Identification and Characterization of Citrus Chlorotic Spot Virus, a New Dichorhavirus Associated with Citrus Leprosis-Like Symptoms.

Local chlorotic spots resembling early lesions characteristic of citrus leprosis (CL) were observed in leaves of two sweet orange (Citrus sinensis L.) trees in Teresina, State of Piauí, Brazil, in early 2017. However, despite the similarities, these spots were generally larger than those of a typical CL and showed rare or no necrosis symptoms. In symptomatic tissues, transmission electron microscopy revealed the presence of viroplasms in the nuclei of the infected parenchymal cells and rod-shaped particles with an average size of approximately 40 × 100 nm, resembling those typically observed during infection by dichorhaviruses. A bipartite genome of the putative novel virus, tentatively named citrus chlorotic spot virus (CiCSV) (RNA1 = 6,518 nucleotides [nt] and RNA2 = 5,987 nt), revealed the highest nucleotide sequence identity values with the dichorhaviruses coffee ringspot virus strain Lavras (73.8%), citrus leprosis virus N strain Ibi1 (58.6%), and orchid fleck virus strain So (56.9%). In addition to citrus, CiCSV was also found in local chlorotic lesions on leaves of the ornamental plant beach hibiscus (Talipariti tiliaceum (L.) Fryxell). Morphological characterization of mites recovered from the infected plants revealed at least two different types of Brevipalpus. One of them corresponds to Brevipalpus yothersi. The other is slightly different from B. yothersi mites but comprises traits that possibly place it as another species. A mix of the two mite types collected on beach hibiscus successfully transmitted CiCSV to arabidopsis plants but additional work is required to verify whether both types of flat mite may act as viral vectors. The current study reveals a newly described dichorhavirus associated with a citrus disease in the northeastern region of Brazil.

Diversity and Genetic Variation among Brevipalpus Populations from Brazil and Mexico.

Brevipalpus phoenicis s.l. is an economically important vector of the Citrus leprosis virus-C (CiLV-C), one of the most severe diseases attacking citrus orchards worldwide. Effective control strategies for this mite should be designed based on basic information including its population structure, and particularly the factors that influence its dynamics. We sampled sweet orange orchards extensively in eight locations in Brazil and 12 in Mexico. Population genetic structure and genetic variation between both countries, among locations and among sampling sites within locations were evaluated by analysing nucleotide sequence data from fragments of the mitochondrial cytochrome oxidase subunit I (COI). In both countries, B. yothersi was the most common species and was found in almost all locations. Individuals from B. papayensis were found in two locations in Brazil. Brevipalpus yothersi populations collected in Brazil were more genetically diverse (14 haplotypes) than Mexican populations (four haplotypes). Although geographical origin had a low but significant effect (ca. 25%) on the population structure, the greatest effect was from the within location comparison (37.02 %). Potential factors driving our results were discussed.

Common Bean: Experimental Indicator Plant for Citrus leprosis virus C and Some Other Cytoplasmic-Type Brevipalpus-Transmitted Viruses.

Citrus leprosis (CL) caused by Citrus leprosis virus C (CiLV-C) is present in Latin America from Mexico to Argentina, where citrus plants are grown. CiLV-C is transmitted by the tenuipalpid mite, Brevipalpus phoenicis, causing localized lesions on citrus leaves, fruit, and stems. One limitation to study of the virus-vector-host relationship in this pathosystem is the lack of a suitable assay plant. On Citrus spp. used as susceptible hosts, symptoms may take weeks or months to appear after experimental inoculation by viruliferous mites. Common bean (Phaseolus vulgaris) was found to respond with localized necrotic lesions after inoculation with viruliferous B. phoenicis in 5 days. Thus far, 113 tested common bean varieties and lines and some recent accessions of varied genetic background behaved in a similar way. Black bean 'IAC Una' was adopted as a standard test variety. When inoculated leaves were left at 28 to 30°C, the period for the lesion appearance was reduced to only 2 days. Confirmation that the lesions on common bean leaves are caused by CiLV-C were made by transmission electron microscopy, immunofluorescence, enzyme-linked immunosorbent assay, and reverse-transcription polymerase chain reaction specific for CiLV-C. Common bean plants mite-inoculated with some other cytoplasmic-type Brevipalpus-transmitted viruses (BrTVs) (Passion fruit green spot virus, Solanum violaefolium ringspot virus, Ligustrum ringspot virus, and Hibiscus green spot virus) also responded with necrotic local lesions and may serve as test plants for these viruses. Two nuclear types of BrTV (Coffee ringspot virus and Clerodendrum chlorotic spot virus) were unable to produce symptoms on common bean.

