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Carvalho VL, Prakoso D, Schwarz ER, Logan TD, Nunes BTD, Beachboard SE, Long MT. Negevirus Piura Suppresses Zika Virus Replication in Mosquito Cells. Viruses 2024; 16:350. [PMID: 38543716 PMCID: PMC10976066 DOI: 10.3390/v16030350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 05/23/2024] Open
Abstract
We investigated the interaction between the insect-specific virus, Piura virus (PIUV), and the arbovirus Zika virus (ZIKV) in Aedes albopictus cells. We performed coinfection experiments in C6/36 cells. Piura virus (Cor 33 strain, Colombia) and ZIKV (PRVABC58 strain, Puerto Rico) were co-inoculated into C6/36 cells using two multiplicity of infection (MOI) combinations: 0.1 for both viruses and 1.0 for ZIKV, 0.1 for PIUV. Wells were infected in triplicate with either PIUV and ZIKV coinfection, ZIKV-only, or PIUV-only. Mock infected cells served as control wells. The cell suspension was collected daily 7 days post-infection. Zika virus load was titrated by TCID50 on Vero 76 cells. The ZIKV-only infection and PIUV and ZIKV coinfection experiments were also quantified by RT-qPCR. We also investigated whether ZIKV interfered in the PIUV replication. PIUV suppressed the replication of ZIKV, resulting in a 10,000-fold reduction in ZIKV titers within 3 days post-infection. PIUV viral loads were not reduced in the presence of ZIKV. We conclude that, when concurrently infected, PIUV suppresses ZIKV in C6/36 cells while ZIKV does not interfere in PIUV replication.
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Affiliation(s)
- Valéria L. Carvalho
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Rodovia BR-316, Km 7, s/n, Ananindeua 67030-000, PA, Brazil
| | - Dhani Prakoso
- Professor Nidom Foundation, Surabaya, East Java 60236, Indonesia;
| | - Erika R. Schwarz
- Montana Veterinary Diagnostic Laboratory, 1911 W Lincoln St., Bozeman, MT 59718, USA
| | - Tracey D. Logan
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, 1225 Center Dr. Suite 4101, Gainesville, FL 32611, USA
| | - Bruno Tardelli Diniz Nunes
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Rodovia BR-316, Km 7, s/n, Ananindeua 67030-000, PA, Brazil
| | - Sarah E. Beachboard
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 1945 SW 16th Ave., Gainesville, FL 32608, USA
| | - Maureen T. Long
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 1945 SW 16th Ave., Gainesville, FL 32608, USA
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, Gainesville, FL 32610, USA
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2
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Roy A, Grinstead S, Leon Martínez G, Pinzón JCC, Nunziata SO, Padmanabhan C, Hammond J. Meta-Transcriptomic Analysis Uncovers the Presence of Four Novel Viruses and Multiple Known Virus Genera in a Single Hibiscus rosa-sinensis Plant in Colombia. Viruses 2024; 16:267. [PMID: 38400042 PMCID: PMC10891833 DOI: 10.3390/v16020267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Hibiscus is not native to Colombia but well suited to its arid soil and dry climates. A single hibiscus plant from Risaralda, showing black spots on upper and lower sides of its leaves, was collected for virome analysis using meta-transcriptomic high-throughput sequencing technology. Bioinformatic analysis identified 12.5% of the total reads in the Ribo-Zero cDNA library which mapped to viral genomes. BLAST searches revealed the presence of carlavirus, potexvirus, and of known members of the genera Betacarmovirus, Cilevirus, Nepovirus, and Tobamovirus in the sample; confirmed by RT-PCR with virus-specific primers followed by amplicon sequencing. Furthermore, in silico analysis suggested the possibility of a novel soymovirus, and a new hibiscus strain of citrus leprosis virus C2 in the mixed infection. Both RNA dependent RNA polymerase and coat protein gene sequences of the potex and carla viruses shared less than 72% nucleotide and 80% amino acid identities with any alphaflexi- and betaflexi-virus sequences available in GenBank, identifying three novel carlavirus and one potexvirus species in the Hibiscus rosa-sinensis plant. The detection of physalis vein necrosis nepovirus and passion fruit green spot cilevirus in hibiscus are also new reports from Colombia. Overall, the meta-transcriptome analysis identified the complex virome associated with the black spot symptoms on hibiscus leaves and demonstrated the diversity of virus genera tolerated in the mixed infection of a single H. rosa-sinensis plant.
