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A number of important citrus pathogens are spread by graft propagation, arthropod vector transmission and inadvertent import and dissemination of infected plants. For these reasons, citrus disease management and clean stock programs require pathogen detection systems which are economical and sensitive to maintain a healthy industry. To this end, multiplex quantitative real-time PCR (qPCR) assays were developed allowing high-throughput and simultaneous detection of some major invasive citrus pathogens. Automated high-throughput extraction comparing several bead-based commercial extraction kits were tested and compared with tissue print and manual extraction to obtain nucleic acids from healthy and pathogen-infected citrus trees from greenhouse in planta collections and field. Total nucleic acids were used as templates for pathogen detection. Multiplex reverse transcription-qPCR (RT-qPCR) assays were developed for simultaneous detection of six targets including a virus, two viroids, a bacterium associated with huanglongbing and a citrus RNA internal control. Specifically, two one-step TaqMan-based multiplex RT-qPCR assays were developed and tested with target templates to determine sensitivity and detection efficiency. The first assay included primers and probes for 'Candidatus Liberibacter asiaticus' (CLas) and Citrus tristeza virus (CTV) broad spectrum detection and genotype differentiation (VT- and T3-like genotypes). The second assay contained primers and probes for Hop stunt viroid (HSVd), Citrus exocortis viroid (CEVd) and the mitochondrial NADH dehydrogenase (nad5) mRNA as an internal citrus host control. Primers and TaqMan probes for the viroids were designed in this work; whereas those for the other pathogens were from reports of others. Based on quantitation cycle values, automated high-throughput extraction of samples proved to be as suitable as manual extraction. The multiplex RT-qPCR assays detected both RNA and DNA pathogens in the same dilution series as singleplex assays and yielded similar quantitation cycle values. Taken together, high throughput extraction and multiplex RT-qPCR assays reported in this study provided a rapid and standardized method for routine and simultaneous diagnosis of different RNA and DNA citrus pathogens., (Published by Elsevier B.V.)

The 3699 nt genome of olive latent virus 1 (OLV-1), described years ago from Southern Italy as a putative sobemovirus, was completely sequenced. OLV-1 genomic RNA was not polyadenylated and had a structure virtually identical to that of species of the Necrovirus rather than the Sobemovirus genus. Five open reading frames (ORFs) were identified, of which the 5'-proximal encoded a 23K protein and ended with an amber codon whose readthrough could yield a putative 82K product. This polypeptide had extensive sequence similarity with polymerases of serotypes A and D of tobacco necrosis necrovirus (TNV-A and TNV-D) and species of the family Tombusviridae and related genera (Dianthovirus and Machlomovirus). Two small ORFs followed, which encoded polypeptides of 8K and 6K, respectively. The 6K product had extensive homology with the comparable 6K protein of TNV-A and was also related to the 11K protein of shallot latent carlavirus, one of the "triple block" polypeptides involved in cell-to-cell virus movement. The 3'-proximal ORF was in the same position as the coat protein (CP) cistron of necroviruses and encoded a 30K product related to CP of both TNV-A and -D. Computer-assisted comparative analysis of structural and non-structural proteins of OLV-1, TNV-A and TNV-D disclosed on overall distant relationship between OLV-1 and TNV-D. OLV-1 genome appeared homologous to that of TNV-A, but differences from TNV-A were the absence of the small ORF downstream of the CP cistron and in the low degree of sequence identity in CP (39% aa identity). OLV-1 is serologically distantly related to TNV-A and even more distantly related to TNV-D. We propose that OLV-1 is a necrovirus species in its own right.

Olive latent virus 2 (OLV2), a virus with particle shapes resembling those of alfalfa mosaic alfamovirus (AMV), has four major RNA species, two of which (RNA3 and RNA4) were completely sequenced. RNA3 was a bicistronic molecule containing two clear-cut ORFs, one of which (ORF1) coded for a 36.5 kDa polypeptide with conserved motifs of the '30K superfamily' movement proteins and the other (ORF2) encoded a 20 kDa polypeptide identified as the viral coat protein. RNA4, which was a little smaller than RNA3 (2078 nt versus 2438 nt), also differed from RNA3 in a few positions, but its in vitro translation did not produce any protein. By contrast, an additional RNA, 1042 nt in size with strong sequence homology with RNA3 and RNA4, was identified in RNA extracts from infected plants. This RNA, which may be a subgenomic form of RNA3 carrying the coat protein cistron, is apparently encapsidated to a very small extent, or not at all. Comparative computer-assisted analysis of virus-coded protein sequences disclosed homologies suggesting that OLV2 may belong to the family Bromoviridae, but as an entity separated from the currently known genera.

