Identification and characterization of citrus yellow vein clearing virus, a putative new member of the genus Mandarivirus.

Molecular features and genomic organization were determined for Citrus yellow vein clearing virus (CYVCV), the putative viral causal agent of yellow vein clearing disease of lemon trees, reported in Pakistan, India, and more recently in Turkey and China. CYVCV isolate Y1 from Adana, Turkey, was used for deep sequencing analysis of the virus-induced small RNA fractions and for mechanical and graft inoculation of herbaceous and citrus indicator plants. A polyclonal antiserum was developed from CYVCV-Y1 purified from Phaseolus vulgaris and used in western blot assays to characterize the coat protein of CYVCV-Y1 and determine its serological relationship with related viruses. Contigs assembled from the Illumina sequenced short reads were used to construct the whole genome of Citrus yellow vein clearing virus (CYVCV), consisting in a positive-sense RNA of 7,529 nucleotides and containing six predicted open reading frames. The CYVCV genome organization and size resembled that of flexiviruses, and search for sequence homologies revealed that Indian citrus ringspot virus (ICRSV) (Mandarivirus, Alphaflexiviridae) is the most closely related virus. However, CYVCV had an overall nucleotide sequence identity of ≈74% with ICRSV. Although the two viruses were similar with regard to genome organization, viral particles, and herbaceous host range, CYVCV caused different symptoms in citrus and was serologically distinct from ICRSV. Primer pairs were designed and used to detect the virus by conventional and quantitative reverse transcription-polymerase chain reaction on yellow vein clearing symptomatic field trees as well as graft- and mechanically inoculated host plants. Collectively, these data suggest that CYVCV is the causal agent of yellow vein clearing disease and represents a new species in the genus Mandarivirus.

Calculation of diagnostic parameters of advanced serological and molecular tissue-print methods for detection of Citrus tristeza virus: a model for other plant pathogens.

Citrus tristeza virus (CTV) is one of the most important virus diseases that affect citrus. Control of CTV is achieved by grafting selected virus-free citrus scions onto CTV-tolerant or -resistant rootstocks. Quarantine and certification programs are essential for avoiding the entry and propagation of severe strains of CTV. Citrus nurseries in Spain and central California (United States) maintain zero-tolerance policies for CTV that require sensitive, specific, and reliable pathogen-detection methods. Tissue-print (TP) real-time reverse-transcriptase polymerase chain reaction (RT-PCR) assay was compared with the validated TP enzyme-linked immunosorbent assay (ELISA), using the CTV-specific monoclonal antibodies 3DF1 and 3CA5, for CTV detection. In total, 1,395 samples from healthy and CTV-infected nursery and mature tree plants were analyzed with both methods. The total agreement between both detection methods was substantial (Cohen's kappa index of 0.77 ± 0.03). The diagnostic parameters of each technique (i.e., the sensitivity, specificity, and likelihood ratios) were evaluated in a second test involving 658 Citrus macrophylla nursery plants. Mexican lime indexing was used to evaluate samples with discrepant results in the analysis. For TP-ELISA, a sensitivity of 0.8015, a specificity of 0.9963, and a positive and negative likelihood ratio of 216.42 and 0.199, respectively, were estimated. For TP real-time RT-PCR, a sensitivity of 0.9820, a specificity of 0.8519, and a positive and negative likelihood ratio of 6.63 and 0.021, respectively, were estimated. These diagnostic parameters show that TP real-time RT-PCR was the most sensitive technique, whereas TP-ELISA showed the highest specificity, validating the use of the molecular technique for routine CTV-detection purposes. In addition, our results show that the combination of both techniques can accurately substitute for the conventional biological Mexican lime index for the detection of CTV. The calculation of diagnostic parameters is discussed, as a necessary tool, to validate detection or diagnostic methods in plant pathology. Furthermore, assessment of the post-test probability of disease after a diagnostic result and CTV prevalence allows selection of the best method for accurate and reliable diagnosis.

Rapid differentiation and identification of potential severe strains of Citrus tristeza virus by real-time reverse transcription-polymerase chain reaction assays.

A multiplex Taqman-based real-time reverse transcription (RT) polymerase chain reaction (PCR) assay was developed to identify potential severe strains of Citrus tristeza virus (CTV) and separate genotypes that react with the monoclonal antibody MCA13. Three strain-specific probes were developed using intergene sequences between the major and minor coat protein genes (CPi) in a multiplex reaction. Probe CPi-VT3 was designed for VT and T3 genotypes; probe CPi-T36 for T36 genotypes; and probe CPi-T36-NS to identify isolates in an outgroup clade of T36-like genotypes mild in California. Total nucleic acids extracted by chromatography on silica particles, sodium dodecyl sulfate-potassium acetate, and CTV virion immunocapture all yielded high quality templates for real-time PCR detection of CTV. These assays successfully differentiated CTV isolates from California, Florida, and a large panel of CTV isolates from an international collection maintained in Beltsville, MD. The utility of the assay was validated using field isolates collected in California and Florida.

