletion of the host, dsRNA, and siRNA extractions, which increase the relative pathogen titer in a metagenomic sample. However, these solutions are costly and time-consuming. Here we present a faster and cost-effective alternative method with lower HTS-LoD similar to or lower than PCR. The technique is called TArget-SPecific Reverse Transcript (TASPERT) pool. It relies on pathogen-specific reverse primers, targeting all RNA viruses of interest, pooled and used in double-stranded cDNA synthesis. These reverse primers enrich the sample for only pathogens of interest. Evidence on how TASPERT is significantly superior to oligodT, random 6-mer, and 20-mer in generating metagenomic libraries containing the pathogen of interest is presented in this proof of concept.

Studies on the Occurrence of Viruses in Planting Material of Grapevines in Southwestern Germany

Viral diseases in viticulture lead to annual losses in the quantity and quality of grape production. Since no direct control measures are available in practice, preventive measures are taken to keep the vines healthy. These include, for example, the testing of propagation material for viruses such as Arabis mosaic virus (ArMV), Grapevine fanleaf virus (GFLV) or Grapevine leafroll-associated virus 1 (GLRaV-1) and 3 (GLRaV-3). As long-term investigations have shown, GLRaV-1 (2.1%) occurs most frequently in southwestern German wine-growing regions, whereas GLRaV-3 (<0.1%) is almost never found. However, tests conducted over 12 years indicate that there is no general decline in virus-infected planting material. Thus, it can be assumed that a spread of the viruses via corresponding vectors still takes place unhindered. Beyond the examinations regulated within the German Wine Growing Ordinance, one-time tests were carried out on Grapevine Pinot gris virus (GPGV). This analysis showed that GPGV was found in 17.2% of the samples.

Discovery of Four Novel Viruses Associated with Flower Yellowing Disease of Green Sichuan Pepper (Zanthoxylum Armatum) by Virome Analysis

An emerging virus-like flower yellowing disease (FYD) of green Sichuan pepper (Zanthoxylum armatum v. novemfolius) has been recently reported. Four new RNA viruses were discovered in the FYD-affected plant by the virome analysis using high-throughput sequencing of transcriptome and small RNAs. The complete genomes were determined, and based on the sequence and phylogenetic analysis, they are considered to be new members of the genera Nepovirus (Secoviridae), Idaeovirus (unassigned), Enamovirus (Luteoviridae), and Nucleorhabdovirus (Rhabdoviridae), respectively. Therefore, the tentative names corresponding to these viruses are green Sichuan pepper-nepovirus (GSPNeV), -idaeovirus (GSPIV), -enamovirus (GSPEV), and -nucleorhabdovirus (GSPNuV). The viral population analysis showed that GSPNeV and GSPIV were dominant in the virome. The small RNA profiles of these viruses are in accordance with the typical virus-plant interaction model for Arabidopsis thaliana. Rapid and sensitive RT-PCR assays were developed for viral detection, and used to access the geographical distributions. The results revealed a correlation between GSPNeV and the FYD. The viruses pose potential threats to the normal production of green Sichuan pepper in the affected areas due to their natural transmission and wide spread in fields. Collectively, our results provide useful information regarding taxonomy, transmission and pathogenicity of the viruses as well as management of the FYD.

High Risk Blueberry Viruses by Region in North America; Implications for Certification, Nurseries, and Fruit Production

There is limited information on the distribution of blueberry viruses in the U.S. or around the world other than where the viruses were first discovered and characterized. A survey for blueberry viruses was carried out in the U.S. in 2015⁻2017. Most blueberry viruses have been characterized to the point that sensitive diagnostic assays have been developed. These assays are based on ELISA or variations of PCR, which were employed here to determine the presence of blueberry viruses in major blueberry production and nursery areas of the U.S. The viruses included in this study were: blueberry fruit drop (BFDaV), blueberry latent (BlLV), blueberry leaf mottle (BLMoV), blueberry mosaic (BlMaV), blueberry red ringspot (BRRV), blueberry scorch (BlScV), blueberry shock (BlShV), blueberry shoestring (BlSSV), blueberry virus A (BVA), peach rosette mosaic (PRMV), tobacco ringspot (TRSV), and tomato ringspot (ToRSV). In the Pacific Northwest BlShV was the most widespread virus, with BlScV and ToRSV detected in a limited number of fields in Oregon and Washington, but BlScV was widespread in British Columbia. In the upper midwest, the nematode-borne (ToRSV, TRSV), aphid-transmitted (BlSSV and BVA) and pollen-borne (BLMoV) viruses were most widespread. In the northeast, TRSV, ToRSV, and BlScV, were detected most frequently. In the southeast, BRRV and BNRBV were the most widespread viruses. BlLV, a cryptic virus with no known symptoms or effect on plant growth or yield was present in all regions. There are other viruses present at low levels in each of the areas, but with the lower incidence they pose minimal threat to nursery systems or fruit production. These results indicate that there are hotspots for individual virus groups that normally coincide with the presence of the vectors. The information presented highlights the high risk viruses for nursery and fruit production each pose a different challenge for control.

Molecular characterization and complete genome of a novel nepovirus from red clover

During high throughput sequencing (HTS) of leaves from a symptomatic red clover plant, a new RNA virus, tentatively named red clover nepovirus A (RCNVA), was discovered. The complete genomic sequence was determined and characterized. Particularly noteworthy was that RCNVA shares high sequence identities in RNA1 with a group of phylogenetically related nepoviruses while homologies in the RNA2 segments are markedly lower. Based on the genomic organization and phylogenetic attributes, RCNVA should be classified as a novel virus of the genus Nepovirus (subfamily Comovirinae, family Secoviridae, order Picornavirales).

Rapid detection of fifteen known soybean viruses by dot-immunobinding assay

A dot-immunobinding assay (DIBA) was optimized and used successfully for the rapid detection of 15 known viruses [Alfalfa mosaic virus (AMV), Bean pod mottle virus (BPMV), Bean yellow mosaic virus (BYMV), Cowpea mild mottle virus (CPMMV), Cowpea severe mosaic virus (CPSMV), Cucumber mosaic virus (CMV), Peanut mottle virus (PeMoV), Peanut stunt virus (PSV), Southern bean mosaic virus (SBMV), Soybean dwarf virus (SbDV), Soybean mosaic virus (SMV), Soybean vein necrosis virus (SVNV), Tobacco ringspot virus (TRSV), Tomato ringspot virus (ToRSV), and Tobacco streak virus (TSV)] infecting soybean plants in Oklahoma. More than 1000 leaf samples were collected in approximately 100 commercial soybean fields in 24 counties of Oklahoma, during the 2012-2013 growing seasons. All samples were tested by DIBA using polyclonal antibodies of the above 15 plant viruses. Thirteen viruses were detected, and 8 of them were reported for the first time in soybean crops of Oklahoma. The highest average incidence was recorded for PeMoV (13.5%) followed by SVNV (6.9%), TSV (6.4%), BYMV, (4.5%), and TRSV (3.9%), while the remaining seven viruses were detected in less than 2% of the samples tested. The DIBA was quick, and economical to screen more than 1000 samples against 15 known plant viruses in a very short time.