A virus with highly flexuous filamentous particles c. 800 nm long, showing distinct transverse striations was isolated with high frequency (60%) by inoculation of Nicotiana occidentalis with sap from grapevine accessions indexing positive for corky bark. The virus, for which the name grapevine virus B (GVB) is proposed, has an ssRNA genome with mol. wt. of c. 2.5 x 10(6) Da (c. 7600 nt) and coat protein subunits with mol. wt. of c 23,000 Da. GVB has a very restricted herbaceous host range and was experimentally transmitted by the mealybug Pseudococcus ficus. The physicochemical and ultrastructural properties of GVB resemble those of closteroviruses. However, it is serologically unrelated to other grapevine closteroviruses including grapevine virus A, with which it shares some biological and physicochemical properties.

Four stable hybridoma cell lines secreting monoclonal antibodies to grapevine closterovirus A (GVA) were obtained by fusing spleen cells of immunized BALB/c mice with mouse myeloma cell line Sp2/0-Ag 14. In ELISA all MAbs reacted with virus in leaf extracts from Nicotiana benthamiana, glass-house-, field-, or in vitro-grown grapevines, or with cortical shavings from mature grape canes. In IEM tests, only one of the MAbs (PA3.F5) decorated virus particles on the entire surface. This MAb was likely induced by a surface antigenic determinant, whereas the other three MAbs (PA3.D 11, PA3.C 6, and PA3.B 9) were originated by cryptotopes. Coupling polyclonal antibodies for coating protein A-sensitized plates, and monoclonal antibody conjugates for antigen detection, gave highly efficient and reproducible results for identification of GVA in field-grown grapevines.

A virus with isometric particles c. 30 nm in diameter and angular contour was isolated by inoculation of sap from a Tunisian grapevine with mild mottling and leaf deformation. The virus sedimented in sucrose density gradients as three components: T (empty shells), M (particles containing a molecule of ssRNA with an apparent size of 5,800 nucleotides, constituting 35% of the particle weight) and B (particles containing a molecule of ssRNA with apparent size of 6,800 nucleotides, constituting 41% of the particle weight). Virus particles had buoyant densities of 1.31 (T), 1.45 (M), and 1.49 g/cm3 (B) in cesium chloride equilibrium gradients. The coat protein subunits consisted of a single polypeptide with mol. wt. of c. 59,000 daltons. An antiserum was produced with a titer of 1:256, which did not react with healthy plant antigens. Cells of artificially infected herbaceous hosts showed cytoplasmic vesiculate-vacuolate inclusion bodies, virus-containing tubules, mostly associated with plasmodesmata and/or cell wall protrusions, and crystalline aggregates of virus particles and empty capsids. The physicochemical and ultrastructural properties of this virus resemble very much those of nepoviruses. However, it was serologically unrelated to 19 different members of the group, including all those reported to infect grapevines. Therefore, the virus is possibly a hitherto unreported nepovirus for which the name of grapevine Tunisian ringspot virus (GTRV) is proposed.

A non-radioactive dot-blot hybridization assay for the successful detection of Citrus tristeza virus (CTV) RNA in total nucleic acid extracts of infected citrus was developed. Two digoxigenin (DIG)-labelled minus-sense riboprobes, complementary to the coat protein gene sequence of a Chinese and an Apulian CTV isolate were synthesized. Several citrus tissues were evaluated as optimal virus source and leaf petioles were found appropriate material for reliable detection. The hybridization assay showed a detection limit corresponding to 0.2 mg of fresh infected tissue. The riboprobes allowed CTV detection in isolates from different geographical areas, grown in the screenhouse or in the field, resulting in similar hybridization patterns. The infected trees were tested during different seasons with positive results, although from July to August most of the samples gave a weaker hybridization signal, compared to other seasons. The high sensitivity and reliability of the molecular hybridization assay described make it a good alternative to serological methods for CTV detection. [ABSTRACT FROM AUTHOR]

A survey for viruses was carried out in 2003 in the main olive-growing areas of Lebanon (South Lebanon, North Lebanon, Mount Lebanon and Bekaa). A total of 300 samples was collected in 31 different locations in 76 different commercial orchards and checked by RT-PCR for the presence ofArabis mosaic virus(ArMV),Cherry leaf roll virus(CLRV),Strawberry latent ringspot virus(SLRV),Olive latent virus 1(OLV-1) andOlive leaf yellowing-associated virus(OLYaV), using virus-specific primers reported in the literature. About one third (31%) of the trees were infected. In particular, the closterovirus OLYaV was the most widespread, as it was detected in 23.7% of the samples, followed by the necrovirus OLV-1 (8.3%), the two nepoviruses CLRV (2%) and ArMV (0.3%), and the sadwavirus SLRV (0.3%). A high variability was detected in the HSP70 gene of Lebanese and Italian OLYaV isolates, for at least nine different patterns were obtained when this genomic region was subjected to single-strand conformation polymorphism (SSCP) analysis. [ABSTRACT FROM AUTHOR]

