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Espinoza-Lozano L, Sumba M, Cañada-Bautista MG, Quito-Avila DF. Occurrence, Distribution, and Population Structure of Schlumbergera Virus X in Dragon Fruit in Ecuador. Plant Dis 2024; 108:587-591. [PMID: 37743588 DOI: 10.1094/pdis-03-23-0445-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The occurrence of Schlumbergera virus X (SchVX) in commercial dragon fruit fields in three provinces of Ecuador has been identified in this study. The virus was found in symptomatic and asymptomatic cladodes of the two major species (Hylocereus undatus and H. megalanthus) cultivated in the country. Symptoms in H. undatus included irregular and ring-shaped chlorotic spots that coalesce into large chlorotic patches along the cladodes, whereas small chlorotic spot symptoms on the cladodes were observed in H. megalanthus. Phylogenetic inferences based on 27 partial nucleotide sequences of the RNA-dependent RNA polymerase (RdRp) and three whole genome comparisons showed that Ecuadorean isolates from H. undatus and H. megalanthus share a most recent ancestor with isolates from Spain and Portugal. In addition, an SchVX isolate with a distinct genomic lineage was found in symptomatic H. polyrhizus plants from a single location, suggesting two independent virus introductions into the country.
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Affiliation(s)
- Lisbeth Espinoza-Lozano
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Martha Sumba
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Maria G Cañada-Bautista
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Diego F Quito-Avila
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
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Muñoz V, Curillo D, Gómez S, Moreno-Peña L, Peña D, Chica E, Yánez V, Sánchez-Timm E, Quito-Avila DF. In Vitro-Based Production of Virus-Tested Babaco ( Vasconcellea x heilbornii, syn. Carica pentagona) in Ecuador: An Integrated Approach to an Endangered Crop. Plants (Basel) 2023; 12:2560. [PMID: 37447121 DOI: 10.3390/plants12132560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/09/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
Babaco (Vasconcellea x heilbornii), a fruit-bearing vegetatively propagated crop native to Ecuador, is appreciated for its distinctive flavor and nutritional properties. The aim of this research was to determine a functional protocol for tissue culture propagation of virus-free babaco plants including in vitro establishment, multiplication, rooting, and acclimation. First, symptomless babaco plants from a single commercial nursery were analyzed for virus detection and cared for using different disinfection treatments in the greenhouse to reduce contamination during the in vitro establishing step, and three cytokinins, 6-(γ,γ-Dimethylallylamino) purine (2IP), 6-Benzylaminopurine (BAP), and Thidiazuron (TDZ), were used to determine the best hormone for multiplication. The best treatment for plant disinfection was the weekly application of copper sulfate at the greenhouse and a laboratory disinfection using ethanol (EtOH) (70%), Clorox (2%), and a solution of povidone iodine (2.5%), with an 80% survival during in vitro plant establishment. TDZ showed a better multiplication rate when compared with other hormones, and 70% of the rooted plants were successfully acclimated at the greenhouse. Generated plants were virus-free when tested against babaco mosaic virus (BabMV) and papaya ringspot virus (PRSV), two of the most important viruses that can affect babaco. An efficient protocol to produce virus-free babaco plants was elaborated with an integrated use of viral diagnostic tools to ensure the production of healthy start material to farmers.
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Affiliation(s)
- Valeria Muñoz
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090101, Ecuador
| | - Diana Curillo
- Facultad de Ciencias Agrícolas, Universidad de Cuenca, Campus Yanuncay, Av. October 12 and Diego de Tapia, Cuenca 010107, Ecuador
| | - Sebastián Gómez
- Facultad de Ingeniería y Ciencias Aplicadas, Carrera de Ingeniería en Agroindustrias, Universidad de las Américas, Campus UDLAPARK, Quito 170503, Ecuador
| | - Lissette Moreno-Peña
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090101, Ecuador
| | - Denisse Peña
- Facultad de Ciencias Agrícolas, Universidad de Cuenca, Campus Yanuncay, Av. October 12 and Diego de Tapia, Cuenca 010107, Ecuador
| | - Eduardo Chica
- Facultad de Ciencias Agrícolas, Universidad de Cuenca, Campus Yanuncay, Av. October 12 and Diego de Tapia, Cuenca 010107, Ecuador
| | - Viviana Yánez
- Facultad de Ingeniería y Ciencias Aplicadas, Carrera de Ingeniería en Agroindustrias, Universidad de las Américas, Campus UDLAPARK, Quito 170503, Ecuador
| | - Eduardo Sánchez-Timm
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090101, Ecuador
- Facultad de Ciencias de la Vida, FCV, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090101, Ecuador
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090101, Ecuador
- Facultad de Ciencias de la Vida, FCV, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090101, Ecuador
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Reyes-Proaño EG, Cañada-Bautista MG, Cornejo-Franco JF, Alvarez-Quinto RA, Mollov D, Sanchez-Timm E, Quito-Avila DF. The Virome of Babaco ( Vasconcellea × heilbornii) Expands to Include New Members of the Rhabdoviridae and Bromoviridae. Viruses 2023; 15:1380. [PMID: 37376679 DOI: 10.3390/v15061380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Babaco (Vasconcellea × heilbornii) is a subtropical species in the Caricaceae family. The plant is native to Ecuador and represents an important crop for hundreds of families. The objective of this study was to characterize, at the genomic level, two new babaco viruses identified by high-throughput sequencing. The viruses, an ilarvirus and a nucleorhabdovirus, were found in a symptomatic babaco plant from a commercial nursery in the Azuay province of Ecuador. The tripartite genome of the new ilarvirus, provisionally named babaco ilarvirus 1 (BabIV-1), is related to subgroup 3 ilarviruses, including apple mosaic virus, apple necrotic mosaic virus, and prunus necrotic ringspot virus as the closest relatives. The genome of the nucleorhabdovirus, provisionally named babaco nucleorhabdovirus 1 (BabRV-1), showed the closest relation with joa yellow blotch-associated virus and potato yellow dwarf nucleorhabdovirus. Molecular-based detection methods found BabIV-1 and BabRV-1 in 21% and 36%, respectively, of plants surveyed in a commercial babaco nursery, highlighting the importance of enforcing virus testing and nursery certification programs for babaco.