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Affiliation(s)
- Avijit Roy
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture (USDA), Beltsville, MD 20705, USA
| | - Sam Grinstead
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture (USDA), Beltsville, MD 20705, USA
| | - Guillermo Leon Martínez
- AGROSAVIA, Centro de Investigación La Libertad, Km.17 vía Pto. Lopez, Villavicencio, Meta, Colombia
| | | | - Schyler O Nunziata
- Plant Pathogen Confirmatory Diagnostics Laboratory, Science and Technology, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, USDA, Laurel, MD 20708, USA
| | - Chellappan Padmanabhan
- Plant Pathogen Confirmatory Diagnostics Laboratory, Science and Technology, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, USDA, Laurel, MD 20708, USA
| | - John Hammond
- Floral and Nursery Plants Research Unit, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
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3
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Zhang S, Yang C, Qiu Y, Liao R, Xuan Z, Ren F, Dong Y, Xie X, Han Y, Wu D, Ramos-González PL, Freitas-Astúa J, Yang H, Zhou C, Cao M. Conserved untranslated regions of multipartite viruses: Natural markers of novel viral genomic components and tags of viral evolution. Virus Evol 2024; 10:veae004. [PMID: 38361819 PMCID: PMC10868557 DOI: 10.1093/ve/veae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024] Open
Abstract
Viruses with split genomes are classified as being either segmented or multipartite based on whether their genomic segments occur within a single virion or across different virions. Despite variations in number and sequence during evolution, the genomic segments of many viruses are conserved within the untranslated regions (UTRs). In this study, we present a methodology that combines RNA sequencing with iterative BLASTn of UTRs (https://github.com/qq371260/Iterative-blast-v.1.0) to identify new viral genomic segments. Some novel multipartite-like viruses related to the phylum Kitrinoviricota were annotated using sequencing data from field plant samples and public databases. We identified potentially plant-infecting jingmen-related viruses (order Amarillovirales) and jivi-related viruses (order Martellivirales) with at least six genomic components. The number of RNA molecules associated with a genome of the novel viruses in the families Closteroviridae, Kitaviridae, and Virgaviridae within the order Martellivirales reached five. Several of these viruses seem to represent new taxa at the subgenus, genus, and family levels. The diversity of novel genomic components and the multiple duplication of proteins or protein domains within single or multiple genomic components emphasize the evolutionary roles of genetic recombination (horizontal gene transfer), reassortment, and deletion. The relatively conserved UTRs at the genome level might explain the relationships between monopartite and multipartite viruses, as well as how subviral agents such as defective RNAs and satellite viruses can coexist with their helper viruses.
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Affiliation(s)
| | - Caixia Yang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, 21 Huanan Street, Shenyang, Liaoning 110044, China
| | - Yuanjian Qiu
- National Citrus Engineering and Technology Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
| | - Ruiling Liao
- National Citrus Engineering and Technology Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
| | - Zhiyou Xuan
- National Citrus Engineering and Technology Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
| | - Fang Ren
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, 98 Xinghainan Street, Xingcheng, Liaoning 125100, China
| | - Yafeng Dong
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, 98 Xinghainan Street, Xingcheng, Liaoning 125100, China
| | - Xiaoying Xie
- Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, Fujian 350002, China
| | - Yanhong Han
- Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, Fujian 350002, China
| | - Di Wu
- College of Horticulture and Landscape Architecture, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
| | - Pedro Luis Ramos-González
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, Av. Cons. Rodrigues Alves 1252, São Paulo SP, 04014-002, Brazil
| | - Juliana Freitas-Astúa
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, Av. Cons. Rodrigues Alves 1252, São Paulo SP, 04014-002, Brazil
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, Caixa Postal 007, CEP, Cruz das Almas BA, 44380-000, Brazil
| | - Huadong Yang
- Hunan Agricultural University, 1 Nongda Road, Changsha, Hunan 410125, China
| | - Changyong Zhou
- National Citrus Engineering and Technology Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
- Guangxi Citrus Breeding and Cultivation Technology Innovation Center, Guangxi Academy of Specialty Crops, 40 Putuo Road, Guilin, Guangxi 541010, China
- Guangxi Key Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guangxi Academy of Specialty Crops, 40 Putuo Road, Guilin, Guangxi 541010, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
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Olmedo-Velarde A, Larrea-Sarmiento A, Wang X, Hu J, Melzer M. A Breakthrough in Kitavirids: Genetic Variability, Reverse Genetics, Koch's Postulates, and Transmission of Hibiscus Green Spot Virus 2. PHYTOPATHOLOGY 2024; 114:282-293. [PMID: 37366568 DOI: 10.1094/phyto-04-23-0110-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Hibiscus green spot virus 2 (HGSV-2), a member of the genus Higrevirus (family Kitaviridae), is a positive-stranded RNA virus associated with leprosis-like symptoms in citrus and green spots on leaves in hibiscus. HGSV-2 has only been reported in Hawaii, and while it is speculated that mites in the genus Brevipalpus might be responsible for its transmission, proper transmission assays have yet to be conducted. This study characterizes additional citrus and hibiscus isolates of HGSV-2 collected from two Hawaiian Islands. We constructed an infectious cDNA clone from a hibiscus isolate of HGSV-2 collected on Oahu and demonstrated its ability to infect several experimental hosts, including Phaseolus vulgaris, Nicotiana tabacum, and N. benthamiana, as well as natural hosts, Citrus reticulata and Hibiscus arnottianus. Bacilliform virions with varied sizes of 33 to 120 nm (length) and 14 to 70 nm (diameter) were observed in partially purified preparations obtained from agroinoculated leaves. Virus progeny from the infectious cDNA clone was found to be infectious after mechanical transmission to N. benthamiana and to cause local lesions. Finally, an isoline colony of the mite Brevipalpus azores had vector competence to transmit a citrus isolate of HGSV-2 collected from Maui to citrus and hibiscus plants, demonstrating the mite-borne nature of HGSV-2. The infectious cDNA clone developed in this study is the first reverse-genetics system for a kitavirid and will be fundamental to better characterize basic biology of HGSV-2 and its interactions with host plants and mite vectors.