Field surveys were carried out in the main stone-fruit growing areas of Morocco to evaluate the sanitary status of commercial orchards, varietal collections and nurseries. The presence of virus and virus-like diseases was checked by ELISA, sap transmission to herbaceous hosts, testing on woody indicators and molecular hybridization (dot-blot and tissue-printing). 1211 samples (382 almond, 339 peach, 291 plum, 150 apricot and 49 cherry) were tested by ELISA for the presence ofPrunus necrotic ring spot virus(PNRSV),Prune dwarf virus(PDV),Apple chlorotic leaf spot virus(ACLSV),Apple mosaic virus(ApMV) andPlum pox virus(PPV). The overall average of virus infection rate was 16.4%, whereas that of single species was: 22.6% for almond, 17.8% for plum, 15% for peach, 10.2% for cherry, and 2.7% for apricot. The following viruses were detected: PNRSV, PDV, ACLSV and ApMV. 565 samples were tested by dot-blot and tissue-printing hybridization for the presence ofPeach latent mosaic viroid(PLMVd) andHop stunt viroid(HSVd). 48 samples were infected, 41 by PLMVd and 7 by HSVd. In addition, nested-PCR tests identified Plum bark necrosis and stem-pitting associated virus (PBNSPaV) in a few almond trees affected by stem pitting. [ABSTRACT FROM AUTHOR]

Field surveys were carried out in the main stone fruit-growing areas of Syria to evaluate the sanitary status of mother blocks, varietal collections and commercial orchards. The presence of vires and vires-like diseases was checked by enzyme-linked immunosorbent assay (ELISA), sap transmission to herbaceous hosts, testing on the woody indicators Prunus persica cv. GF 305 and Prunus serrulata cv. Kwanzan and dot-blot hybridization tests. A total of 1337 samples was tested by ELISA (444 apricot, 283 peach, 246 cherry, 222 almond and 142 plum). The overall mean infection rate was 13%, and the percentage infection level of single species was: peach 24%, cherry 16%, almond 13.5%, apricot 6%, plum 5%. The following viruses and viroids were detected: PNRSV, PDV, ACLSV, PPV, ApMV, PLMVd and HSVd¹. [ABSTRACT FROM AUTHOR]

Studies viruses and virus diseases of grapevine in Palestine. Symptoms observed in grapevines; Field surveys conducted.

When the first foci of sharka were discovered in Puglia region (south-east Italy) in the late 1980s, the regional agricultural authorities launched a programme for Plum pox virus (PPV) monitoring and disease eradication. The infecting virus strain was identified as PPV-D. From 1989 to 1993, a strong eradication campaign was successfully carried out involving 13 plum and 2 apricot orchards with different levels of infection. During 1994–2000, besides plum, apricot and peach, monitoring was extended to sweet cherry. At that time, surveys and testing did not reveal any new PPV focus, but the eradication of infected trees continued in a couple of orchards. In 2001–05, particular attention was paid to peach, as devastating PPV-M outbreaks had developed in other areas of the country. A new PPV focus was found in apricot, caused by PPV-Rec, which was promptly eradicated. In the following two years, surveys in the once infected orchard and surrounding peach plantings did not detect any virus spread. The endeavour has taken 15 years making this PPV monitoring and eradication programme the longest in Italy. Its overall results indicate that the fruit tree industry in Puglia region can now be regarded as essentially PPV-free. [ABSTRACT FROM AUTHOR]

The advent of next generation sequencing (NGS) technologies has dramatically advanced our ability to comprehensively investigate diseases of unknown aetiology and expedited the entire process of virus discovery, identification, viral genome sequencing and, subsequently, the development of routine assays for new viral pathogens. Unlike traditional techniques, these novel approaches require no preliminary knowledge of the suspected virus(es). Currently, the RNA-Seq approach is widely used to identify new viruses in infected plants, by analyzing virus-derived small interfering RNA populations, or single- and double-stranded RNA (dsRNA) molecules extracted from infected plants. The method generates sequence in an unbiased fashion, thus allowing the detection of all viruses that are present in a sample. We applied the Illumina NGS, coupled with metagenomic analysis, to generate large sequence dataset in different woody crops affected by diseases of unknown origin or infected with uncharacterized viruses or new virus strains. This approach has allowed the identification of five novel viral species and the sequencing of the whole genome of several viruses and viroids infecting Citrus spp., Prunus spp., grapevines, fig, hazelnut, olive, persimmon and mulberry. Combined analysis of the datasets generated by using either siRNA fractions or dsRNA templates, favoured the characterization of the whole virus-derived sequences in infected tissues. Furthermore, profiling small RNAs from virus-infected plants led to a better understanding of host-plant response to virus and viroid infections in perennial plants. A general bioinformatic pipeline and an experimental validation strategy were developed. [ABSTRACT FROM AUTHOR]