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Affiliation(s)
- Edison G Reyes-Proaño
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
- Department of Entomology and Plant Pathology, University of Idaho, Moscow, ID 83843, USA
| | - Maria G Cañada-Bautista
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
| | - Juan F Cornejo-Franco
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, CIBE-ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
| | | | | | - Eduardo Sanchez-Timm
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, CIBE-ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
| | - Diego F Quito-Avila
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, CIBE-ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
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Quito-Avila DF, Reyes-Proaño E, Cañada G, Cornejo-Franco JF, Alvarez-Quinto R, Moreira L, Grinstead S, Mollov D, Karasev AV. Papaya Sticky Disease Caused by Virus "Couples": A Challenge for Disease Detection and Management. Plant Dis 2023:PDIS11222565FE. [PMID: 36572970 DOI: 10.1094/pdis-11-22-2565-fe] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Papaya sticky disease (PSD) is a major virus disorder of papaya (Carica papaya). The disease is characterized by fruit damage caused by the oxidation of spontaneously exuded latex. In Brazil, PSD is caused by the coinfection of two viruses, papaya meleira virus (PMeV), a toti-like virus, and papaya meleira virus-2 (PMeV-2), an umbra-like virus. The disorder has also been reported in Mexico and, more recently, in Australia, but the presence of both PMeV and PMeV-2 in symptomatic plants has been documented only in Brazil. In 2021, 2-year-old papaya plants (cultivar Passion Red) exhibiting PSD-like symptoms were observed in Santa Elena Province, Ecuador. Molecular tests of leaf tissue and fruit latex from symptomatic plants failed to detect PMeV. However, papaya virus Q (PpVQ), an umbra-like virus related to but distinct from PMeV-2, and a novel virus, tentatively named papaya sticky fruit-associated virus (PSFaV), were found in the symptomatic samples. PSFaV shares 56% nucleotide identity with the genome of PMeV, suggesting that PSD symptoms can be caused by "couples" of viruses related to but distinct from PMeV (a toti-like virus) and PMeV-2 (an umbra-like virus). This review discusses the history and epidemiology of PSD and the genomic features of newly discovered virus couples involved in this syndrome. Given the unusual etiology of PSD, which involves distinct virus species, the importance of implementing proper diagnostic approaches for PSD is highlighted.
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Affiliation(s)
- Diego F Quito-Avila
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Guayas, Ecuador
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Guayas, Ecuador
| | - Edison Reyes-Proaño
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Guayas, Ecuador
| | - Gabriela Cañada
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Guayas, Ecuador
| | - Juan F Cornejo-Franco
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Guayas, Ecuador
| | - Robert Alvarez-Quinto
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, U.S.A
| | - Lisela Moreira
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, UCR, San José, Costa Rica
- Escuela de Agronomía, Universidad de Costa Rica, UCR, San José, Costa Rica
| | - Sam Grinstead
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) National Germplasm Resources Laboratory, Beltsville, MD, U.S.A
| | - Dimitre Mollov
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, U.S.A
| | - Alexander V Karasev
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, U.S.A
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Reyes-Proaño E, Alvarez-Quinto R, Delgado-Jiménez JA, Cornejo-Franco JF, Mollov D, Bejerman N, Quito-Avila DF. Genome Characterization and Pathogenicity of Two New Hyptis pectinata Viruses Transmitted by Distinct Insect Vectors. Phytopathology 2022; 112:2440-2448. [PMID: 35694887 DOI: 10.1094/phyto-04-22-0130-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Two newly described viruses belonging to distinct families, Rhabdoviridae and Geminiviridae, were discovered co-infecting Hyptis pectinata from a tropical dry forest of Ecuador. The negative-sense RNA genome of the rhabdovirus, tentatively named Hyptis latent virus (HpLV), comprises 13,765 nucleotides with seven open reading frames separated by the conserved intergenic region 3'-AAUUAUUUUGAU-5'. Sequence analyses showed identities as high as 56% for the polymerase and 38% for the nucleocapsid to members of the genus Cytorhabdovirus. Efficient transmission of HpLV was mediated by the pea aphid (Acyrthosiphon pisum) in a persistent replicative manner. The single-stranded DNA genome of the virus tentatively named Hyptis golden mosaic virus (HpGMV) shared homology with members of the genus Begomovirus with bipartite genomes. The DNA-A component consists of 2,716 nucleotides (nt), whereas the DNA-B component contains 2,666 nt. Pairwise alignments using the complete genomic sequence of DNA-A of HpGMV and closest relatives showed identities below the cutoff (<91% shared nt) established by the ICTV as species demarcation, indicating that HpGMV should be classified in a distinct begomovirus species. Transmission experiments confirmed that the whitefly Bemisia tabaci Middle East-Asia Minor 1 (MEAM1) is a vector of HpGMV.
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Affiliation(s)
- Edison Reyes-Proaño
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Guayas, Ecuador
| | - Robert Alvarez-Quinto
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, U.S.A
| | - José A Delgado-Jiménez
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Guayas, Ecuador
| | - Juan F Cornejo-Franco
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Guayas, Ecuador
| | - Dimitre Mollov
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, U.S.A
| | - Nicolás Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, Córdoba X5020ICA, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Camino 60 Cuadras Km 5.5, Córdoba X5020ICA, Argentina
| | - Diego F Quito-Avila
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Guayas, Ecuador
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Guayas, Ecuador
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Quito-Avila DF, Reyes-Proaño EG, Mendoza A, Margaria P, Menzel W, Bera S, Simon AE. Two new umbravirus-like associated RNAs (ulaRNAs) discovered in maize and johnsongrass from Ecuador. Arch Virol 2022; 167:2093-2098. [PMID: 35821148 DOI: 10.1007/s00705-022-05525-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/22/2022] [Indexed: 11/02/2022]
Abstract
Two new umbravirus-like associated RNAs (ulaRNAs) were found, respectively, in maize and Johnsongrass samples from Ecuador. The complete sequences consist of 3,053 and 3,025 nucleotides, respectively, and contain four open reading frames (ORFs). Their genome sequences were 58% identical to each other and 28 to 60% identical to the most closely related viruses. Phylogenetic analysis using full genome sequences and amino acid sequence of the RNA-dependent-RNA polymerase (RdRp) placed both sequences in a clade sharing the most recent common ancestor with ulaRNAs from sugarcane and maize, suggesting that they belong to a monophyletic grass-infecting lineage. Their terminal regions exhibit features common to umbraviruses and ulaRNAs.