Transmission of Citrus leprosis virus C by Brevipalpus phoenicis (Geijskes) to Alternative Host Plants Found in Citrus Orchards.

The equivalent of US$75 million is spent each year in Brazil to control Brevipalpus phoenicis, a mite vector of Citrus leprosis virus C (CiLV-C). In this study, we investigated the possibility that hedgerows and windbreaks normally found in citrus orchards could host CiLV-C. Mites confined by an adhesive barrier were reared on sweet orange fruit with leprosis symptoms then were transferred to leaves of Hibiscus rosa-sinensis, Malvaviscus arboreus, Grevilea robusta, Bixa orellana, and Citrus sinensis. Ninety days post infestation, the descendant mites were transferred to Pera sweet orange plants to verify the transmissibility of the virus back to citrus. Nonviruliferous mites which had no feeding access to diseased tissue were used as controls. Local chlorotic or necrotic spots and ringspots, symptoms of leprosis disease, appeared in most plants tested. Results generated by reversetranscription polymerase chain reaction with primers specific for CiLV-C and by electron microscope analyses confirmed the susceptibility of these plants to CiLV-C.

Citrus leprosis virus C Naturally Infecting Commelina benghalensis, a Prevalent Monocot Weed of Citrus Orchards in Brazil.

There are two bacilliform, rhabdo-like viruses that cause citrus leprosis: Citrus leprosis virus C (CiLV-C), which accumulates in the cytoplasm of infected cells, and Citrus leprosis virus nuclear type (CiLV-N), which accumulates in their nucleus. The first one, the prototype of the new genus Cilevirus, is prevalent and occurs in several countries of the American continent, from Argentina to Mexico (1). The second type, still a tentative member of the Rhabdoviridae family, is of rare occurrence, with a few reports in Brazil and one in Panama (1). Leprosis is particularly important to the Brazilian citrus industry because of the 60 to 80 million dollars spent yearly for the control of Brevipalpus phoenicis (Geijskes, 1939) (Acari: Tenuipalpidae), the vector of the virus (1). For decades, the disease was considered unique to citrus plants; however, greenhouse experiments conducted in the 1990s demonstrated the mechanical transmission of CiLV-C to noncitrus plants (1). Years later, researchers were able to transmit the virus to nonrutaceous hosts using viruliferous mites (1,4). Recently, León et al. (2) reported the occurrence of the first noncitrus plant naturally infected by CiLV-C, the rutaceous Swinglea glutinosa Blanco (Merr.). Tropical spiderworts (Commelina benghalensis L.; Commelinaceae) are monocot weeds commonly found in citrus orchards in Brazil. In a survey conducted in orchards with high incidences of leprosis in the municipalities of Borborema and São José do Rio Preto, State of Sao Paulo, Brazil, tropical spiderworts were found exhibiting necrotic spots with a yellow halo in green leaves and green spots with necrotic center in senescent leaves. Since these symptoms are similar to those caused by CiLV-C in citrus, symptomatic plants were collected and subjected to transmission electron microscopy analyses and reverse transcription-PCR using primers that specifically amplify a region within the putative movement protein gene of the virus (3). Bacilliform virus particles and typical inclusions were seen in the lesions. Bands of the expected 344 bp size were seen in agarose gels of symptomatic samples only. The analysis of the consensus sequence showed 100% identity with CiLV-C sequence available in the GenBank (Accession No. YP_654542.1). Experimental transmission of CiLV-C by B. phoenicis reproduced the lesions in inoculated tropical spiderwort. Also, the virus could be easily transmitted back from C. benghalensis to sweet orange plants. Our data show that this widespread weed is the first monocot as a natural host for CiLV-C. Since tropical spiderwort is a host for B. phoenicis and symptomatic plants were found in two municipalities 130 km apart from each other, it is possible that this weed may serve as reservoir for the virus and play a relevant role in the spread of the disease in the field, but this issue still needs to be addressed in further experiments. References: (1) M. A. Bastianel et al. Plant Dis. 94:284, 2010. (2) M. G. A. Leon et al. Plant Dis. 90:682, 2008. (3) E. C. Locali-Fabris et al. Plant Dis. 87:1317. (4) M. A. Nunes et al. Plant Dis. Online publication. doi:10.1094/PDIS-06-11-0538, 2011.