Molecular characterization of a new soybean-infecting member of the genus Nepovirus identified by high-throughput sequencing

The complete nucleotide sequence of a new soybean-infecting member of the genus Nepovirus (provisionally named "soybean latent spherical virus" [SLSV]) was identified by high-throughput sequencing of RNAs from soybean leaf samples from North Dakota, USA. The sequences of RNAs 1 (8,190 nt) and 2 (5,788 nt) were completed by rapid amplification of cDNA ends. Each contained a single long open reading frame and a 3' nontranslated region of greater than 1,500 nt. The predicted amino acid sequences of the two ORFs were most closely related to nepoviruses in subgroup C. Full-length cDNAs of RNAs 1 and 2 were cloned and used to inoculate soybean plants, which did not display obvious symptoms. These results suggest that SLSV represents a new species in the genus Nepovirus.

Next generation sequencing and molecular analysis of artichoke Italian latent virus

Next-generation sequencing (NGS) allowed the assembly of the complete RNA-1 and RNA-2 sequences of a grapevine isolate of artichoke Italian latent virus (AILV). RNA-1 and RNA-2 are 7,338 and 4,630 nucleotides in length excluding the 3' terminal poly(A) tail, and encode two putative polyproteins of 255.8 kDa (p1) and 149.6 kDa (p2), respectively. All conserved motifs and predicted cleavage sites, typical for nepovirus polyproteins, were found in p1 and p2. AILV p1 and p2 share high amino acid identity with their homologues in beet ringspot virus (p1, 81% and p2, 71%), tomato black ring virus (p1, 79% and p2, 63%), grapevine Anatolian ringspot virus (p1, 65% and p2, 63%), and grapevine chrome mosaic virus (p1, 60% and p2, 54%), and to a lesser extent with other grapevine nepoviruses of subgroup A and C. Phylogenetic and sequence analyses, all confirmed the strict relationship of AILV with members classified in subgroup B of genus Nepovirus.

Complete nucleotide sequence of a new variant of grapevine fanleaf virus from northeastern China

The complete RNA1 and RNA2 sequences of a new grapevine fanleaf virus isolate (GFLV-SDHN) from northeastern China were determined. The two RNAs are 7,367 and 3,788 nucleotides (nt) in length, respectively, excluding the poly(A) tails. Compared to other GFLV isolates, GFLV-SDHN has a 22- to 24-nt insertion in the RNA1 5' untranslated region, and there was 19.1-20.1 % and 11.7 %-13.0 % sequence divergence in RNA1, and 15.5 %-20.5 % and 8.5-13.5 % in RNA2, at the nt and amino acid level, respectively. Phylogenetic analysis revealed that the origins of GFLV-SDHN are distinct from those of other GFLV isolates. One recombination event was identified in the 2A^HP region of RNA2 in GFLV-SDHN.

Detection and genetic variation analysis of grapevine fanleaf virus (GFLV) isolates in China

To investigate the prevalence and genetic variation of grapevine fanleaf virus (GFLV) in China, 142 grapevine samples from 13 provinces and regions were tested using DAS-ELISA, RT-PCR, and nested RT-PCR. Of the samples, 38% tested positive for GFLV by DAS-ELISA, and 26.8% tested positive by RT-PCR and nested RT-PCR. Movement protein (MP) and coat protein (CP) gene PCR products were cloned and sequenced. The MP or CP nucleotide and protein sequences shared identities that ranged from 94.9% to 100%. Phylogenetic analysis revealed that Chinese GFLV isolates obtained in this study were distinct from the isolates reported in GenBank.

Complete genome sequence and construction of infectious full-length cDNA clones of tobacco ringspot Nepovirus, a viral pathogen causing bud blight in soybean

Tobacco ringspot virus (TRSV, genus Nepovirus), causes severe diseases in soybean and tobacco plants. TRSV-induced bud blight disease significantly reduced both the yield and quality of soybeans. The function of the encoded viral gene product involved in TRSV infection was unclear due to the limitation of reverse genetics studies on the viral genome. Here, we represent the successful construction of infectious full-length cDNA clones of TRSV genome (RNA1 and RNA2). The cDNAs of TRSV RNA1 and RNA2 were cloned into the binary vector pPZP211 immediately downstream of a double cauliflower mosaic virus 35S promoter and upstream of the nopaline synthase terminator. Seven days after agrobacterium-mediated co-inoculation of these two constructs, Nicotiana benthamiana plants developed a systemic infection with necrotic ringspot symptoms and weak stunting of the leaves, similar to that induced by natural TRSV. The systemic infection was confirmed by transmission electron microscopy and Western blot analysis. Simultaneously, soybean, tomato, and Arabidopsis ecotype Estland were mechanically inoculated with sap prepared from TRSV-agroinfiltrated N. benthamiana leaves, showing typical symptoms of bud blight, necrotic spots, and lethal systemic necrosis, respectively. The system developed herein will be an appealing way to determine TRSV viral gene functions and study host-TRSV interactions.

Complete genome sequence of three tomato ringspot virus isolates: evidence for reassortment and recombination

The genome sequence of tomato ringspot virus (ToRSV, a subgroup C nepovirus) is currently available for one raspberry isolate. In this study, we describe the complete genome sequence of three additional isolates from raspberry (Rasp1-2014), grapevine (GYV-2014) and prunus (13C280). The degree of nucleotide sequence identity shared between RNA1 and RNA2 in the 5'-terminal 900 nucleotides and 3' untranslated region varied from 98-99 % (13C280, GYV-2014) to 80 % (Rasp1-2014). Phylogenetic studies revealed distinct origins for Rasp1-2014 RNA1 and RNA2, suggesting reassortment. Two recombination events were also identified in the 3' UTR and 5'-terminal region of RNA1.