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Affiliation(s)
- Diego F Quito-Avila
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil, Ecuador. .,Centro de Investigaciones Biotecnológicas del Ecuador, CIBE, Escuela Superior Politécnica del Litoral, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil, Ecuador.
| | - Edison G Reyes-Proaño
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil, Ecuador
| | - Alma Mendoza
- INIAP, Estación Experimental Portoviejo, Km 12, Via a Santa Ana, Manabí, Ecuador
| | - Paolo Margaria
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, Braunschweig, Germany
| | - Wulf Menzel
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, Braunschweig, Germany
| | - Sayanta Bera
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD, 20742, USA
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD, 20742, USA
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Cornejo-Franco JF, Reyes-Proaño E, Mollov D, Mowery J, Quito-Avila DF. Transmission and Pathogenicity of Papaya Virus E: Insights from an Experimental Papaya Orchard. Plant Dis 2022; 106:685-690. [PMID: 34601954 DOI: 10.1094/pdis-08-21-1785-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A study was conducted to investigate epidemiological aspects of papaya virus E (PpVE), a cytorhabdovirus commonly found in papaya (Carica papaya L.) plantings in Ecuador. Besides papaya, PpVE was found in three Fabaceae weeds, including Rhynchosia minima, Centrosema plumieri, and Macroptilium lathyroides, the latter being the species with the highest virus prevalence. Greenhouse experiments showed that in M. lathyroides, single infections of PpVE induce only mild leaf mosaic, whereas in mixed infections with cowpea severe mosaic virus, PpVE contributes to severe mosaic. In papaya, PpVE did not induce noticeable symptoms in single or mixed infections with papaya ringspot virus. Transmission experiments confirmed that whiteflies (Bemisia tabaci) transmit PpVE in a semipersistent, nonpropagative manner.
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Affiliation(s)
- Juan F Cornejo-Franco
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, Guayaquil 090101, Guayas, Ecuador
| | - Edison Reyes-Proaño
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil 090101, Guayas, Ecuador
| | - Dimitre Mollov
- U.S. Department of Agriculture-Agricultural Research Center, Horticultural Crops Research Unit, Corvallis, OR 97331, U.S.A
| | - Joseph Mowery
- U.S. Department of Agriculture-Agricultural Research Center, Electron and Confocal Microscopy Unit, Beltsville, MD 20705, U.S.A
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, Guayaquil 090101, Guayas, Ecuador
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil 090101, Guayas, Ecuador
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Cornejo-Franco JF, Flores F, Mollov D, Quito-Avila DF. An umbra-related virus found in babaco (Vasconcellea × heilbornii). Arch Virol 2021; 166:2321-2324. [PMID: 34046760 DOI: 10.1007/s00705-021-05117-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/11/2021] [Indexed: 11/24/2022]
Abstract
The complete sequence of a new viral RNA from babaco (Vasconcellea × heilbornii) was determined. The genome consisted of 4,584 nucleotides, containing two open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5' terminus, and an unusually long (1,843 nt) NCR at the 3' terminus. The presence of a potential heptameric slippery signal located 12 nt upstream the stop codon of ORF 1 suggests a -1 ribosomal frameshift mechanism for the translation of ORF 2. Sequence comparisons of ORF 2 revealed similarity to the RNA-dependent RNA polymerase (RdRp) of several umbra- and umbra-like viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported in papaya, citrus, opuntia, maize, and sugarcane hosts. Viruses of this clade share a most recent ancestor with the umbraviruses but have different genomic features. The creation of a new genus within the family Tombusviridae is proposed for the classification of these novel viruses.
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Affiliation(s)
- Juan F Cornejo-Franco
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
| | - Francisco Flores
- Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador.,Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Dimitre Mollov
- National Germplasm Resources Laboratory, USDA-ARS, Beltsville, MD, USA
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador. .,Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador.
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Green KJ, Funke CN, Chojnacky J, Alvarez-Quinto RA, Ochoa JB, Quito-Avila DF, Karasev AV. Potato Virus Y (PVY) Isolates from Solanum betaceum Represent Three Novel Recombinants Within the PVY N Strain Group and Are Unable to Systemically Spread in Potato. Phytopathology 2020; 110:1588-1596. [PMID: 32370660 DOI: 10.1094/phyto-04-20-0111-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tamarillo, or tree tomato (Solanum betaceum), is a perennial small tree or shrub species cultivated in subtropical areas for fresh fruit and juice production. In Ecuador, tamarillo orchards are affected by several viruses, with one previously identified as potato virus Y (PVY); however, the specific strain composition of PVY in tamarillo was not determined. In 2015 and 2016, eight tamarillo plants exhibiting symptoms of leaf drop, mosaic, and mottled fruit were sampled near Tumbaco and Quito, Ecuador. These tamarillo PVY isolates were able to systemically infect tobacco, Nicotiana benthamiana, naranjilla, and tamarillo. Seven of the eight PVY isolates from tamarillo exhibited N-serotype, while one of the PVY isolates studied, Tam15, had no identifiable serotype. One isolate, Tam17, had N-serotype but produced asymptomatic systemic infection in tobacco. In tamarillo, four tamarillo isolates induced mosaic and slight growth retardation and were unable to systemically infect pepper or potato. Tamarillo, on the other hand, was unable to support systemic infection of PVY isolates belonging to the PVYO and PVYEu-N strains. The whole genomes of eight PVY isolates were sequenced from a series of overlapping RT-PCR fragments. Phylogenetically, tamarillo PVY isolates were found to belong to the large PVYN lineage, in a new tamarillo clade. Recombination analysis revealed that these tamarillo PVY isolates represent at least three novel recombinant types not reported before. The combination of the biological and molecular properties found in these eight PVY isolates suggested the existence of a new tamarillo strain of PVY that may have coevolved with S. betaceum.