First Report of 'Candidatus Liberibacter asiaticus' Associated with Huanglongbing in Sweet Orange in Ethiopia.

Huanglongbing (HLB) is a serious disease of citrus worldwide. Three different 'Candidatus Liberibacter' species are associated with HLB: 'Ca. Liberibacter asiaticus', 'Ca. L. africanus', and 'Ca. L. americanus' (1). 'Ca. L. africanus' and its vector, Trioza erytreae, are both heat sensitive, and when present, occur in citrus when temperatures remain below 30 to 32°C. In Africa, 'Ca. L. africanus' and T. erytreae have been reported in South Africa, Zimbabwe, Malawi, Burundi, Kenya, Somalia, Ethiopia, Cameroon, and Madagascar (1). Inspection of citrus trees in orchards and budwood sources in nurseries located in the warmer citrus-growing areas of Tigray and North Wollo in northern Ethiopia revealed nearly 100 trees with symptoms of leaf yellowing with a blotchy mottle pattern, dead branches, and decreased fruit quality and yield. Two symptomatic sweet orange budwood trees and three symptomatic orchard plants were sampled in April 2009, along with three healthy-looking sweet orange plants. DNA was extracted from 200 mg of desiccated leaf midribs using the CTAB method (4) and subjected to conventional PCR using the primer pairs A2/J5 (2) and OI2/23S1 (3) that amplify the ribosomal protein gene in the rplKAJL-rpoBC operon and the 16S/23S ribosomal intergenic regions, respectively, of 'Ca. L. africanus' and 'Ca. L. asiaticus'. Positive PCR reactions were obtained for all five symptomatic samples with both primer pairs. PCR amplicons of 703 bp (A2/J5) and 892 bp (OI2/23S) recovered from two of these samples were purified, cloned, and sequenced. BLAST analysis revealed that the nucleotide sequences we obtained for the ribosomal protein (GenBank Accessions Nos. GQ890155 and GQ890156) shared 100% identity with each other and 99% identity with sequences of 'Ca. L. asiaticus' from Brazil (DQ471904), Indonesia (AB480161), China (DQ157277), and Florida (CP001677). Similarly, the 16S/23S ribosomal intergenic sequences (GU296538 and GU296539) shared 100% identity with each other and 99% identity with homologous 'Ca. L. asiaticus' sequences from Brazil (DQ471903), Indonesia (AB480102), China (DQ778016), and Florida (CP001677) and contained two tRNA genes as occurs in 'Ca. L. asiaticus' but not in 'Ca. L. africanus' (3). To our knowledge, this is the first report of 'Ca. L. asiaticus' in Africa. The presence of 'Ca. L. asiaticus' is a threat for warmer citrus-growing areas of Africa that are less favorable for 'Ca. L. africanus' and T. erytreae. In areas where 'Ca. L. asiaticus' was confirmed, symptomatic trees must be promptly eradicated and surveys to determine spread of the disease and its vectors are necessary. References: (1) J. M. Bove. J. Plant Pathol. 88:7, 2006. (2) A. Hocquellet et al. Mol. Cell. Probes 13:373, 1999. (3) S. Jagoueix et al. Int. J. Syst. Bacteriol. 47:224, 1997. (4) M. G. Murray and W. F Thompson. Nucleic Acids Res. 8:4321, 1980.

Transmission of different isolates of Spiroplasma citri to carrot and citrus by Circulifer tenellus (Hemiptera: Cicadellidae).

Carrot purple leaf disease was first reported in 2006 in the state of Washington and was associated with Spiroplasma citri. The disease also was reported in California in 2008. The objectives of this work were to fulfill Koch's postulates and to determine 1) whether the beet leafhopper, Circulifer tenellus (Baker) (Hemiptera: Cicadellidae), transmits carrot [Daucus carota L. subsp. Sativus (Hoffm.) Arcang] isolates of S. citri; and 2) whether carrot and citrus [Citrus sinensis (L.) Osb.]-derived spiroplasmas are pathogenic to both plant species. C. tenellus adults received a 24-h acquisition access period to a diet containing carrot-derived S. citri. After 30 d, insects were transferred to healthy carrot seedlings (five per plant). Negative controls were carrot and periwinkle [Catharanthus roseus (L.) G. Don] plants exposed to diet-only-fed insects, and positive controls were periwinkle plants exposed to insects fed on spiroplasma-supplemented diet. Purple carrot leaves and small, chlorotic periwinkle leaves were evident 10-45 d after exposure. Spiroplasmas were reisolated only from symptomatic plants, and polymerase chain reaction (PCR) confirmed their identity as S. citri. No symptoms occurred, and no spiroplasma-specific PCR amplifications or spiroplasma cultures were obtained from plants exposed to diet only-fed insects. Carrot-derived S. citri was transmitted to 15 and 50% of carrot and periwinkle plants exposed, respectively. Insects exposed to S. citri isolates from carrot or citrus transmitted the pathogen to both their host of origin and to the other plant host (carrot or citrus), showing no isolate-host specificity. Our findings confirm that carrot is a host of S. citri. Although carrot is not a preferred host of C. tenellus, it is likely that inoculative leafhoppers feed on carrot during seasonal migration.