A strain-specific segment of the RNA-dependent RNA polymerase of grapevine fanleaf virus determines symptoms in Nicotiana species

Factors involved in symptom expression of viruses from the genus Nepovirus in the family Secoviridae such as grapevine fanleaf virus (GFLV) are poorly characterized. To identify symptom determinants encoded by GFLV, infectious cDNA clones of RNA1 and RNA2 of strain GHu were developed and used alongside existing infectious cDNA clones of strain F13 in a reverse genetics approach. In vitro transcripts of homologous combinations of RNA1 and RNA2 induced systemic infection in Nicotiana benthamiana and Nicotiana clevelandii with identical phenotypes to WT virus strains, i.e. vein clearing and chlorotic spots on N. benthamiana and N. clevelandii for GHu, respectively, and lack of symptoms on both hosts for F13. The use of assorted transcripts mapped symptom determinants on RNA1 of GFLV strain GHu, in particular within the distal 408 nt of the RNA-dependent RNA polymerase (1E(Pol)), as shown by RNA1 transcripts for which coding regions or fragments derived thereof were swapped. Semi-quantitative analyses indicated no significant differences in virus titre between symptomatic and asymptomatic plants infected with various recombinants. Also, unlike the nepovirus tomato ringspot virus, no apparent proteolytic cleavage of GFLV protein 1E(Pol) was detected upon virus infection or transient expression in N. benthamiana. In addition, GFLV protein 1E(Pol) failed to suppress silencing of EGFP in transgenic N. benthamiana expressing EGFP or to enhance GFP expression in patch assays in WT N. benthamiana. Together, our results suggest the existence of strain-specific functional domains, including a symptom determinant module, on the RNA-dependent RNA polymerase of GFLV.

Genetic variability, evolution, and biological effects of Grapevine fanleaf virus satellite RNAs

Large satellite RNAs (type B satRNAs) of Grapevine fanleaf virus (GFLV) from the genus Nepovirus, family Secoviridae were identified in a naturally infected vineyard and a grapevine germplasm collection. These GFLV satRNA variants had a higher nucleotide sequence identity with satRNAs of Arabis mosaic virus (ArMV) strains NW and J86 (93.8 to 94.6%) than with the satRNA of GFLV strain F13 and those of other ArMV strains (68.3 to 75.0%). Phylogenetic analyses showed no distinction of GFLV and ArMV satRNAs with respect to the identity of the helper virus. Seven stretches of 8 to 15 conserved nucleotides (I-VII) were identified in the 5' region of subgroup A nepovirus genomic RNAs GFLV, ArMV, and Grapevine deformation virus) and nepovirus type B satRNAs, including previously reported motif I, suggesting that large satRNAs might have originated from recombination between an ancestral subgroup A nepovirus RNA and an unknown RNA sequence with the 5' region acting as a putative cis-replication element. A comparative analysis of two GFLV strains carrying or absent of satRNAs showed no discernable effect on virus accumulation and symptom expression in Chenopodium quinoa, a systemic herbaceous host. This work sheds light on the origin and biological effects of large satRNAs associated with subgroup A nepoviruses.

Complete nucleotide sequence of a South African isolate of Grapevine fanleaf virus and its associated satellite RNA

The complete sequences of RNA1, RNA2 and satellite RNA have been determined for a South African isolate of Grapevine fanleaf virus (GFLV-SACH44). The two RNAs of GFLV-SACH44 are 7,341 nucleotides (nt) and 3,816 nt in length, respectively, and its satellite RNA (satRNA) is 1,104 nt in length, all excluding the poly(A) tail. Multiple sequence alignment of these sequences showed that GFLV-SACH44 RNA1 and RNA2 were the closest to the South African isolate, GFLV-SAPCS3 (98.2% and 98.6% nt identity, respectively), followed by the French isolate, GFLV-F13 (87.3% and 90.1% nt identity, respectively). Interestingly, the GFLV-SACH44 satRNA is more similar to three Arabis mosaic virus satRNAs (85%–87.4% nt identity) than to the satRNA of GFLV-F13 (81.8% nt identity) and was most distantly related to the satRNA of GFLV-R2 (71.0% nt identity). Full-length infectious clones of GFLV-SACH44 satRNA were constructed. The infectivity of the clones was tested with three nepovirus isolates, GFLV-NW, Arabis mosaic virus (ArMV)-NW and GFLV-SAPCS3. The clones were mechanically inoculated in Chenopodium quinoa and were infectious when co-inoculated with the two GFLV helper viruses, but not when co-inoculated with ArMV-NW.

Complete nucleotide sequence of a South African isolate of Grapevine fanleaf virus

The complete sequences of RNA1 and RNA2 have been determined for a South African isolate of Grapevine fanleaf virus (GFLV-SAPCS3). The two RNAs are, respectively, 7,342 and 3,817 nucleotides in length, excluding the poly(A) tails. RNA1 has a large open reading frame (ORF) of 6,852 nucleotides and a 5'-UTR and a 3'-UTR of 243 and 244 nucleotides, respectively. RNA2 encodes for an ORF of 3,330 nucleotides and has the highest nucleotide identity (90.4 %) with GFLV-F13. The full length nucleotide sequence of GFLV-SAPCS3 RNA1 had the highest nucleotide identity (86.5 %) to the French isolate GFLV-F13. The 5'- and 3'-UTRs of GFLV-SAPCS3 RNA2 are 272 nucleotides and 212 nucleotides (nt) in length, respectively. The GFLV-SAPCS3 RNA2 5'-UTR is 32-53 nt longer compared to other GFLV isolates. The GFLV-SAPCS3 RNA2 5'-UTR is also more closely related to GFLV-GHu and Arabis mosaic virus (ArMV) isolates than to other GFLV isolates. Putative intra- and interspecies recombination events between GFLV and ArMV isolates involving GFLV-SAPCS3 RNA1 and RNA2 were investigated. Recombination analysis software has indicated that the GFLV-SAPCS3 5'-UTR might have evolved from a recombinational event between GFLV-F13-type and ArMV-Ta-type isolate.

A novel member of the genus Nepovirus isolated from Cucumis melo in Japan

An unusual virus was isolated from a Japanese Cucumis melo cv. Prince melon plant showing mild mottling of the leaves. The virus had a broad experimental host range including at least 19 plant species in five families, with most infected plants showing no symptoms on inoculated and uninoculated systemically infected leaves. The virus particles were spherical, approximately 28 nm in diameter, and the coat protein (CP) had an apparent molecular mass of about 55 kDa. The virus possessed a bi-partite genome with two RNA species, of approximately 8,000 and 4,000 nucleotides. Both genome components for the new virus were sequenced. Amino acid sequence identities in CP between the new virus and previously characterized nepoviruses were found to be low (less than 27%); however, in phylogenetic reconstructions the closest relationship was revealed between the new virus and subgroup A nepoviruses. These results suggest that the new virus represents a novel member of the genus Nepovirus. A new name, Melon mild mottle virus, has been proposed for this new virus.