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Affiliation(s)
- Alejandro Olmedo-Velarde
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Adriana Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Xupeng Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - John Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Michael Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
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5
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Ramos-González PL, Dias Arena G, Tassi AD, Chabi-Jesus C, Watanabe Kitajima E, Freitas-Astúa J. Kitaviruses: A Window to Atypical Plant Viruses Causing Nonsystemic Diseases. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:97-118. [PMID: 37217202 DOI: 10.1146/annurev-phyto-021622-121351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Kitaviridae is a family of plant-infecting viruses that have multiple positive-sense, single-stranded RNA genomic segments. Kitaviruses are assigned into the genera Cilevirus, Higrevirus, and Blunervirus, mainly on the basis of the diversity of their genomic organization. Cell-to-cell movement of most kitaviruses is provided by the 30K family of proteins or the binary movement block, considered an alternative movement module among plant viruses. Kitaviruses stand out for producing conspicuously unusual locally restricted infections and showing deficient or nonsystemic movement likely resulting from incompatible or suboptimal interactions with their hosts. Transmission of kitaviruses is mediated by mites of many species of the genus Brevipalpus and at least one species of eriophyids. Kitavirus genomes encode numerous orphan open reading frames but RNA-dependent RNA polymerase and the transmembrane helix-containing protein, generically called SP24, typify a close phylogenetic link with arthropod viruses. Kitaviruses infect a large range of host plants and cause diseases of economic concern in crops such as citrus, tomato, passion fruit, tea, and blueberry.
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Affiliation(s)
| | - Gabriella Dias Arena
- Instituto Biológico, URL Biologia Molecular Aplicada, São Paulo, Brazil; ,
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Aline Daniele Tassi
- Instituto Biológico, URL Biologia Molecular Aplicada, São Paulo, Brazil; ,
- Tropical Research and Education Center, University of Florida, Homestead, Florida, USA
| | - Camila Chabi-Jesus
- Instituto Biológico, URL Biologia Molecular Aplicada, São Paulo, Brazil; ,
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Elliot Watanabe Kitajima
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Juliana Freitas-Astúa
- Instituto Biológico, URL Biologia Molecular Aplicada, São Paulo, Brazil; ,
- Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia, Brazil
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6
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Chabi-Jesus C, Ramos-González PL, Tassi AD, Rossetto Pereira L, Bastianel M, Lau D, Canale MC, Harakava R, Novelli VM, Kitajima EW, Freitas-Astúa J. Citrus Bright Spot Virus: A New Dichorhavirus, Transmitted by Brevipalpus azores, Causing Citrus Leprosis Disease in Brazil. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12061371. [PMID: 36987059 PMCID: PMC10053991 DOI: 10.3390/plants12061371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 06/01/2023]
Abstract
Citrus leprosis (CL) is the main viral disease affecting the Brazilian citriculture. Sweet orange (Citrus sinensis L. Osbeck) trees affected by CL were identified in small orchards in Southern Brazil. Rod-like particles of 40 × 100 nm and electron lucent viroplasm were observed in the nucleus of infected cells in symptomatic tissues. RNA extracts from three plants, which proved negative by RT-PCR for known CL-causing viruses, were analyzed by high throughput sequencing and Sanger sequencing after RT-PCR. The genomes of bi-segmented ss(-)RNA viruses, with ORFs in a typical organization of members of the genus Dichorhavirus, were recovered. These genomes shared 98-99% nt sequence identity among them but <73% with those of known dichorhavirids, a value below the threshold for new species demarcation within that genus. Phylogenetically, the three haplotypes of the new virus called citrus bright spot virus (CiBSV) are clustered with citrus leprosis virus N, which is a dichorhavirus transmitted by Brevipalpus phoenicis sensu stricto. In CiBSV-infected citrus plants, B. papayensis and B. azores were found, but the virus could only be transmitted to Arabidopsis plants by B. azores. The study provides the first evidence of the role of B. azores as a viral vector and supports the assignment of CiBSV to the tentative new species Dichorhavirus australis.