Detection of Brevipalpus-transmitted viruses in their mite vectors by RT-PCR.

The diagnosis of plant diseases caused by Brevipalpus-transmitted viruses (BrTVs) has been done through the analyses of symptoms, transmission electron microscopy, and RT-PCR of infected plant tissues. Here, we report the detection of Citrus leprosis virus C, Orchid fleck virus, Clerodendrum chlorotic spot virus and Solanum violaefolium ringspot virus in their viruliferous vectors Brevipalpus spp. using specific primer pairs for each of the viruses. The efficiency of virus transmission by Brevipalpus mites is low, so the detection of these pathogens in their vectors could constitute an important tool for studies involving virus-vector relationships, transmission, and monitoring the pathogen prior to the appearance of symptoms in the field.

Evaluation of the genetic variability of orchid fleck virus by single-strand conformational polymorphism analysis and nucleotide sequencing of a fragment from the nucleocapsid gene.

The variability of a fragment of the nucleocapsid gene of orchid fleck virus (OFV) was investigated by single-strand conformational polymorphism (SSCP) analysis and nucleotide sequencing. Forty-eight samples of 18 genera of orchids were collected from Brazil, Costa Rica and Australia. The SSCP analysis yielded six different band patterns, and phylogenetic analysis based on the nucleotide fragment sequence obtained in this work and six available in GenBank showed two different groups, one with isolates 023Germany and So-Japan, and other with the rest of the isolates. None of the analyses showed geographic correlation among the Brazilian strains. The data obtained in this study showed a low genetic variation in this region of the genome; the d(N)/d(S) ratio of 0.251-0.405 demonstrated a negative selective pressure that maintains the stability of the analyzed fragments.

Natural Infection of Swinglea glutinosa by the Citrus leprosis virus Cytoplasmic Type (CiLV-C) in Colombia.

Swinglea glutinosa (Blanco) Merr., a perennial plant in the family Rutaceae, is originally from southeast Asia but which is now grown worldwide. In Colombia, it is used as an ornamental and principally as a living fence around rural properties and farms in several regions of the country. Citrus leprosis virus cytoplasmic type (CiLV-C) was recently detected in orange groves of the Colombian Piedmont eastern plains, an area known as the Llanos Orientales (2). Because of the potential for country-wide infection of citrus, some measures are being taken to avoid CiLV-C spread to other regions of Colombia. Further surveys made from June to December 2005 to evaluate the extent of the spread of CiLV-C in the Llanos Orientales revealed some plants in S. glutinosa hedges surrounding citrus orchards exhibiting chlorotic spots and ringspots of varied size on the leaves, similar to those caused by CiLV-C on sweet oranges leaves. These plants were found near citrus orchards in the municipalities of Guamal and in some urban areas of Villavicencio City in the Meta Department. The possibility that these symptoms were caused by CiLV-C was investigated soon after sample collection by the same procedures as described previously for sweet orange (2). In the leaf lesions of S. glutinosa, typical bacilliform particles and dense cytoplasmic viroplasm were found with electron microscopy. Total RNA extracted from symptomatic leaves was subjected to reverse transcription-PCR (RT) using primers (Fwd. 5'GATACGGGACGCATAACA-3'/Rev. 5'-TTCTGGCTCAACATCTGG-3') that specifically amplify a region within the CiLV-C putative methyltransferase gene and this yielded a single fragment of the expected 402 bp (3). Analysis of the consensus sequence derived from 20 RT-PCR products (GenBank Accession No. EU689106) showed 96% nucleotide and 92% amino acid sequence identity to the sequence of a Brazilian CiLV-C isolate (GenBank Accession Nos. DQ352194.1 and YP_654565.1), respectively. Recently, published work described mite transmission of CiLV-C to some nonrutaceous plants (1), but to our knowledge, this is the first report of a nonCitrus rutaceous plant naturally infected by CiLV-C. Mites found in citrus orchards and previously identified as Brevipalpus phoenicis (Geijskes) (2), which are likely the most important vector of CiLV-C in citrus in Colombia, were observed feeding on healthy and symptomatic S. glutinosa, indicating that S. glutinosa is a host for B. phoenicis. Because the use of S. glutinosa as a living fence or hedge is a common practice in Colombia, CiLV-C-infected S. glutinosa plants may play a role in the epidemiology of leprosis in commercial citrus by serving as an inoculum source for this lethal virus. References: (1) M. Bastianel et al. Summa Phytopathol. 32:211, 2006. (2) G. A. León et al. Plant Dis. 90:682, 2006. (3) E. C. Locali et al. Plant Dis. 87:1317, 2003.