Detection of Tomato black ring virus by real-time one-step RT-PCR

A TaqMan-based real-time one-step RT-PCR assay was developed for the rapid detection of Tomato black ring virus (TBRV), a significant plant pathogen which infects a wide range of economically important crops. Primers and a probe were designed against existing genomic sequences to amplify a 72 bp fragment from RNA-2. The assay amplified all isolates of TBRV tested, but no amplification was observed from the RNA of other nepovirus species or healthy host plants. The detection limit of the assay was estimated to be around nine copies of the TBRV target region in total RNA. A comparison with conventional RT-PCR and ELISA, indicated that ELISA, the current standard test method, lacked specificity and reacted to all nepovirus species tested, while conventional RT-PCR was approximately ten-fold less sensitive than the real-time RT-PCR assay. Finally, the real-time RT-PCR assay was tested using five different RT-PCR reagent kits and was found to be robust and reliable, with no significant differences in sensitivity being found. The development of this rapid assay should aid in quarantine and post-border surveys for regulatory agencies.

Genome diversity and intra- and interspecies recombination events in Grapevine fanleaf virus

ABSTRACT Grapevine fanleaf virus (GFLV) was documented in self-rooted vines of four grapevine (Vitis vinifera) cultivars in eastern Washington. GFLV was found as mixed infection in cvs. Pinot Noir, Chardonnay, and Cabernet Franc and as single infections in cv. Merlot. Fanleaf disease symptoms were only observed in the first two cultivars. The spatial distribution of GFLV-infected grapevines was random, suggesting primary spread through planting virus-infected cuttings rather than infield transmission. RNA1 sequences of Washington isolates showed 87 to 89% nucleotide sequence identity between them and with strain F13. RNA2 of Washington isolates was variable in size, showing 85 to 99% sequence identity between them and 81 to 92% with other isolates. As in other GFLV isolates, three conserved putative stem-loop structures were present in the 5' noncoding regions of both RNAs of Washington isolates. Phylogenetic incongruence of GFLV isolates from Washington in 2A(HP)- and 2B(MP)-based trees and identification of putative recombination events suggested that their genomic RNA2 originated from inter- and intraspecies recombination events between GFLV, Grapevine deformation virus, and Arabis mosaic virus. These results confirm interspecies recombination in RNA2 of grapevine-infecting nepoviruses as an important strategy for GFLV evolution.

Virus diseases in the tobacco fields of Guilan and Western Azerbaijan provinces of Iran

Tobacco (Nicotiana tabacum L.) is one of the important industrial plants in Iran. Viruses as an important group of plant pathogens cause many losses on the quality and quantity of tobacco crop. There was few information on the types of plant viruses infecting the tobacco fields of Guilan and almost no information for Western Azerbaijan province. During 2005-2007, leaf samples were taken from symptomatic plants in the growing areas of these two provinces. The observed symptoms on plants in the fields varied from mild mosaics to severe necrosis. The regions of sampling were including Rasht, Bazar-jomeh, Soumae-Sara, Talesh and Astara in Guilan and Ourmia, Sardasht and Ghara-Ziaeddin in Western Azerbaijan. The tobacco types and varieties from which the samples were taken included air-cured burley variety Burley 21 and to a lesser extent, oriental tobacco variety Basma Serres in W. Azerbaijan and flue-cured varieties Coker 347 and Virginia El in Guilan province. Samples were tested by DAS-ELISA method (Clark and Adams, 1977) using the polyclonal antibodies for a set of tobacco viruses. Some samples with positive reactions in DAS-ELISA were inoculated to indicator test plants such as Chenopodium amaranticolor, Datura metel, D. stramonium, Physalis floridana, Nicotiana rustica, N. glutinosa, and tobacco (varieties White burley and Samsun). The results of greenhouse experiments were consistent with serological tests. The following viruses which are listed in order of their overall abundance within the tested samples were detected: Tobacco streak virus (TSV), Tomato spotted wilt virus (TSWV), Tobacco etch virus (TEV), Tobacco ringspot virus (TRSV), Potato virus Y (PVY), Cucumber mosaic virus (CMV) and Tobacco mosaic virus (TMV). In all samples more than one virus infection was detected. The most severe mosaic type symptoms including the deformation and blistering on leaves were mainly seen in the infections by CMV and TMV. The most severe necrotic type symptoms including necrosis of midribs or veins and in some cases stem necrosis were generally associated with the infections by PVY and TSWV. Except TMV infection which was not detected in the Burley 21 variety in W. Azerbaijan, the above mentioned viruses were present in all sampling regions. The lack of TMV infection on Burley 21 is due to the presence of N gene, conferring resistance in this variety.

Diversity of Grapevine fanleaf virus isolates from Iran

Enzyme-linked immunosorbent assay (ELISA) testing of 126 grapevine samples, from vineyards in the northwest region of Iran, detected Grapevine fanleaf virus (GFLV) in 33 samples. Total RNA from eight of the infected samples were subjected to reverse transcription polymerase chain reaction (RT-PCR) analysis using primers which corresponded to the virus coat protein and 3' non coding region of RNA 2. An expected 1620 bp DNA fragment was amplified from all the tested samples. PCR products from isolates B5, S1 and SH3 were cloned and the nucleotide sequences of three clones from each isolate were determined. The sequences showed that a DNA fragment of 1623 bp from isolate S1 and 1629bp from isolates B5 and SH3 were amplified. The fragments covered 1481 nucleotides of the 3' proximal region of the CP gene plus 142 or 148 nucleotides of the 3' non coding region. Alignment of the sequences revealed over 99% identities among clones from each isolate and 83-93% among clones from different isolates. Identities of 83-94% were found between the isolates from Iran and previously reported GFLV strains/isolates. Phylogenetic analysis based on CP sequences showed that isolates S1 and SH3 formed a distinct cluster but isolate B5 clustered with previously reported GFLV strains. This is the first report on sequence analysis of nearly full-length CP cDNA clones of GFLV isolates from Iran.

The RNA2 5' leader of Blackcurrant reversion virus mediates efficient in vivo translation through an internal ribosomal entry site mechanism

The 5' and 3' non-translated regions (NTRs) of mRNAs of eukaryotes and their viruses often contain translational enhancers, including internal ribosomal entry sites (IRESs) comprised in the 5' leaders of many uncapped viral mRNAs. Blackcurrant reversion virus (BRV) has a genome composed of two uncapped, polyadenylated RNAs with relatively short 5' NTRs, almost devoid of secondary structure. In this work, a role of the RNA2 5' NTR in translation was studied by using mono- and dicistronic Photinus pyralis and Renilla reniformis luciferase reporter mRNAs in protoplasts of Nicotiana benthamiana. The RNA2 5' leader was found to confer efficient in vivo translation compared with the control 5' NTR, and each half of the BRV leader was essential for stimulatory function. Such efficient translational enhancement was mediated, at least in part, through an IRES mechanism. Multiple RNA2 5' NTR regions, complementary to a fragment of plant 18S rRNA demonstrated previously to be accessible for intermolecular mRNA-rRNA interactions and conserved between eukaryotes, were shown to be important for efficient translation. Similar mRNA-rRNA base-pairing potential was also predicted for the 5' leaders of other nepoviruses.