Genetic diversity of Spiroplasma citri strains from different regions, hosts, and isolation dates.

Spiroplasma citri, a phloem-limited pathogen, causes citrus stubborn disease (CSD). Losses due to CSD in California orchards have grown over the past decade. To investigate the possibility of introduction or emergence of a new strain, a study of genetic diversity among S. citri strains from various locations was conducted using random amplified polymorphism DNA-polymerase chain reaction (RAPD-PCR) of 35 strains cultured from 1980 to 1993, and of 35 strains cultured from 2005 to 2006. Analysis using 20 primer pairs revealed considerable diversity among strains. However, no unique genetic signatures were associated with recently collected strains compared with those collected 15 to 28 years ago, and no geographically associated pattern was distinguishable. S. citri strains from carrot and daikon radish contain some unique DNA fragments, suggesting some host plant influence. Multiple strains from single trees also showed genetic diversity. Sequencing of five RAPD bands that differed among strains showed that diversity-related gene sequences include virus fragments, and fragments potentially encoding a membrane lipoprotein, a DNA modification enzyme, and a mobilization element. No differences in colony morphology were observed among the strains. The lack of correlation between PCR patterns and isolation date or collection site is inconsistent with the hypothesis that recent infections are due to the introduction or emergence of novel pathogen strains.

Incidence, Transmissibility, and Genotype Analysis of Citrus tristeza virus (CTV) Isolates from CTV Eradicative and Noneradicative Districts in Central California.

Growers in 45% (44,100 ha) of the citrus acreage in California stopped eradicating Citrus tristeza virus (CTV)-infected trees from their fields in 1995-96. The impact of leaving infected trees on the rate of CTV spread was determined by comparing temporal incidence of CTV in plots in Strathmore, Tulare County without eradication with incidence in a plot in McFarland, Kern County with eradication. From 1997 to 2003, CTV incidence in the Strathmore plots ranged from 6 to 42%, with annual spread rates from 1.6 to 3.6%. CTV incidence in the McFarland plot increased from 0 to 5% between 2001 and 2003 before infected trees were removed. Using a subplot hierarchical bulk sampling method, virus incidence over a 3-year period in a 6.5 km2 area near McFarland was estimated to range from 0.09 to 0.69%, which indicated that CTV suppression was still being achieved in this area. Vector tests using the cotton aphid, Aphis gossypii, identified highly transmissible isolates (30 to 61% transmission rate) and a larger proportion of highly transmissible isolates were found in the McFarland plots. Thirty-six CTV isolates from recently infected plot trees were obtained and analyzed. None of these isolates reacted with monoclonal antibody MCA13 that detects presumptive CTV severe strains. Molecular analysis using polymerase chain reaction and sequence-specific primers showed that all isolates had a genotype identical to the T30 mild isolate from Florida.

Reverse-Transcription Polymerase Chain Reaction Detection of Citrus Tristeza Virus in Aphids.

A rapid and simple reverse-transcription polymerase chain reaction (RT-PCR) method was developed for the detection of citrus tristeza virus (CTV) in three aphid species. Seven CTV isolates from a worldwide isolate collection were used for aphid acquisition feeding by three aphid species. These included the most efficient CTV vector, the brown citrus aphid, Toxoptera citricida; the melon aphid, Aphis gossypii; and the green peach aphid, Myzus persicae, a non-vector for CTV. A short procedure for nucleic acid extraction from single or groups of aphids was developed. Nucleic acid extracts from 1, 3, 5, and 10 aphids with acquisition-access periods of 24 and 48 h were reverse transcribed and amplified using primers for the coat protein gene of the Florida B3 (T-36) isolate of CTV. PCR-amplified fragments of approximately 670 bp were obtained from all the isolates tested and the amplified product from the aphids fed on citrus infected with isolate B3 was confirmed as the CTV coat protein gene by digesting with various restriction enzymes. This technique will be useful in investigations of CTV-vector-plant interactions and CTV epidemiology.