Complete nucleotide sequence, genomic organization and phylogenetic analysis of Citrus leprosis virus cytoplasmic type.

The complete nucleotide sequence of the genomic RNA 1 (8745 nt) and RNA 2 (4986 nt) of Citrus leprosis virus cytoplasmic type (CiLV-C) was determined using cloned cDNA. RNA 1 contains two open reading frames (ORFs), which correspond to 286 and 29 kDa proteins. The 286 kDa protein is a polyprotein putatively involved in virus replication, which contains four conserved domains: methyltransferase, protease, helicase and polymerase. RNA 2 contains four ORFs corresponding to 15, 61, 32 and 24 kDa proteins, respectively. The 32 kDa protein is apparently involved in cell-to-cell movement of the virus, but none of the other putative proteins exhibit any conserved domain. The 5' regions of the two genomic RNAs contain a 'cap' structure and poly(A) tails were identified in the 3'-terminals. Sequence analyses and searches for structural and non-structural protein similarities revealed conserved domains with members of the genera Furovirus, Bromovirus, Tobravirus and Tobamovirus, although phylogenetic analyses strongly suggest that CiLV-C is a member of a distinct, novel virus genus and family, and definitely demonstrate that it does not belong to the family Rhabdoviridae, as previously proposed. Based on these results it was proposed that Citrus leprosis virus be considered as the type member of a new genus of viruses, Cilevirus.

Occurrence of Citrus leprosis virus in Llanos Orientales, Colombia.

In Colombia, citrus is cultivated in mostly small plantings that total 55,000 ha by approximately 25,000 farmers. Production includes 1,200 tons of fresh fruits and 60 tons of juice for domestic consumption, resulting in a net worth of US$650,000 per year. Most of the production comes from areas located between the Cordillera Occidental and Cordillera Central mountain ranges (departments of Antioquia, Caldas, Quindio, and Risaralda) near coffee plantations. The departments of Meta and Casanare, located at the east plains (Llanos Orientales), include a zone parallel (4 to 5°N, 72 to 74°W) to the east mountain range and generate approximately 10% of the total Colombian citrus production. Suspected citrus leprosis symptoms on leaves and fruits of sweet oranges (Citrus sinensis (L.) Osb.) were first observed by plant pathologists for CORPOICA (Colombian National Agricultural Research Organization) in citrus orchards in Casanare in 2003, and later in 2004, in Meta. To confirm the visual identification, leaves and fruits from Valencia sweet orange exhibiting typical lesions of leprosis were collected from several locations in the departments of Casanare (Yopal, Aguazul) and Meta (Guamal, Villavicencio, and Cumaral). Samples were fixed in cacodylate-buffered paraformaldehyde/glutaraldehyde solution and subsequently processed for examination in thin sections using electron microscopy. Samples were processed and examined at the Citrus Research and Educational Center (CREC) of the University of Florida, Lake Alfred, and the Agricultural College (ESALQ) of the Universidade de São Paulo at Piracicaba, SP, Brazil. Some leaf samples collected in Meta were also dried and used for detection of Citrus leprosis virus, cytoplasmic type (CiLV-C) by reverse transcription-polymerase chain reaction (RT-PCR) at the Centro APTA Citros Sylvio Moreira at Cordeirópolis (CAPTACSM). The RT-PCR was performed with primers that specifically amplify a fragment of the viral genome that codes for the putative cell-to-cell movement protein (1). Locations at CREC and ESALQ each observed, using electron microscopy, cell changes characteristic of CiLV-C that include short bacilliform particles in the endoplasmic reticulum and dense, vacuolated, and irregularly shaped viroplasm in the cytoplasm (2) in samples from Casanare and Meta. RT-PCR amplified cDNA fragments of the expected size for samples collected in Meta and one of the amplicons was sequenced (GenBank Accession No. DQ272491). The sequence obtained was found to have 98% nucleotide sequence identity to the Brazilian CiLV-C isolate (GenBank Accession No. AY289190.1). Mites collected from affected plants from the department of Meta were identified at ESALQ as Brevipalpus phoenicis (Geijskes), a known principal vector of CiLV-C (2). These several lines of evidence confirmed that the symptoms observed in sweet oranges at Meta and Casanare are due to the infection by CiLV-C. To our knowledge, this is the first report of this virus in Colombia. References:(1) E. C. Locali et al. Plant Dis. 87:1317, 2003, (2) J. C. V. Rodrigues et al. Exp. Appl. Acarol. 30:161, 2003.