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Affiliation(s)
| | | | | | - Robert A Alvarez-Quinto
- Centro de Investigaciones Biotecnologicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
| | - Jose B Ochoa
- Instituto Nacional Autónomo de Investigaciones Agropecuarias (INIAP), Quito, Ecuador
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnologicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
| | - Alexander V Karasev
- Department of EPPN, University of Idaho, Moscow, ID
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID
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Cornejo-Franco JF, Alvarez-Quinto RA, Grinstead S, Mollov D, Karasev AV, Ochoa J, Quito-Avila DF. A New Tymovirus Isolated From Solanum quitoense: Characterization and Prevalence in Two Solanaceous Crops in Ecuador. Plant Dis 2019; 103:2246-2251. [PMID: 31287777 DOI: 10.1094/pdis-01-19-0113-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Naranjilla (Solanum quitoense Lam.) and tamarillo (S. betaceum Cav.) are two important perennial solanaceous crops grown in Ecuador for the fresh market and juice production. Viruses infecting tamarillo and naranjilla are currently poorly studied, and no clean stock program exists in Ecuador. Here, we report a new virus, provisionally named as naranjilla mild mosaic virus (NarMMV) (genus Tymovirus, family Tymoviridae), isolated from naranjilla grown in an orchard in Pichincha Province, Ecuador. The complete genome of the virus consists of 6,348 nucleotides and encodes three open reading frames typical for members of the genus Tymovirus. Phylogenetically, Chiltepin yellow mosaic virus, Eggplant mosaic virus, and the recently characterized naranjilla chlorotic mosaic virus (NarCMV) were found to be the closest relatives of NarMMV. Unlike NarCMV, the new virus induced mild mosaic in naranjilla and more severe symptoms in tamarillo. Similar to NarCMV, NarMMV was unable to systemically infect potato. Virus surveys found NarMMV prevalent in naranjilla production areas of two provinces of Ecuador, especially where hybrid cultivars of naranjilla were cultivated. NarMMV was also found in field-grown tamarillo. The new virus cross-reacted with antibodies developed against NarCMV. Hence, this antibody will be useful for its field diagnosis using enzyme-linked immunosorbent assay or immunocapture reverse transcription polymerase chain reaction in future virus-free certification programs.
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Affiliation(s)
- Juan F Cornejo-Franco
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, Campus Gustavo Galindo, Guayaquil 090101, Ecuador
| | | | - Samuel Grinstead
- National Germplasm Resources Laboratory, U.S. Department of Agriculture Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Dimitre Mollov
- National Germplasm Resources Laboratory, U.S. Department of Agriculture Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Alexander V Karasev
- Department of Entomology and Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844-2329, U.S.A
| | - Jose Ochoa
- Instituto Nacional Autónomo de Investigaciones Agropecuarias, Quito 170101, Ecuador
- Facultad de Ciencias Agrícolas, Universidad Central del Ecuador, Quito 170101, Ecuador
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, Campus Gustavo Galindo, Guayaquil 090101, Ecuador
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Campus Gustavo Galindo, Guayaquil 090101, Ecuador
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Green KJ, Mollov D, Tran LT, Alvarez-Quinto RA, Ochoa JB, Quito-Avila DF, Karasev AV. Characterization of a New Tymovirus Causing Stunting and Chlorotic Mosaic in Naranjilla (Solanum quitoense). Plant Dis 2018; 102:911-918. [PMID: 30673388 DOI: 10.1094/pdis-10-17-1534-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Naranjilla ("little orange"), also known as lulo (Solanum quitoense Lam.), is a perennial shrub species cultivated in the Andes for fresh fruit and juice production. In 2015, a naranjilla plant exhibiting stunting, mosaic, and chlorotic spots was sampled in the Pastaza province of Ecuador and maintained under greenhouse conditions. An infectious agent was mechanically transmitted to indicator plants and was subjected to biological and molecular characterization. Spherical particles approximately 30 nm in diameter, composed of a single 20-kDa capsid protein, were observed under an electron microscope in infected naranjilla plants. High-throughput sequencing conducted on inoculated Nicotiana benthamiana plants produced a single sequence contig sharing the closest relationship with several tymoviruses. The entire 6,245-nucleotide genome of a new tymovirus was amplified using reverse-transcription polymerase chain reaction and resequenced with the Sanger methodology. The genome had three open reading frames typical of tymoviruses, and displayed a whole-genome nucleotide identity level with the closest tymovirus, Eggplant mosaic virus, at 71% (90% coverage). This tymovirus from naranjilla was able to systemically infect eggplant, tamarillo, N. benthamiana, and naranjilla. In naranjilla, it produced mosaic, chlorotic spots, and stunting, similar to the symptoms observed in the original plant. The virus was unable to infect potato and tobacco and unable to systemically infect pepper plants, replicating only in inoculated leaves. We concluded that this virus represented a new tymovirus infecting naranjilla, and proposed the tentative name Naranjilla chlorotic mosaic virus (NarCMV).