Development of degenerate and species-specific primers for the differential and simultaneous RT-PCR detection of grapevine-infecting nepoviruses of subgroups A, B and C

Based on the nucleotide sequence homology of RNA-1 and RNA-2 of nepoviruses isolated from grapevines, three sets of degenerate primers, one for each of the three subgroups of the genus (A, B and C), were designed and proved effective for RT-PCR detection of subgroups in infected grapevines and herbaceous hosts. Primers designed specifically for detecting subgroup A species amplified a fragment of 255 bp from samples infected by Grapevine fanleaf virus (GFLV), Arabis mosaic virus (ArMV), Tobacco ringspot virus (TRSV) and Grapevine deformation virus (GDefV), but not from samples infected by other nepovirus species. Similarly, primers for detection of subgroup B nepoviruses amplified a 390 bp product from samples infected by Grapevine chrome mosaic virus (GCMV), Tomato black ring virus (TBRV), Grapevine Anatolian ringspot virus (GARSV) and Artichoke Italian latent virus (AILV). The third set of primers amplified a 640 bp fragment, only from samples infected by subgroup C nepoviruses, i.e Tomato ringspot virus (ToRSV) Grapevine Bulgarian latent virus (GBLV), and Grapevine Tunisian ringspot virus (GTRSV). These primers were able to detect simultaneously all viral species belonging to the same subgroup and to discriminate species of different subgroups. Multiplex-PCR detection of subgroup A and B nepoviruses was obtained using a specific primer (sense for subgroup A and antisense for subgroup B) for each of the species of the same subgroup in combination with the degenerate subgroup-specific primers. In this way it was possible to detect four different viral species in single samples containing mixtures of viruses of the same subgroup. In particular, for viruses of subgroup A (TRSV, GFLV, ArMV and GDefV) amplicons of 190, 259, 301 and 371 bp were obtained, whereas amplicons of 190, 278, 425 and 485 bp, respectively, were obtained from samples infected with viruses of subgroup B (GCMV, AILV, GARSV and TBRV).

Plant parasitic and vector nematodes associated with Asiatic and Oriental hybrid lilies

A survey for distribution and abundance of plant parasitic nematodes in fields grown to Lilium in Himachal Pradesh, India at four study sites viz. Nagrota (at 810 m a.s.l.), Palampur (at 1270 m a.s.l.), Sunder Nagar (at 1400 m a.s.l.) and Chail (at 2250 m a.s.l.) was carried out. Moderate (101-500/200 ml soil) to high (501-1000/200 ml soil) populations of phytonematodes including the vectors for plant viruses (Aphelenchoides avenae, Criconemoides spp., Hoplolaimus spp., Longidorus spp., Paratylenchus spp., Pratylenchus spp., Rhabditis spp., Trichodorus spp., Tylenchoryhnchus spp., Tylenchulus spp. and Xiphinema diversicaudatum) were recorded. Mean population of nematodes was positively correlated with pH in all the study sites, negatively correlated with electrical conductivity (EC), percent organic matter (OM%), available potassium (K) and positively correlated with percent carbon (C%), available nitrogen (N) and available phosphorus (P) in all but one study site. The highest incidence of virus-vector nematodes viz. X. diversicaudatum, Longidorus spp. and Trichodorus spp. was recorded at Palampur. Only Strawberry latent ringspot nepovirus (SLRSV) was detected in Lilium cvs. Star Gazer Max and Galeili by Enzyme Linked Immunosorbent Assay (ELISA) and reverse transcription polymerase chain reaction (RT-PCR) and in X. diversicaudatum associated with the cultivars by RT-PCR. Cucumis sativus used as bait plants showed SLRSV symptoms after 15 days of nematode inoculation and further SLRSV was again detected by ELISA and RT-PCR in C. sativus plants confirming the transmission of SLRSV by X. diversicaudatum in Lilium.

Partial molecular characterization of a mild isolate of Grapevine fanleaf virus from South Moravia, Czech Republic

An atypical mild isolate HV5 of Grapevine fanleaf virus (GFLV) was found in a South Moravian viticulture region in Czech Republic. Partial sequence of its RNA2 was determined and compared with available sequences of typical GFLV isolates. Two genomic regions, namely a 814 nt-long one spanning the movement protein (MP) gene and a 5'-part of the coat protein (CP) gene. and a 1426 nt-long one covering a part of the CP gene and the adjacent 3'-non-coding region (3'-NCR) were analyzed. Although no HV5-specific molecular features could be found in the two regions, marked differences were observed in the 3'-NCR. There was a 54 nt-long portion in which the sequence identity of some compared isolates was only 54.7%. Moreover, an unique one-nucleotide deletion occurred in the HV5 3'-NCR. These changes were also reflected in the predicted RNA secondary structure of this region. Particular biological behavior of GFLV HV5 isolate, namely a symptomless infection, could be related to the observed molecular differences.

Sequence analysis of grapevine isolates of Raspberry ringspot nepovirus

The nucleotide sequences of RNAs 1 and 2 of a German isolate of Raspberry ringspot virus (RpRSV) infecting grapevine (RpRSV-Grapevine), as well as partial sequences of another grapevine isolate from Switzerland (RAC815) were determined. The sequences of the protease-polymerase region encoded by RNA1, and the movement protein and coat protein genes encoded by RNA 2, of these isolates were compared with those of other isolates available in databases. The coat proteins of the grapevine isolates formed a sister group to all those from other RpRSV isolates, but whether this resulted from divergence or recombination was uncertain.

A RT/PCR-partial restriction enzymatic mapping (PREM) method for the molecular characterisation of the large satellite RNAs of Arabis mosaic virus isolates

The satellite RNA of the grapevine isolate NW of Arabis mosaic virus (ArMV) was cloned and sequenced, and showed 75% identity at the nucleotide level to the satellite RNA of the lilac isolate of ArMV. In order to survey ArMV isolates from various geographical origins and natural hosts for the presence of large satellite RNAs and analyse their degree of variability, a RT/PCR-partial restriction enzymatic mapping (PREM) method was developed. The method is based on the incorporation of 5-methyl-dCTP in the RT/PCR reaction, and the subsequent digestion of the RT/PCR products by methyl-sensitive restriction enzymes. Satellites RNAs were detected by RT/PCR in eight isolates out of 47, six of them originating from grapevine, one from hop and one from lilac. The partial restriction digestion patterns allowed to distinguish six different types of satellites. Cloning and sequencing of the different satellites confirmed these results, the PREM proving able to discriminate sequences with 96% identity. The sizes of the different satellites varied between 1092 and 1139 nucleotides, their encoded proteins between 338 and 360 amino acids. Conserved domains were found in the amino and carboxy-termini between the sequences of the proteins encoded by the satellites of the different isolates of ArMV.