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Affiliation(s)
- Camila Chabi-Jesus
- Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (Esalq/USP), Piracicaba 13418-900, São Paulo, Brazil
- Instituto Biológico/IB, São Paulo 04014-002, São Paulo, Brazil
| | | | | | | | - Marinês Bastianel
- Centro de Citricultura Sylvio Moreira/IAC, Cordeirópolis 13490-970, São Paulo, Brazil
| | - Douglas Lau
- Embrapa Trigo, Passo Fundo 99050-970, Rio Grande do Sul, Brazil
| | - Maria Cristina Canale
- Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina/Epagri, Paulo Lopes 88490-000, Santa Catarina, Brazil
| | | | | | - Elliot Watanabe Kitajima
- Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (Esalq/USP), Piracicaba 13418-900, São Paulo, Brazil
| | - Juliana Freitas-Astúa
- Instituto Biológico/IB, São Paulo 04014-002, São Paulo, Brazil
- Embrapa Mandioca e Fruticultura, Cruz das Almas 44380-000, Bahia, Brazil
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Vidal AH, Lacorte C, Sanches MM, Alves-Freitas DMT, Abreu EFM, Pinheiro-Lima B, Rosa RCC, Jesus ON, Campos MA, Felix GP, Abreu ACR, Santos YS, Lacerda ALM, Varsani A, Melo FL, Ribeiro SG. Characterization of Cucurbit Aphid-Borne Yellows Virus (CABYV) from Passion Fruit in Brazil: Evidence of a Complex of Species within CABYV Isolates. Viruses 2023; 15:v15020410. [PMID: 36851624 PMCID: PMC9965994 DOI: 10.3390/v15020410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
High-throughput sequencing (HTS) has been an important tool for the discovery of plant viruses and their surveillance. In 2015, several virus-like symptoms were observed in passion fruit (PF) plants in Bahia state, Brazil. Using HTS technology, bioinformatics tools, RT-PCR, and Sanger sequencing, we identified the cucurbit aphid-borne yellows virus (CABYV, Polerovirus, Solemoviridae) in co-infection with cowpea aphid-borne mosaic virus (CABMV, Potyvirus, Potyviridae) in PF, in green manure, and spontaneous plants in several localities in Bahia. Complete genomes of CABYV-PF isolates were determined and analyzed with other CABYV isolates available in GenBank that have been identified in various countries. Phylogenetic analysis and pairwise identity comparison with CABYV isolates showed that CABYV-PFs are more closely related to French and Spanish isolates. Overall, analyses of all the CABYV genomes revealed that these could represent ten distinct species, and we thus proposed reclassifying these CABYV as isolates into ten species, tentatively named "Polerovirus curcubitaeprimum" to "Polerovirus curcubitaenonum", and "Polerovirus melo". CABYV-PF is a member of "Polerovirus curcubitaeprimum".
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Affiliation(s)
- Andreza H. Vidal
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Instituto de Ciências Biológicas—IB, PPG BIOMOL, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Cristiano Lacorte
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
| | - Marcio M. Sanches
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Embrapa Gado de Corte, Campo Grande 79106-550, MS, Brazil
| | | | | | - Bruna Pinheiro-Lima
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Instituto de Ciências Biológicas—IB, PPG BIOMOL, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | | | - Onildo N. Jesus
- Embrapa Mandioca e Fruticultura, Cruz das Almas 44380-000, BA, Brazil
| | - Magnólia A. Campos
- Centro de Educação e Saúde, Universidade Federal de Campina Grande, Cuité 58175-000, PB, Brazil
| | - Gustavo P. Felix
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Instituto de Ciências Biológicas—IB, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Ana Clara R. Abreu
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Instituto de Ciências Biológicas—IB, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Yam S. Santos
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa (UFV), Viçosa 36570-900, MG, Brazil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Fernando L. Melo
- Instituto de Ciências Biológicas—IB, PPG BIOMOL, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Simone G. Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Instituto de Ciências Biológicas—IB, PPG BIOMOL, Universidade de Brasília, Brasília 70910-900, DF, Brazil