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Affiliation(s)
- Kelsie J Green
- Department of Entomology, Plant Pathology and Nematology (EPPN), University of Idaho, Moscow
| | - Dimitre Mollov
- United States Department of Agriculture-Agricultural Research Service, National Germplasm Resources Laboratory, Beltsville, MD
| | | | - Robert A Alvarez-Quinto
- Centro de Investigaciones Biotecnológicas del Ecuador and Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
| | - Jose B Ochoa
- Instituto Nacional Autónomo de Investigaciones Agropecuarias, Quito, Ecuador
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnológicas del Ecuador and Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral
| | - Alexander V Karasev
- Department of EPPN and Bioinformatics and Computational Biology Program, University of Idaho
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Braidwood L, Quito-Avila DF, Cabanas D, Bressan A, Wangai A, Baulcombe DC. Maize chlorotic mottle virus exhibits low divergence between differentiated regional sub-populations. Sci Rep 2018; 8:1173. [PMID: 29352173 PMCID: PMC5775324 DOI: 10.1038/s41598-018-19607-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/29/2017] [Indexed: 12/01/2022] Open
Abstract
Maize chlorotic mottle virus has been rapidly spreading around the globe over the past decade. The interactions of maize chlorotic mottle virus with Potyviridae viruses causes an aggressive synergistic viral condition - maize lethal necrosis, which can cause total yield loss. Maize production in sub-Saharan Africa, where it is the most important cereal, is threatened by the arrival of maize lethal necrosis. We obtained maize chlorotic mottle virus genome sequences from across East Africa and for the first time from Ecuador and Hawaii, and constructed a phylogeny which highlights the similarity of Chinese to African isolates, and Ecuadorian to Hawaiian isolates. We used a measure of clustering, the adjusted Rand index, to extract region-specific SNPs and coding variation that can be used for diagnostics. The population genetics analysis we performed shows that the majority of sequence diversity is partitioned between populations, with diversity extremely low within China and East Africa.
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Affiliation(s)
- Luke Braidwood
- University of Cambridge, Plant Sciences, Cambridge, CB2 3EA, United Kingdom.
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnologicas del Ecuador, Facultad de Ciencias de la Vida, Escuela Superior Politecnica del Litoral, ESPOL, Guayaquil, Ecuador
| | - Darlene Cabanas
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 3050 Maile Way, Gilmore Hall 310, Honolulu, Hawaii, USA
| | - Alberto Bressan
- Department of Plant and Environmental Protection Sciences, University of Hawaii, 3050 Maile Way, Gilmore Hall 310, Honolulu, Hawaii, USA
- Bayer CropScience LP, R&D Trait Research, 3500 Paramount Parkway, Morrisville, USA
| | - Anne Wangai
- Kenya Agricultural and Livestock Research Organization (KALRO), Nairobi, Kenya
| | - David C Baulcombe
- University of Cambridge, Plant Sciences, Cambridge, CB2 3EA, United Kingdom
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Alvarez-Quinto RA, Cornejo-Franco JF, Quito-Avila DF. Characterization of a not so new potexvirus from babaco (Vasconcellea x heilbornii). PLoS One 2017; 12:e0189519. [PMID: 29244846 PMCID: PMC5731686 DOI: 10.1371/journal.pone.0189519] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/28/2017] [Indexed: 11/19/2022] Open
Abstract
A new member of the genus Potexvirus was fully sequenced and characterized. The virus was isolated from babaco (Vasconcellea x heilbornii), a natural hybrid native to Ecuador. The virus contains a 6,692 nt long genome organized in five open reading frames in an arrangement typical of other potexviruses. Sequence comparisons revealed close relatedness with Papaya mosaic virus (PapMV), Alternathera mosaic virus (AltMV) and Senna mosaic virus (SenMV), exhibiting nucleotide identities up to 67% for the polymerase (Pol) and 68% for the coat protein (CP), with deduced amino acid identities of 70% and 72% for the Pol and CP, respectively. The presence of an AlkB domain, in the polymerase region, was observed. Terminal nucleotide sequences were conserved across potexviruses with characteristic motifs and predicted secondary structures at the 3' UTR. Although serologically undistinguishable from PapMV and AltMV, the new virus showed differences in host range and symptom induction. The name babaco mosaic virus is proposed for this newly characterized Potexvirus. The complete genome sequence of the new virus has been deposited in NCBI GenBank under accession number MF978248.
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Affiliation(s)
- Robert A. Alvarez-Quinto
- Centro de Investigaciones Biotecnológicas del Ecuador, CIBE, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
| | - Juan F. Cornejo-Franco
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
| | - Diego F. Quito-Avila
- Centro de Investigaciones Biotecnológicas del Ecuador, CIBE, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
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Quito-Avila DF, Ibarra MA, Alvarez R, Peralta EL, Martin RR. A raspberry bushy dwarf virus isolate from Ecuadorean Rubus glaucus contains an additional RNA that is a rearrangement of RNA-2. Arch Virol 2014; 159:2519-21. [PMID: 24719196 DOI: 10.1007/s00705-014-2069-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
Sequencing of the complete genome of a raspberry bushy dwarf virus isolate from Rubus glaucus in Ecuador revealed that its RNA-1 and RNA-2 were 5449 and 2231 nucleotides (nt) long, respectively, and phylogenetically closest to isolates from Sweden and Slovenia. In dsRNA analysis of infected plants, an additional band of 3 kbp was observed. Sequencing of this band revealed that it was 3279 nt long. BLAST searches revealed that this band contained a modified version of RNA-2, which consisted of RNA-2 (2231 nt) plus an additional 1048-nt fragment that was concatenated in a reverse-complement fashion to its 5' terminus.