Transmissibility of Citrus leprosis virus by Brevipalpus phoenicis to Solanum violaefolium.

Citrus leprosis virus (CiLV) constitutes one of the most important viruses in citrus in the areas where it occurs. Two morphological types of virus particles have been described from associated leprosis symptoms, nuclear (CiLV-N) and cytoplasmic (CiLV-C) (4). The CiLV-C is more common, representing more than 99% of samples collected from South and Central America (E. W. Kitajima and J. C. V. Rodrigues, unpublished). Both virus types are associated with the mite vector, Brevipalpus phoenicis (Geijskes) (Acari: Tenuipalpidae). So far, CiLV-C has only been naturally transmitted by these mites to citrus (3). Plants of Solanum violaefolium Schott (Solanaceae) and ornamental and sweet orange seedlings were infested with viruliferous adult female mites, colony no. 61 (GenBank Accession No. AY320027) that were previously maintained on citrus seedlings infected with CiLV-C according to Rodrigues et al. (3). Fifteen days after the mites were transferred, spotted yellowish symptoms were observed on leaves of plants of S. violaefolium and similar symptoms were observed after 25 days on citrus leaves. The symptomatic tissues were studied using transmission electron microscopy. Particles typical of CiLV-C were observed in samples from both plant species. To our knowledge, this is the first reported case of mites transmitting CiLV-C to a noncitrus host. Subsequent experiments showed that mites were able to transmit the virus between plants of S. violaefolium. Attempts to transmit the virus by mites from S. violaefolium to citrus were unsuccessful. The dsRNA viral electrophoresis profile showed differences between the two host plants. Reverse transcription-polymerase chain reaction (RT-PCR) and sequencing assays with primers designed to detect CiLV-C (2) amplified DNA fragments of the expected size and base composition. These data suggest the loss or alteration of some viral components from the Solanum sp. host that might be essential for the transmission or infection in citrus. Such a mechanism may explain why, despite the ever-increasing number of Brevipalpus-transmitted viruses in a large number of different host plant species (1), cross transmission is not common. This information shows one of the potential routes for CiLV to invade citrus orchards, and suggests one alternative host plant that allows rapid multiplication of the virus for characterization. References: (1) E. W. Kitajima et al. Exp. Appl. Acarol. 30:135, 2003. (2) E. C. Locali et al. Plant Dis. 87:1317, 2003. (3) J. C. V. Rodrigues et al. Proc. Int. Org. Citrus Virol. 174, 2000 (4) J. C. V. Rodrigues et al. Exp. Appl. Acarol. 30:161, 2003.

First Report of Citrus leprosis virus on Citrus in Santa Cruz, Bolivia.