- Correspondence:
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Roy A, Guillermo LM, Nunziata S, Padmanabhan C, Rivera Y, Brlansky RH, Hartung J. First report of Passion fruit green spot virus in yellow Passion fruit (Passiflora edulis f. flavicarpa) in Casanare, Colombia. PLANT DISEASE 2022; 107:2270. [PMID: 36471457 DOI: 10.1094/pdis-09-22-2267-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Passiflora edulis, commonly known as passion fruit, is a vine species of passionflower native to South America. In Colombia, yellow passion fruit (P. edulis f. flavicarpa) is the most important species in terms of net production and local consumption. Recently two brevipalpus transmitted cileviruses, (i) passion fruit green spot virus (PfGSV) and (ii) hibiscus strain of citrus leprosis virus C2 (CiLV-C2H) were detected in passion fruit in Brazil and Hawaii, respectively (Ramos-González et al., 2020, Olmedo-Velarde et al., 2022). CiLV-C2H infects both citrus and hibiscus in Colombia (Roy et al., 2015, 2018) but there was no report of PfGSV elsewhere apart from Brazil and Paraguay (Costa-Rodrigues et al., 2022). Apart from emerging begomovirus diseases, five major viruses are known to infect passion fruit in Colombia: soybean mosaic virus (SMV), cowpea aphid-borne mosaic virus, passion fruit yellow mosaic virus, cucumber mosaic virus, and a tentative Gulupa bacilliform badnavirus A (Cardona et al., 2022). Current findings of CiLV-C2H in passion fruit and PfGSV in hibiscus motivated us to investigate the possibilities of cilevirus infection in passion fruit in Colombia. During surveys, along with healthy yellow passion fruit leaves, five symptomatic plant samples from Meta and three from Casanare were collected before sent to the Molecular Plant Pathology Laboratory at Beltsville, MD under APHIS permit. Passion fruit samples from Meta showed leaf mottling, rugose mosaic, and leaf distortion, whereas leaf variegation, chlorotic spots, yellowing, green spots in senescent leaves and green vein banding were observed in the Casanare samples (Supp. Fig. 1). Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen, USA). To know the potential cilevirus infection in these samples, three PfGSV specific (Ramos-González et al. 2020) and a CiLV-C2 generic primer pairs (Olmedo-Velarde et al. 2021) were used in the RT-PCR assays. All five passion fruit samples from Meta failed to produce either CiLV-C2 or CiLV-C2H or PfGSV amplicon whereas all three Casanare samples successfully amplified 321, 244 and 299 nts of PfGSV-RNA1 and -RNA2 amplicons using C13F/C13R, C6F/C6R and C8F/C8R primers, respectively. Bi-directional amplicon sequencing followed by BlastN analysis revealed ≥99% nt identity with the PfGSV-RNA1 (MK804173) and -RNA2 (MK804174) genome sequences. An optimized ribo-depleted library preparation protocol was utilized to prepare two cDNA libraries using the RNA extracts of a PfGSV suspected positive (Casanare) and a negative (Meta) samples (Chellappan et al., 2022). HTS libraries of Casanare and Meta samples resulted in 22.7 to 29.5 million raw reads, respectively. After adapter trimming and filtering, clean reads were mapped to the Arabidopsis thaliana reference genome and unmapped reads were de novo assembled (Chellappan et al., 2022). BlastN analysis from the assembled contigs identified 1-3 contigs corresponding to PfGSV-RNA1 and -RNA2, respectively, from Casanare sample whereas 3 contigs of SMV were identified in Meta passion fruit sample. No other virus sequence was obtained from either of the libraries. Assembled contigs covered 99.33% of the RNA1 and 94.42% of the RNA2 genome, with read depths of 64,474 and 119,549, respectively. Meta sample contigs (OP564897) covered >99% of the SMV genome, which shared >99% nt identity with the Colombian SMV isolates (KY249378, MW655827). Both RNA-1 (OP564895) and -2 (OP564896) segments of the Casanare isolate shared 99% nt identity with PfGSV isolate (MK804173-74). Our discovery identified PfGSV in Colombia, for the first-time outside Brazil and Paraguay. The findings of PfGSV in yellow passion fruit increases the potential threat and possibility of PfGSV movement via Brevipalpus sp. from passion fruit to other hosts.