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Affiliation(s)
- D F Quito-Avila
- Centro de Investigaciones Biotecnologicas del Ecuador, Escuela Superior Politecnica del Litoral (CIBE-ESPOL), Km 30.5 Via Perimetral Campus Gustavo Galindo. Apartado 09-01-5863, Guayaquil, Ecuador,
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Quito-Avila DF, Lightle D, Martin RR. Effect of Raspberry bushy dwarf virus, Raspberry leaf mottle virus, and Raspberry latent virus on Plant Growth and Fruit Crumbliness in 'Meeker' Red Raspberry. Plant Dis 2014; 98:176-183. [PMID: 30708766 DOI: 10.1094/pdis-05-13-0562-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Raspberry crumbly fruit in red raspberry (Rubus idaeus), widespread in the Pacific Northwest of the United States and British Columbia, Canada, is most commonly caused by a virus infection. Raspberry bushy dwarf virus (RBDV) has long been attributed as the causal agent of the disease. Recently, the identification of two additional viruses, Raspberry leaf mottle virus (RLMV) and Raspberry latent virus (RpLV), in northern Washington and British Columbia, suggested the existence of a possible new virus complex responsible for the increased severity of the disease. Virus testing of crumbly fruited plants from five fields in northern Washington revealed the presence of RLMV and RpLV, in addition to RBDV. Plants with less severe crumbly fruit symptoms had a much lower incidence of RLMV or RpLV. Field trials using replicated plots of 'Meeker' plants containing single and mixed infections of RBDV, RLMV, or RpLV, along with a virus-free control, were developed to determine the role of RLMV and RpLV in crumbly fruit. Field evaluations during establishment and two fruiting years revealed that plants infected with the three viruses or the combinations RBDV+RLMV and RBDV+RpLV had the greatest reduction in cane growth, or fruit firmness and fruit weight, respectively. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) showed that the titer of RBDV was increased ~400-fold when it occurred in mixed infections with RLMV compared to RBDV in single infections. In addition, a virus survey revealed that RLMV and RpLV are present at high incidence in northern Washington; whereas the incidence in southern Washington and Oregon, where crumbly fruit is not as serious a problem, was considerably lower.
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Affiliation(s)
- Diego F Quito-Avila
- Centro de Investigaciones Biotecnologicas del Ecuador, Escuela Superior Politecnica del Litoral, CIBE-ESPOL, Plant Pathology-Virology, Guayaquil, Ecuador
| | - Danielle Lightle
- Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| | - Robert R Martin
- Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
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Quito-Avila DF, Ibarra MA, Alvarez RA, Espinoza L, Ratti MF, Peralta EL, Martin RR. First Report of Raspberry bushy dwarf virus in Andean Blackberry (Rubus glaucus) in Central Ecuador. Plant Dis 2013; 97:1003. [PMID: 30722554 DOI: 10.1094/pdis-12-12-1198-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During the past two decades, several viruses have been identified from Rubus spp. in wild and commercial plantings around the world (2). In Ecuador, approximately 14 tons of blackberries are produced each year from an estimated area of 5,500 ha. In 2012, a preliminary survey was conducted to determine the presence of RNA viruses in Rubus glaucus, the most prevalent blackberry in Ecuador. Fifteen plants showing leaf mottling and severe mosaic were leaf-sampled from each of five different fields in Azuay Province. A total of 12 pooled samples of 20 g were obtained from the collected symptomatic tissue and used for dsRNA extraction using a cellulose-based protocol for detection of RNA viruses in plants (3). Three dsRNA segments of approximately 5 kbp, 2 kbp, and 900 bp were observed from all 12 dsRNA preparations. The dsRNA was heat-denatured and used as template for the generation of cDNA library using the universal random primer 5'-GCCGGAGCTCTGCAGAATTCNNNNNN-3', for reverse transcription (RT), and the anchor primer 5'-GCCGGAGCTCTGCAGAATTC-3'for PCR as described (1). The PCR products were cloned using a StrataClone Kit (Agilent, CA) and sequenced (Macrogen, Korea). Sequence analysis revealed the presence of Raspberry bushy dwarf virus (RBDV), a pollen-borne Idaeovirus naturally found in several Rubus spp. worldwide. Approximately 120 RBDV sequences obtained from the Ecuadorean isolate were assembled into two contigs belonging to RNA1 and RNA2. Both sequences were re-confirmed by RT-PCR using specific primers. Partial sequences were assigned GenBank Accessions KC315894, KC315893, and KC315892 for the replicase, MP and CP, respectively. Furthermore, BLAST searches showed that the nucleotide sequence corresponding to the replicase was 95% similar to an isolate from the resistance breaking R15 strain (S51557.1), whereas the MP and CP nucleotide sequences were up to 98% similar to a Slovenian isolate (EU796088.1). Primers designed to amplify a 427-bp portion of the CP were used to detect RBDV from four blackberry plantings in two distant production areas: Ambato in Tungurahua Province and Paute in Azuay Province. Leaf mottling and severe mosaic was observed in 90% of blackberry fields in those two locations. Leaf samples (n = 90) were randomly collected from both symptomatic and asymptomatic plants in each location. In Ambato, RBDV was detected in 50% and 40% of symptomatic and asymptomatic plants, respectively. In Paute, RBDV was present in 70% of symptomatic plants and 29% of asymptomatic plants. The presence of RBDV in asymptomatic plants suggests the virus might not be the sole causal agent of the disorder. Further studies are needed to determine the role of RBDV in the observed symptoms, since virus complexes responsible for increased severity of symptoms have been commonly reported in Rubus spp. (4). R. glaucus is native to the tropical highlands (from Ecuador to Mexico) and differs from blackberries commercially grown in the United States and Europe. Therefore, RBDV-induced symptoms reported in blackberry grown in the United States and Europe may not be extrapolated to the Andes berry. To the best of our knowledge, this is the first report of RBDV from blackberry in Ecuador. References: (1) P. Froussard. Nucleic Acids Res. 20:2900, 1992. (2) R. R. Martin et al. Plant Dis. 97:168, 2013. (3). T. J. Morris and J. A. Dodds. Phytopathology 69:854. 1979. (4) D. F. Quito-Avila et al. J. Virol. Methods 179:38, 2012.