Characterization of a naturally occurring recombinant isolate of Grapevine fanleaf virus

The naturally occurring Grapevine fanleaf virus (GFLV) recombinant isolate A17b was recovered from its grapevine host by sap inoculation and serial passages onto Gomphrena globosa, a pseudo local lesion herbaceous host, and Chenopodium quinoa, a systemic herbaceous host, to characterize some of its biological properties. Sequence analysis of the CP gene, in which a recombinational event was previously detected, demonstrated the genetic stability of recombinant isolate A17b over a 5-year period in its natural host as well as in C. quinoa. Also, recombinant isolate A17b was graft transmissible, as shown by an in vitro heterologous approach, and transmitted by the nematode Xiphinema index as readily as nonrecombinant GFLV isolates. Furthermore, despite a lower pathogenicity on Chenopodium amaranticolor, recombinant isolate A17b had a similar host range and induced similar symptoms in type and severity to nonrecombinant GFLV isolates. Interestingly, the use of infectious chimeric RNA2 transcripts in combination to RNA1 transcripts of GFLV strain F13 suggested no implication of the recombination event in the CP gene of isolate A17b in the reduced pathogenicity on C. amaranticolor. Altogether, recombinant isolate A17b had similar biological properties to GFLV nonrecombinant isolates.

Sensitive and reliable detection of grapevine fanleaf virus in a single Xiphinema index nematode vector

Grapevine fanleaf virus (GFLV) is specifically transmitted from plant to plant by the ectoparasitic nematode Xiphinema index. A sensitive and reliable procedure was developed to readily detect GFLV in a single viruliferous X. index, regardless of the nematode origin, i.e. greenhouse rearings or vineyard soils. The assay is based on bead milling to disrupt nematodes extracted from soil samples, solid-phase extraction of total nematode RNAs, and amplification of a 555bp fragment of the coat protein (CP) gene by reverse transcription-polymerase chain reaction with two primers designed from conserved sequences. This procedure is sensitive since the CP gene fragment is amplified from an artificial sample consisting of one viruliferous nematode mixed with 3000 aviruliferous individuals. In addition, StyI RFLP analysis of the CP amplicon enables the GFLV isolate carried by a single viruliferous X. index to be characterized. This GFLV detection assay opens new avenues for epidemiological studies and for molecular investigations on the mechanism of X. index-mediated GFLV transmission.

The long 3' non-translated regions of Blackcurrant reversion virus RNAs are highly conserved between virus isolates representing different phenotypes and geographic origins

Blackcurrant reversion virus (BRV) belongs in the subgroup c of nepoviruses. The 3' NTRs of RNAs 1 and 2 of BRV are 1360 and 1363 nucleotides long, respectively, and highly similar (94.8%). In this study we have compared the sequences of the 3' NTRs of ten BRV isolates, originating from different geographic regions or hosts. All deduced sequences were 94.1-98.8% identical with each other, and with the previously deduced 3' NTR sequences of RNAsl and 2 of the type isolate. The proceeding 480 nucleotides of the CP coding region were 86.9-97.9% identical between the same isolates.

Complete nucleotide sequence of an isolate of the nepovirus raspberry ringspot virus from grapevine

The complete nucleotide sequence of the RNAs 1 and 2 of the nepovirus Raspberry ringspot virus cherry isolate (RpRSV-ch) from grapevine was determined. The RNA 1 is 7935 nucleotides (nt) long excluding the poly(A) tail, and contains one long open reading frame (ORF) encoding a polypeptide of 2367 amino acids. This ORF is preceeded by a 136nt 5' non-coding region, and followed by a 695nt 3' non-coding region. Conserved amino acid motifs, characteristic of the viral protease cofactor, the NTP-binding protein, proteinase and polymerase, were found in the sequence of the RNA 1-encoded polyprotein. The RNA 2 is 3915nt long excluding the poly(A) tail, and contains one long ORF encoding a polypeptide of 1106 amino acids. This ORF is preceeded by a 203nt 5' non-coding region, and followed by a 390nt 3' non-coding region. When compared to the corresponding sequences of other nepoviruses, a maximum level of 34% identity was found between the RNA 1-encoded polypetides of RpRSV-ch and other nepoviruses. For the RNA 2-encoded polypeptide, 88% identity was found between RpRSV-ch and RpRSV-S, a Scottish isolate of RpRSV from raspberry, and a maximum 29% identity between RpRSV-ch and other nepoviruses.

Transgenic resistance to tobacco ringspot virus

The coat protein (CP) gene including the 3'-untranslated region (UTR) of RNA2 of a cherry isolate of Tobacco ringspot virus (TRSV) was utilized in a CP-mediated resistance (CP-MR) strategy. To facilitate construction of plant expression vectors the sequence context of the CP gene translation initiation codon was modified at the 5'-end of the coding sequence by including an initiation codon. The gene was ligated to a version of the Cauliflower mosaic virus (CaMV) 35S promoter with a duplicated enhancer. The cloned CP gene was used to transform Nicotiana tabacum cv. Xanthi, as a systemic and local lesion host. The transgenic plants showed different level of resistance ranging from complete resistance to reduction in symptom severity post inoculation with the cherry isolate of TRSV. A CP gene transcript was detected in different tissue of transgenic lines, but translation product was undetectable by Western blot analysis or enzyme-linked immunosorbent assay (ELISA). Interestingly, 100% of seed transmission was blocked in a resistant line, which offers important prospects for engineering TRSV into economically important crops as soybean with 100% seed transmission.

Restriction analysis of genetic variability of Polish isolates of Tomato black ring virus

Several different isolates of Tomato black ring virus (TBRV) have been collected in Poland from cucumber, tomato, potato and black locust plants. Biological tests showed some differences in the range of infected plants and the type of symptoms, which was the basis for selection of seven the most biologically different TBRV isolates. According to the sequence of TBRV-MJ, several primer pairs were designed and almost the entire sequence of both genomic RNAs was amplified. The RT-PCR products derived from all tested TBRV isolates were digested by restriction enzymes. On the basis of the restriction patterns, the variable and the conserved regions of the TBRV genome were defined and the relationships between the Polish TBRV isolates established.