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Affiliation(s)
- Avijit Roy
- USDA Agricultural Research Service, 17123, Molecular Plant Pathology Laboratory, Building 004, Room 117, BARC-West, 10300 Baltimore Avenue, Washington, District of Columbia, United States, 20250;
| | - Leon M Guillermo
- AGROSAVIA, 70126, Centro de Investigación La Libertad. Km.17 vía Pto. Lopez. Villavicencio, Bogota, Meta, Colombia;
| | - Schyler Nunziata
- USDA APHIS PPQ, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, Maryland, United States;
| | - Chellappan Padmanabhan
- USDA APHIS , PPCDL, USDA APHIS PPQ, Science and Technology, Bldg 580, BARC-East,, 9901 Powder Mill Road, Laurel, Maryland, United States, 20708;
| | - Yazmin Rivera
- USDA, Animal Plant Health Inspection Service; Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Plant Pathogen Confirmatory Diagnostics Laboratory, 9901 Powder Mill Rd, Laurel, Maryland, United States, 20705;
| | - Ronald H Brlansky
- University of Florida Citrus Research and Education Center, 57513, Department of Plant Pathology, Lake Alfred, Florida, United States;
| | - John Hartung
- USDA-ARS BARC, 57604, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States;
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9
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Tassi AD, Ramos-González PL, Sinico TE, Kitajima EW, Freitas-Astúa J. Circulative Transmission of Cileviruses in Brevipalpus Mites May Involve the Paracellular Movement of Virions. Front Microbiol 2022; 13:836743. [PMID: 35464977 PMCID: PMC9019602 DOI: 10.3389/fmicb.2022.836743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Plant viruses transmitted by mites of the genus Brevipalpus are members of the genera Cilevirus, family Kitaviridae, or Dichorhavirus, family Rhabdoviridae. They produce non-systemic infections that typically display necrotic and/or chlorotic lesions around the inoculation loci. The cilevirus citrus leprosis virus C (CiLV-C) causes citrus leprosis, rated as one of the most destructive diseases affecting this crop in the Americas. CiLV-C is vectored in a persistent manner by the flat mite Brevipalpus yothersi. Upon the ingestion of viral particles with the content of the infected plant cell, virions must pass through the midgut epithelium and the anterior podocephalic gland of the mites. Following the duct from this gland, virions reach the salivary canal before their inoculation into a new plant cell through the stylet canal. It is still unclear whether CiLV-C multiplies in mite cells and what mechanisms contribute to its movement through mite tissues. In this study, based on direct observation of histological sections from viruliferous mites using the transmission electron microscope, we posit the hypothesis of the paracellular movement of CiLV-C in mites which may involve the manipulation of septate junctions. We detail the presence of viral particles aligned in the intercellular spaces between cells and the gastrovascular system of Brevipalpus mites. Accordingly, we propose putative genes that could control either active or passive paracellular circulation of viral particles inside the mites.
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Affiliation(s)
- Aline Daniele Tassi
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, São Paulo, Brazil.,Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | | | - Thais Elise Sinico
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, São Paulo, Brazil.,Centro de Citricultura Sylvio Moreira, Cordeirópolis, Brazil
| | - Elliot Watanabe Kitajima
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - Juliana Freitas-Astúa
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, São Paulo, Brazil.,Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
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10
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Ramos-González PL, Chabi-Jesus C, Tassi AD, Calegario RF, Harakava R, Nome CF, Kitajima EW, Freitas-Astua J. A Novel Lineage of Cile-Like Viruses Discloses the Phylogenetic Continuum Across the Family Kitaviridae. Front Microbiol 2022; 13:836076. [PMID: 35418952 PMCID: PMC8996159 DOI: 10.3389/fmicb.2022.836076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/15/2022] [Indexed: 12/12/2022] Open
Abstract
An increasing number of plant species have been recognized or considered likely reservoirs of viruses transmitted by Brevipalpus mites. A tiny fraction of these viruses, primarily those causing severe economic burden to prominent crops, have been fully characterized. In this study, based on high-throughput sequencing, transmission electron microscopy analyses of virions in plant-infected tissues, viral transmission experiments, and the morphoanatomical identification of the involved Brevipalpus mites, we describe molecular and biological features of viruses representing three new tentative species of the family Kitaviridae. The genomes of Solanum violifolium ringspot virus (SvRSV, previously partially characterized), Ligustrum chlorotic spot virus (LigCSV), and Ligustrum leprosis virus (LigLV) have five open reading frames (ORFs) > 500 nts, two distributed in RNA1 and three in RNA2. RNA1 of these three viruses display the same genomic organization found in RNA1 of typical cileviruses, while their RNA2 are shorter, possessing only orthologs of genes p61, p32, and p24. LigCSV and LigLV are more closely related to each other than to SvRSV, but the identities between their genomic RNAs were lower than 70%. In gene-by-gene comparisons, ORFs from LigCSV and LigLV had the highest sequence identity values (nt sequences: 70–76% and deduced amino acid sequences: 74–83%). The next higher identity values were with ORFs from typical cileviruses, with values below 66%. Virions of LigLV (≈ 40 nm × 55 nm) and LigCSV (≈ 54 nm × 66 nm) appear almost spherical, contrasting with the bacilliform shape of SvRSV virions (≈ 47 nm × 101 nm). Mites collected from the virus-infected plants were identified as Brevipalpus papayensis, B. tucuman, and B. obovatus. Viruliferous B. papayensis mites successfully transmitted LigCSV to Arabidopsis thaliana. SvRSV, LigCSV, and LigLV seem to represent novel sub-lineages of kitaviruses that descent on parallel evolutionary branches from a common ancestor shared with the tentative cile-like virus hibiscus yellow blotch virus and typical cileviruses. Biological and molecular data, notably, the phylogenetic reconstruction based on the RdRp proteins in which strong support for monophyly of the family Kitaviridae is observed, mark an advance in the understanding of kitavirids.