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Affiliation(s)
- D F Quito-Avila
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil-Ecuador
| | - M A Ibarra
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil-Ecuador
| | - R A Alvarez
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil-Ecuador
| | - L Espinoza
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil-Ecuador
| | - M F Ratti
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil-Ecuador
| | - E L Peralta
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil-Ecuador
| | - R R Martin
- USDA-ARS, Horticultural Crops Research Unit, Corvallis, OR, 97331
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Quito-Avila DF, Ibarra MA, Alvarez RA, Ratti MF, Espinoza L, Cevallos-Cevallos JM, Peralta EL. First Report of Banana bract mosaic virus in 'Cavendish' Banana in Ecuador. Plant Dis 2013; 97:1003. [PMID: 30722549 DOI: 10.1094/pdis-12-12-1154-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Banana bract mosaic virus (BBrMV), a member of the genus Potyvirus, family Potyviridae, is the causal agent of bract mosaic disease. The disorder has been considered a serious constraint to banana and plantain production in India and the Philippines, where the virus was first identified (3). To date, the presence of BBrMV has been reported only in a few banana-growing countries in Asia (3). In the Americas, BBrMV has been detected by ELISA tests in Colombia only (1). The efficient spread of BBrMV through aphids and vegetative material increases the quarantine risk and requires strict measures to prevent entrance of the virus to new areas. In Ecuador-the world's number one banana exporter-the banana industry represents the main agricultural income source. Thus, early detection of banana pathogens is a priority. In June of 2012, mosaic symptoms in bracts and bunch distortion of 'Cavendish' banana were observed in a commercial field in the province of Guayas, Ecuador. Leaves from 35 symptomatic plants were tested for Cucumber mosaic virus (CMV), Banana streak virus (BSV), and BBrMV using double antibody sandwich ELISA kits from Adgen (Scotland, UK). Twenty-one plants tested positive for BBrMV but not for CMV or BSV. In order to confirm the ELISA results, fresh or lyophilized leaf extracts were used for immunocapture reverse transcription (IC-RT)-PCR. In addition, total RNA was extracted from the ELISA-positive samples and subjected to RT-PCR. The RT reactions were done using both random and oligo dT primers. Several sets of primers, flanking conserved regions of the virus coat protein (CP), have been used for PCR-detection of BBrMV (2,3,4). The Ecuadorian BBrMV isolate was successfully detected by three primer sets with reported amplification products of 324, 280, and 260 nucleotides long, respectively (3,4). Amplification products of the expected size were purified and sequenced. All the nucleotide sequences obtained from 20 PCR-positive symptomatic plants were 100% identical between each other. However, 99% identity was observed when PCR products from the Ecuadorian isolate were compared with the corresponding fragment of a BBrMV isolate from the Philippines (NCBI Accession No. DQ851496.1). PCR products of the Ecuadorian isolate, amplified by the different CP primers described above, were assembled into a 408-bp fragment and deposited in the NCBI GenBank (KC247746). Further testing confirmed the presence of BBrMV in symptomatic plants from four different provinces. To our knowledge, this is the first report of BBrMV in Ecuador and the first BBrMV partial nucleotide sequence reported from the Americas. It is worth mentioning that primer set Bract 1/Bract 2, which amplifies a 604-bp product (2), was not effective in detecting the Ecuadorian isolate. It is hypothesized that nucleotide variation at the reverse primer site is the cause of the lack of amplification with this primer set, since the forward primer is part of the sequenced product and no variation was found. Sequencing of the entire CP region is underway to conduct phylogenetic analysis and determine genetic relationships across several other BBrMV isolates. References: (1) J. J. Alarcon et al. Agron 14:65, 2006. (2) M. F. Bateson and J. L. Dale. Arch. Virol 140:515, 1995. (3) E. M. Dassanayake. Ann. Sri Lanka Dept. Agric. 3:19, 2001. (4) M. L. Iskra-Caruana et al. J. Virol. Methods 153:223, 2008.
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Affiliation(s)
- D F Quito-Avila
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil, Ecuador
| | - M A Ibarra
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil, Ecuador
| | - R A Alvarez
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil, Ecuador
| | - M F Ratti
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil, Ecuador
| | - L Espinoza
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil, Ecuador
| | - J M Cevallos-Cevallos
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil, Ecuador
| | - E L Peralta
- Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo Km 30.5 vía Perimetral, apartado 09-01-5863, Guayaquil, Ecuador
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Quito-Avila DF, Brannen PM, Cline WO, Harmon PF, Martin RR. Genetic characterization of Blueberry necrotic ring blotch virus, a novel RNA virus with unique genetic features. J Gen Virol 2013; 94:1426-1434. [PMID: 23486668 DOI: 10.1099/vir.0.050393-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new disorder was observed on southern highbush blueberries in several south-eastern states in the USA. Symptoms included irregularly shaped circular spots or blotches with green centres on the upper and lower surfaces of leaves. Double-stranded RNA was extracted from symptomatic leaves suggesting the presence of virus(es) possibly involved in the disease. Sequencing revealed the presence of a novel RNA virus with a ~14 kb genome divided into four RNA segments. Sequence analyses showed that the virus, for which we propose the name Blueberry necrotic ring blotch virus (BNRBV), possesses protein domains conserved across RNA viruses in the alpha-virus-like supergroup. Phylogenetic inferences using different genes placed BNRBV in a clade that includes the Bromoviridae, the genus Cilevirus (CiLV) and the recently characterized Hibiscus green spot virus (HGSV). Despite the strong genetic relationships found among BNRBV, Cilevirus and HGSV, the genome of BNRBV contains three features that distinguish it significantly from its closest relatives: (i) the presence of two helicase domains with different evolutionary pathways, (ii) the existence of three conserved nucleotide stretches located at the 3' non-coding regions of each RNA segment and (iii) the conservation of terminal nucleotide motifs across each segment. Furthermore, CiLV and HGSV possess poly(A)-tailed bipartite and tripartite genomes, respectively, whereas BNRBV has a quadra-partite genome lacking a poly(A) tail. Based on these genetic features a new genus is proposed for the classification of BNRBV.