Elimination of PPV and PNRSV through thermotherapy and meristem-tip culture in nectarine

The plum pox virus (PPV) and prunus necrotic ringspot virus (PNRSV) cause serious disease problems in stone-fruit trees. In this work, the possibility of obtaining plant material free from these viruses through thermotherapy and meristem-tip culture from infected nectarine shoots (Prunus persica var. nectarina Max, cv. 'Arm King') was studied. In addition, the detection of these viruses in in vitro cultures and young acclimatized plantlets with double antibody sandwich-enzyme-linked immunosorbent assay (DAS-ELISA) and multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) was studied. Meristem-tip explants (0.8-1.3 mm) derived from sprouted buds of winter wood and spring shoots from field grown plants had a 2-5% regeneration response. However, application of thermotherapy to potted nectarine trees (3 weeks at a maximum temperature of 35 degrees C) facilitated excision of longer meristem tips (1.3-2.0 mm) that resulted in a significantly higher regeneration response (38%) in woody plant medium (WPM) without plant growth regulators. Such explants formed multiple shoots with the addition of 8 microM benzylaminopurine and 0.8 microM indoleacetic acid. When they were tested for the presence of PPV and PNRSV, 86% and 81% were found to be virus-free as detected by DAS-ELISA and multiplex RT-PCR, respectively. Individual shoots excised from virus-free cultures readily rooted in vitro (half-strength WPM plus 2 microM indolebutyric acid) and grew to plantlets. The combination of an efficient protocol for virus elimination and the establishment of highly sensitive diagnostics resulted in the production of nectarine plants free from PPV and PNRSV.

Mixed infection of black currant (Ribes nigrum L.) plants with Blackcurrant reversion associated virus and rhabdovirus-like particles with symptoms of black currant reversion disease

Black currant plants of cvs. Black Smith and Karlstejnský dlouhohrozen showing symptoms of severe Russian (R) form of black currant reversion disease (BCRD) were found in 1999-2000 in the Czech Republic. Five selected plants of both cultivars originating from two distant loci were tested by polymerase chain reaction (PCR) for presence of the Blackcurrant reversion associated virus (BRAV), the causal agent of BCRD. In all plants, virus-specific 215 nt cDNA fragments proving the presence of BRAV were obtained. Moreover, in two of those five black currant plants, rhabdovirus-like particles were found in ultrathin sections by electron microscopical examinations. The particles measured 200-347 nm by 64-90 nm. They occurred mostly within nuclei of parenchyma cells of vascular bundles as single particles, rafts of particles, but also in aggregates. They were found also in the perinuclear space and occasionally directly in the cytoplasm. Clusters of particles either within the nucleus or in the perinuclear space were membrane-bound. We bring evidence on the occurrence of the severe (R) form of BCRD and the first evidence of BRAV in the Czech Republic.

Brevipalpus-transmitted plant virus and virus-like diseases: cytopathology and some recent cases

An increasing number of diseases transmitted by Brevipalpus mite species (Acari: Tenuipalpidae) is being identified that affect economically important plants such as citrus, coffee, passion fruit, orchids, and several ornamentals. All of these diseases are characterized by localized lesions (chlorotic, green spots, or ringspots) on leaves, stems, and fruits. Virus or virus-like agents are considered to be the causal agents, possibly transmitted in a circulative-propagative manner by Brevipalpus mites. The virus or virus-like particles are short, rod-like, or bacilliform, that induce two characteristic types of cell alteration: (1) 'Nuclear type'--nuclei of parenchyma and epidermal cells in the lesions often contain a large electron lucent inclusion. Short, naked, rod-like (40-50 nm x 100-110 nm) particles may be seen in the viroplasm or nucleoplasm and in the cytoplasm. These particles are commonly arranged perpendicularly on the membranes of the nuclear envelope or endoplasmic reticulum (ER). In a very few instances, they were found to be membrane-bound, within the ER cavities. (2) 'Cytoplasmic type'--short bacilliform particles (60-70 nm x 110-120 nm) are present within the cisternae of the ER and often have electron dense viroplasm of varied shapes present in the cytoplasm. Bacilliform particles may be seen budding into the ER lumen near the viroplasm. These particles resemble those of members of the Rhabdoviridae, but are shorter. The only sequenced virus of this group, orchid fleck virus (OFV), has a negative sense (bipartite) type ssRNA genome, but its organization is similar to known rhabdoviruses, which are monopartite. Both types of cytopathological effects have been found associated with citrus leprosis. In orchids, OFV has a 'nuclear type' of cytopathology, but in some species the 'cytoplasmic type' has been found associated with ringspot symptoms. In Hibiscus and Clerodendron, green spot symptoms have been associated with the cytoplasmic type of cell alteration, while chlorotic spots, in the same species, are associated with the nuclear type. In a few cases, both types of cytopathological effects have been found in the same tissue and cell.

Simultaneous RT/PCR detection and differentiation of arabis mosaic and grapevine fanleaf nepoviruses in grapevines with a single pair of primers

The movement protein genes from several isolates of ArMV and GFLV of different geographical origins were amplified by RT/PCR using degenerate primers, cloned and sequenced. A single pair of degenerate primers was designed from these sequences to allow the simultaneous amplification of parts of the movement protein genes of ArMV and GFLV. Their use in an immunocapture-RT/PCR for the detection of ArMV or GFLV in infected grapevines proved to be ten times more sensitive than the corresponding ArMV or GFLV ELISA tests. A Sph1 restriction site found in the sequences corresponding to the amplified products from the GFLV isolates, but not in the amplified products from the ArMV isolates, allowed the differentiation between ArMV and GFLV in the infected grapevines by a Sph1 restriction digestion of the amplified products.

Sequence diversity and interrelationships among isolates of satsuma dwarf-related viruses

The 3'-region of RNA2 of three viruses (Natsudaidai dwarf virus (isolate ND-1), and two unidentified isolates (LB-1, Az-1)), which were related to Satsuma dwarf virus (SDV), were sequenced. Phylogenetic analysis including the previously reported SDV-related viruses (Citrus mosaic virus (CiMV, Ci-968), Navel orange infectious mottling virus (NIMV, NI-1)) showed that they were classified into three groups, SDV (S-58), CiMV (Ci-968, LB-1, Az-1, ND-1), and NIMV (NI-1). The results suggested these groups might correspond to the three distinct virus species. ND-1, LB-1, and Az-1 were considered strains of CiMV, although they do not induce citrus mosaic on the fruit rind.

Complete nucleotide sequences of the RNAs 2 of German isolates of grapevine fanleaf and Arabis mosaic nepoviruses

The RNAs 2 of an Arabis mosaic virus (ArMV) and a grapevine fanleaf virus (GFLV) isolate, originating from South West of Germany near Neustadt an der Weinstrasse (NW), were sequenced. They are 3820 and 3775 nucleotides long respectively, and both contain one open reading frame encoding a polypeptide of 1110 amino acids. Their 5' non-coding regions contain conserved and repeated sequences, which are able to form stem-loop structures. Nucleotide sequence comparisons between the full-length RNAs 2 revealed homology levels of 84 and 82% between the ArMV-NW and the ArMV-L and -U, respectively, 90% between GFLV-NW and GFLV-F13, and 72% between ArMV-NW and GFLV-NW. Amino acid sequence comparisons showed that the greatest difference was found between the 2A proteins of the different ArMV isolates, the 2A protein of the ArMV-NW showing more similarity to the 2A protein of GFLV-NW than to those of ArMV-L2 or -U2.