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Affiliation(s)
- Pedro L Ramos-González
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
| | - Camila Chabi-Jesus
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil.,Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - Aline D Tassi
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil.,Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - Renata Faier Calegario
- Departamento de Fitotecnia e Fitossanidade, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ricardo Harakava
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
| | - Claudia F Nome
- Instituto de Patologia Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| | - Elliot W Kitajima
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
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11
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Olmedo Velarde A, Roy A, Larrea-Sarmiento A, Wang X, Padmanabhan C, Nunziata S, Nakhla MK, Hu J, Melzer M. First report of the hibiscus strain of citrus leprosis virus C2 infecting passionfruit (Passiflora edulis). PLANT DISEASE 2022; 106:2539. [PMID: 35253490 DOI: 10.1094/pdis-10-21-2314-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In Hawaii, passionfruit (Passiflora edulis; Passifloraceae) is grown primarily in residential properties and community gardens (CG). In 2019, passionfruit plants displaying chlorotic spots on young leaves, and green spots in senescing leaves were observed at two CG in Honolulu. Symptoms resembled those of passionfruit green spot virus (PfGSV) infection in Passiflora spp. (Ramos-González et al. 2020) and of the hibiscus strain of citrus leprosis virus C2 (CiLV-C2H) infection in hibiscus in Hawaii (Melzer et al. 2013). Both viruses belong to the genus Cilevirus, family Kitaviridae. Total RNA was extracted from two sample pools comprised of 40 symptomatic leaves collected from both the CG following a CTAB-based procedure (Li et al. 2008). To identify the virus associated with the P. edulis infection, reverse transcription (RT)-polymerase chain reaction (PCR) was performed using CiLV-C2 (Olmedo-Velarde et al. 2021) and PfGSV specific primers (Ramos-González et al. 2020). RT-PCR assay amplified the CiLV-C2 amplicon but failed to produce the PfGSV amplicon from infected leaves. Amplicon sequencing followed by a BLASTn search showed the nucleotide sequence had >99% identity with the CiLV-C2H-RNA1 (KC626783). A ribo-depleted RNA library created using the TruSeq Stranded Total RNA Library Prep kit (Illumina) underwent high throughput sequencing (HTS) on a NextSeq550 Illumina platform (2x75 cycles). The 6.5 million raw reads obtained were trimmed, filtered, and de novo assembled using Metaviral SPAdes v. 3.15.02 (Antipov et al. 2020). The resulting contigs were searched against an in-house database generated from GenBank virus and viroid sequences using BLASTn. This identified 12 and 3 contigs corresponding to CiLV-C2H and watermelon mosaic virus, respectively, with the latter being previously reported in passionfruit (Watanabe et al. 2016). RNA1 contigs covered 80.17% of the CiLV-C2H genome, whereas RNA2 contigs covered 94.5% with an average coverage depth of 31.660 and 57.121, respectively. To obtain the near complete genome of CiLV-C2H, gaps from the assembled HTS data were filled by overlapping RT-PCR followed by Sanger sequencing. RNA1 (8,536 nt, Acc. No. MW413437) and RNA2 (4,878 nt, MW413438) genome sequences shared 99.2% and 97.0% identity with CiLV-C2H-RNA1 (KC626783) and -RNA2 (KC626784). To further confirm the presence of CiLV-C2H in symptomatic P. edulis plants, 40 symptomatic leaf samples were individually tested by RT-PCR, and 30 samples were positive. Brevipalpus mites collected from CiLV-C2H-positive P. edulis leaves were transferred to common bean (Phaseolus vulgaris) seedlings (Garita et al. 2013). At 15-30 days post-transfer, RNA extracted from lesions observed in recipient plants tested positive for CiLV-C2H by RT-PCR. Total RNA from individual Brevipalpus mites was isolated, and cDNA was prepared to tentatively identify the mite species involved in CiLV-C2H transmission in passionfruit (Druciarek et al 2019, Olmedo-Velarde et al. 2021). CiLV-C2H was detected in individual mites, and the 28S ribosomal mite RNA sequence (MZ478051) shared 99-100% nucleotide identity with B. yothersi (MK293678 and MT812697), a vector of CiLV-C2 (Roy et al. 2013). CiLV-C2 currently has a host range limited to the families Malvaceae, Araceae, and Rutaceae (Roy et al. 2015). CiLV-C2H infects hibiscus alone and citrus in mixed infection with CiLV-C2 (Roy et al; 2018) which is responsible for causing citrus leprosis disease. Detection of CiLV-C2H in passionfruit expands the number of host families of CiLV-C2H.