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Affiliation(s)
- Diego F Quito-Avila
- Centro de Investigaciones Biotecnologicas del Ecuador (CIBE), Escuela Superior Politecnica del Litoral (ESPOL), Guayaquil, Guayas EC090150, Ecuador
| | - Philip M Brannen
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| | - William O Cline
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27607, USA
| | - Philip F Harmon
- Department of Plant Pathology, University of Florida, Gainesville, FL 32605, USA
| | - Robert R Martin
- USDA-ARS, Horticultural Crops Research Unit, Corvallis OR 97331, USA
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Abstract
Raspberry latent virus (RpLV) is a newly characterized reovirus found in commercial raspberry fields in the Pacific Northwest (PNW). Thus far, all members of the plant reoviruses are transmitted in a replicative, persistent manner by several species of leafhoppers or planthoppers. After several failed attempts to transmit RpLV using leafhoppers, the large raspberry aphid, commonly found in the PNW, was tested as a vector of the virus. The virus was transmitted to new, healthy raspberry plants when inoculated with groups of at least 50 viruliferous aphids, suggesting that aphids are vectors of RpLV, albeit inefficient ones. Using absolute and relative quantification methods, it was shown that the virus titer in aphids continued to increase after the acquisition period even when aphids were serially transferred onto fresh, healthy plants on a daily basis. Transmission experiments determined that RpLV has a 6-day latent period in the aphid before it becomes transmissible; however, it was not transmitted transovarially to the next generation. To our knowledge, this is the first report of a plant reovirus transmitted by an aphid. Phylogenetic analyses showed that RpLV is related most closely to but distinct from Rice ragged stunt virus (RRSV), the type member of the genus Oryzavirus. Moreover, the conserved nucleotide termini of the genomic segments of RpLV did not match those of RRSV or other plant reoviruses, allowing us to suggest that RpLV is probably the type member of a new genus in the Reoviridae comprising aphid-transmitted reoviruses.
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Affiliation(s)
- Diego F Quito-Avila
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
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Quito-Avila DF, Martin RR. Real-time RT-PCR for detection of Raspberry bushy dwarf virus, Raspberry leaf mottle virus and characterizing synergistic interactions in mixed infections. J Virol Methods 2011; 179:38-44. [PMID: 21968094 DOI: 10.1016/j.jviromet.2011.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/14/2011] [Accepted: 09/19/2011] [Indexed: 10/17/2022]
Abstract
Two TaqMan-based real-time One-Step RT-PCR assays were developed for the rapid and efficient detection of Raspberry bushy dwarf virus (RBDV) and Raspberry leaf mottle virus (RLMV), two of the most common raspberry viruses in North America and Europe. The primers and probes were designed from conserved fragments of the polymerase region of each virus and were effective for the detection of different isolates tested in this study. The RBDV assay amplified a 94bp amplicon and was able to detect as few as 30 viral copies. Whereas the RLMV assay amplified a 180bp amplicon and detected as few as 300 viral copies from plant and aphid RNA extracts. Both assays were significantly more sensitive than their corresponding conventional RT-PCR methods. The sensitivity of the RLMV assay was also tested on single aphids after a fixed acquisition access period (AAP). In addition, the assays revealed a novel synergistic interaction between the two viruses, where the concentration of RBDV was enhanced ∼400-fold when it occurred in combination with RLMV compared to its concentration in single infections. The significance of this finding and the importance of the development of real-time RT-PCR assays for the detection of RBDV and RLMV are discussed.
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Affiliation(s)
- Diego F Quito-Avila
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
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Quito-Avila DF, Jelkmann W, Tzanetakis IE, Keller K, Martin RR. Complete sequence and genetic characterization of Raspberry latent virus, a novel member of the family Reoviridae. Virus Res 2010; 155:397-405. [PMID: 21144872 DOI: 10.1016/j.virusres.2010.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 11/12/2010] [Accepted: 11/19/2010] [Indexed: 12/18/2022]
Abstract
A new virus isolated from red raspberry plants and detected in the main production areas in northern Washington State, USA and British Columbia, Canada was fully sequenced and found to be a novel member of the family Reoviridae. The virus was designated as Raspberry latent virus (RpLV) based on the fact that it is symptomless when present in single infections in several Rubus virus indicators and commercial raspberry cultivars. RpLV genome is 26,128 nucleotides (nt) divided into 10 dsRNA segments. The length of the genomic segments (S) was similar to those of other reoviruses ranging from 3948 nt (S1) to 1141 nt (S10). All of the segments, except S8, have the conserved terminal sequences 5'-AGUU----GAAUAC-3'. A point mutation at each terminus of S8 resulted in the sequences 5'-AGUA----GAUUAC-3'. Inverted repeats adjacent to each conserved terminus as well as stem loops and extended pan handles were identified by analyses of secondary structures of the non-coding sequences. All segments, except S3 and S10, contained a single open reading frame (ORF) on the positive sense RNAs. Two out-of-frame overlapping ORFs were identified in segments S3 (ORF S3a and S3b) and S10 (ORF S10a and S10b). Amino acid (aa) alignments of the putative proteins encoded by the main ORF in each segment revealed a high identity to several proteins encoded by reoviruses from different genera including Oryzavirus, Cypovirus, and Dinovernavirus. Alignments of the polymerase, the most conserved protein among reoviruses, revealed a 36% aa identity between RpLV and Rice ragged stunt virus (RRSV), the type member of the genus Oryzavirus, indicating that these two viruses are closely related. Phylogenetic analyses showed that RpLV clusters with members of the genera Oryzavirus, Cypovirus, Dinovernavirus and Fijivirus. These genera belong to the subfamily Spinareovirinae which includes reoviruses with spiked core particles ('turreted' reoviruses). In addition, two nucleotide binding motifs, regarded as 'signature' sequences among turreted reoviruses, were also found in RpLV P8, suggesting that RpLV is a novel dicot-infecting reovirus in the subfamily Spinareovirinae.
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Affiliation(s)
- Diego F Quito-Avila
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
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