The citrus crop is rapidly expanding in the Province of Santa Cruz de la Sierra, Bolívia. Citrus, mostly planted by small growers, currently comprises approximately 15,000 ha. Sweet oranges (Citrus sinensis) and mandarins (C. reticulate) are the main citrus-types grown primarily for internal consumption. Recently, there has been an increase in incidence of leprosis-like symptoms (round to elliptic lesions on the leaves, chlorotic to necrotic lesions in young twigs, and depressed small lesions on the fruits). These symptoms were associated with infestations by the tenuipalpid mite Brevipalpus sp. To verify if Citrus leprosis virus was the causal agent of the observed symptoms, leaf and fruit samples (mostly from Valencia sweet orange) were collected from commercial groves in El Torno, 32 km south of Santa Cruz, and Yapacani and Colónia San Juan, 130 km northwest of Santa Cruz. Small fragments of these samples were placed immediately in a mixture of glutaraldehyde and paraformaldehyde in cacodylate buffer and later processed with transmission electron microscopy at ESALQ, Piracicaba, SP, Brazil. Some of the leaf samples were dried at 35°C and used for reverse transcription-polymerase chain reaction (RT-PCR) with primers that specifically amplify portions of the genome of Citrus leprosis virus, cytoplasmic type (CiLV-C) (1) at Centro APTA Citros, Cordeirópolis, SP, Brazil. Brevipalpus sp. mites were also collected and kept in 90% ethanol for further identification at the University of Florida, Gainesville and ESALQ. In the samples from the three surveyed areas, transmission electron microscopy confirmed the presence of short bacilliform particles within endoplasmic reticulum cisternae and electron dense viroplasms in the cytoplasm, typical of infection by CiLV-C (2). CiLV-C specific primers amplified DNA fragments of expected sizes in RT-PCR from dried leaf samples that came from these three localities. Direct sequencing of at least three amplicons of each sample confirmed the identity of the virus. The consensus sequence of the putative movement protein gene in samples from Yapacani and Colónia San Juan (GenBank Accessions Nos. AY960216 and AY960215, respectively) were identical and exhibited 99% nucleotide and 98% amino acid homology with the Brazilian isolate sequence available at GenBank (Accession No. AY289190). The consensus sequence of the putative replicase gene found in the sample from El Torno (GenBank Accession No. AY960214) exhibited 96 and 93% nucleotide and amino acid homology, respectively with the Brazilian isolate (GenBank Accession No. AY289191). Sampled mites were identified as B. phoenicis (Geijskes), the known vector of CiLV-C (2). The symptomatology, particle morphology and cytopathology, detection by molecular methods and the association with infestation by B. phoenicis, together indicate that the foliar, stem, and fruit lesions in sweet orange observed in the Santa Cruz region were caused by CiLV-C. To our knowledge, this is the first report of this virus in Bolivia. References: (1) E. C. Locali et al. Plant Dis. 87:1317, 2003. (2) J. C. V. Rodrigues et al. Exp. Appl. Acarol. 30:161, 2003.

Serological Studies Using Polyclonal Antisera Prepared Against the Viral Coat Protein of Four Begomoviruses Expressed in Escherichia coli.

Polyclonal rabbit antisera were produced to the coat protein of Bean golden mosaic virus Brazil isolate (BGMV), Cabbage leaf curl virus (CabLCV), Tomato yellow leaf curl virus (TYLCV), and Tomato mottle virus (ToMoV), all expressed in Escherichia coli by the pETh expression vector. The expressed coat protein of each virus was purified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis for use as an immunogen. The antisera to BGMV, CabLCV, TYLCV, and ToMoV reacted in indirect (plate-trapping) enzyme-linked immunosorbent assay (ELISA) with extracts from begomovirus-infected tissue. The antisera to BGMV, CabLCV, TYLCV, and ToMoV also reacted specifically with the test begomovirus antigens in leaf imprint blots and Western blots. The CabLCV and TYLCV antisera were used to detect Bean golden yellow mosaic virus antigens by immunogold labeling of thin sections of infected bean tissues. In tissue blot immunoassays, the TYLCV antiserum reacted well with TYLCV antigens but not with ToMoV antigens, while CabLCV antiserum reacted well with ToMoV antigens and weakly with TYLCV antigens. The results indicate that polyclonal antisera prepared to expressed begomovirus coat proteins were useful for the detection of begomoviruses in an array of assays.