Cloning and sequencing of the coat protein gene of tobacco ringspot virus isolates from UK and Iran

The coat protein (CP) gene and the 3' untranslated region (UTR) of genomic RNA 2 of Tobacco ringspot virus (TRSV, the genus Nepovirus, subgroup a) isolates from the UK and Iran were cloned from total viral RNA and sequenced. Comparison of these isolates with an isolate from the USA revealed a high degree of nucleotide and amino acid identity which extends the knowledge of molecular relationships between these three TRSV isolates. The UK isolate shared the highest nucleotide identity (95%) with the US isolate as compared to a lower identity with the Iranian isolate (92%). The highest identity (98%) was found between the UK and US isolates at amino acid level. Comparative analysis of the Iranian, UK and US isolates revealed some differences concerning some members of other subgroups of nepoviruses. For example, the N-terminal FDAYXR and the C-terminal FYGRXS motifs conserved among some nepoviruses, which occur adjacent to each other in folded CP molecules, were not detected in the Iranian, UK or US TSRV isolates. These isolates shared similarity only with Tomato ringspot virus (TomRSV) belonging to the subgroup c of nepoviruses. Another similarity of these isolates with TomRSV and Raspberry ringspot virus (RRSV) was the presence of a 34 nucleotide (nt) long sequence within the 3'-UTR.

Cloning and sequencing of peach rosette mosaic virus RNA1

The complete nucleotide sequence of peach rosette mosaic nepovirus (PRMV) RNA1 has been determined. A grapevine isolate of PRMV from Michigan was propagated and purified and cDNA clones representing 99. 5% of the RNA1 were constructed. The cDNA and direct RNA sequence analysis revealed a RNA species of 8004 nucleotides, excluding a 3' polyadenylated tail. The 5'- and 3'-untranslated regions were 52 and 1474 nucleotides, respectively. Computer analysis of the PRMV RNA1 nucleotide sequence unveiled a single long open reading frame of 6477 nucleotides, which is capable of encoding a 240 kDa polyprotein. Analysis of the predicted amino acid sequence of RNA1 revealed amino acid motifs characteristic of a replicase, proteinase, NTP-binding protein and a proteinase cofactor. The order and identity of these putative proteins are consistent with other nepoviruses. Analysis of PRMV RNA1 further distinguishes the taxonomic subdivisions within the nepovirus group, confirms the subgroup three status of PRMV and lays the groundwork for a replicase-mediated resistance strategy.

[Grapevine viruses in Tunisia]

Tunisian grapevine culture is affected by many viruses caused by some phytovirus belonging to nepovirus, closterovirus and trichovirus groups. The present work deal with the economically important viroses identified in tunisian grapevines. We present here the development methods to detect these viruses in propagating material. The important viruses biologically, biochemically, serologically and using molecular techniques, characterised are: GFLV, GLRaV3 and GVB. The genetic polymorphism analysis was also carried and tunisian isolates were compared to previously described ones in literature.

Occurrence of nepoviruses in Rubus species in the Czech Republic

The occurrence of arabis mosaic virus (AMV), raspberry ringspot virus (RRV), tomato black ring virus (TBRV), strawberry latent ringspot virus (SLRV) and cherry leaf roll virus (CLRV) in cultivated and wild plants of raspberry and blackberry has been studied in the Czech Republic in 1993-1996. Five hundred and seventy samples were collected at 51 localities and assayed by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA). The results represent the first evidence on the occurrence of AMV, RRV, TBRV and SLRV in cultivated Rubus species in the Czech Republic. Isolates AMV M20 and TBRV ML15 which were successfully transmitted by mechanical inoculation and characterized by reactions of differential host plants and by electron microscopy are the first isolates from Rubus from this territory. CLRV was not detected in either cultivated or wild Rubus species.

Detection and isolation of nepoviruses on strawberry in the Czech Republic

Arabis mosaic, strawberry latent ringspot, tomato black ring and raspberry ringspot nepoviruses were monitored using double sandwich enzyme-linked immunosorbent assay (DAS-ELISA) in 18 cultivars of strawberry Fragaria x ananassa Duch. in the Czech Republic. Arabis mosaic and strawberry latent ringspot viruses were detected, isolated and characterized on differential host plants and by electron microscopy. Both viruses were purified and antisera to them were prepared.

The 119 kDa and 124 kDa polyproteins of arabis mosaic nepovirus (isolate S) are encoded by two distinct RNA2 species

Arabis mosaic virus (ArMV) is a nepovirus that is serologically distantly related to grapevine fanleaf virus (GFLV). Both ArMV and GFLV induce grapevine degeneration disease. Several ArMV isolates, unlike isolates of GFLV, produce upon in vitro translation of RNA2 a polyprotein (P2) that forms a double band in polyacrylamide-SDS gels. Cloning of full-length copies of RNA2 of an ArMV isolate from grapevine (ArMV-S) revealed that this isolate contained two RNA2s of different length, called RNA2-U and RNA2-L. The two species were not readily separated by electrophoresis of the virion RNA under denaturing gel electrophoresis conditions but could be distinguished by analysis of primer extension and in vitro translation products. The size difference of the two RNA2s is due mostly if not exclusively to differences in their coding regions. The 124 kDa RNA2-U-encoded polyprotein P2' and the 119 kDa RNA2-L-encoded polyprotein P2", which co-migrate, respectively, with the upper and lower polyprotein bands produced by RNA2 of ArMV-S, were more than 95% identical except in their N-terminal domains. In vitro maturation experiments and sequence comparisons indicate that the N-terminal products of P2' and P2" have a molecular mass of 31 kDa and 26 kDa. The genomic organization proposed is similar to that of GFLV RNA2.

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

Digoxigenin-labeled RNA probes were used to detect cherry leaf roll virus in infected plants. A dot-blot hybridization immunoenzymatic assay in both crude sap extracts and partially purified tissue with a colorigenic and chemiluminescent detection was developed. The use of the new AMPPD substrate was found to be effective in clarified sap extracts in conditions were the colorigenic detection method failed. Both detection assays were effective when using unfractionated nucleic acid preparations, the chemiluminescent being five times more sensitive than the colorigenic. The chemiluminescent hybridization assay makes it possible to detect the virus at the picogram level. The non-radioactive dot-blot hybridization techniques described here turned out to be very suitable for plant virus diagnosis. The sensitivity of this method and those obtained by ELISA or radioactive dot-blot described previously is compared.