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Affiliation(s)
- Alejandro Olmedo Velarde
- University of Hawaii System, 3939, Plant & Environmental Protection Sciences, 3190 Maile Way, St John 315, Honolulu, Hawaii, United States, 96822;
| | - Avijit Roy
- USDA Agricultural Research Service, 17123, Molecular Plant Pathology Laboratory, Building 004, Room 117, BARC-West, 10300 Baltimore Avenue, Washington, District of Columbia, United States, 20250;
| | - Adriana Larrea-Sarmiento
- University of Hawai'i at Manoa, 3949, PEPS, 3190 Maile Way, St John 310, Honolulu, Honolulu, Hawaii, United States, 96822-2217;
| | - Xupeng Wang
- University of Hawai'i at Manoa, 3949, Department of Plant and Environmental Protection Sciences, 3190 Maile Way, Room 310, Honolulu, Hawaii, United States, 96822
- University of Hawai'i at Manoa, 3949, Department of Plant and Environmental Protection Sciences, 3190 Maile Way, Room 310, Honolulu, Hawaii, United States, 96822;
| | - Chellappan Padmanabhan
- PPQ, CPHST, National Plant Germplasm and Biotechnology Laboratory, Laurel, Maryland, United States;
| | - Schyler Nunziata
- PPQ, CPHST, National Plant Germplasm and Biotechnology Laboratory, Laurel, Maryland, United States;
| | - Mark K Nakhla
- PPQ, CPHST, National Plant Germplasm and Biotechnology Laboratory, BARC-East, Bldg-580, Powder Mill Rd, Beltsville, Maryland, United States, 20705;
| | - John Hu
- 3190 Maile WayRm 310C310CHonolulu, Hawaii, United States, 96822
- United States;
| | - Michael Melzer
- University of Hawaii, Plant and Environmental Protection Sciences, 3190 Maile Way, St. John 310, Honolulu, Hawaii, United States, 96822;
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12
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Ramos-González PL, Pons T, Chabi-Jesus C, Arena GD, Freitas-Astua J. Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:771983. [PMID: 34804105 PMCID: PMC8602818 DOI: 10.3389/fpls.2021.771983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
The genus Cilevirus groups enveloped single-stranded (+) RNA virus members of the family Kitaviridae, order Martellivirales. Proteins P15, scarcely conserved polypeptides encoded by cileviruses, have no apparent homologs in public databases. Accordingly, the open reading frames (ORFs) p15, located at the 5'-end of the viral RNA2 molecules, are considered orphan genes (ORFans). In this study, we have delved into ORFs p15 and the relatively poorly understood biochemical properties of the proteins P15 to posit their importance for viruses across the genus and theorize on their origin. We detected that the ORFs p15 are under purifying selection and that, in some viral strains, the use of synonymous codons is biased, which might be a sign of adaptation to their plant hosts. Despite the high amino acid sequence divergence, proteins P15 show the conserved motif [FY]-L-x(3)-[FL]-H-x-x-[LIV]-S-C-x-C-x(2)-C-x-G-x-C, which occurs exclusively in members of this protein family. Proteins P15 also show a common predicted 3D structure that resembles the helical scaffold of the protein ORF49 encoded by radinoviruses and the phosphoprotein C-terminal domain of mononegavirids. Based on the 3D structural similarities of P15, we suggest elements of common ancestry, conserved functionality, and relevant amino acid residues. We conclude by postulating a plausible evolutionary trajectory of ORFans p15 and the 5'-end of the RNA2 of cileviruses considering both protein fold superpositions and comparative genomic analyses with the closest kitaviruses, negeviruses, nege/kita-like viruses, and unrelated viruses that share the ecological niches of cileviruses.
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Affiliation(s)
- Pedro L. Ramos-González
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
| | - Tirso Pons
- National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Camila Chabi-Jesus
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - Gabriella Dias Arena
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
| | - Juliana Freitas-Astua
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
- Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
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13
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Olmedo-Velarde A, Hu J, Melzer MJ. A Virus Infecting Hibiscus rosa-sinensis Represents an Evolutionary Link Between Cileviruses and Higreviruses. Front Microbiol 2021; 12:660237. [PMID: 34012426 PMCID: PMC8126721 DOI: 10.3389/fmicb.2021.660237] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/06/2021] [Indexed: 11/30/2022] Open
Abstract
Hibiscus (Hibiscus spp.) are popular ornamental and landscape plants in Hawaii which are susceptible to foliar diseases caused by viruses belonging to the genera Cilevirus and Higrevirus (family Kitaviridae). In this study, a virus infecting H. rosa-sinensis plants displaying foliar symptoms consistent with infection by a kitavirus, including yellow chlorotic blotches with a green perimeter, was characterized. The genome consisted of two RNAs 8.4 and 4.4 kb in length, and was organized most similarly to cileviruses, but with important distinctions. These included the location of the p29 homolog as the 3′-terminal open reading frame (ORF) of RNA2 instead of its typical locus at the 3′-end of RNA1; the absence of a p15 homolog on RNA2 and the adjacent intergenic region which also harbors small putative ORFs of unknown function; and the presence of an ORF encoding a 10 kDa protein at the 3′-terminal end of RNA1 that was also found to be present in the hibiscus green spot virus 2 genome. Spherical particles approximately 55–65 nm in diameter were observed in infected leaf tissue, and viral RNA was detected by reverse-transcription PCR in individual mites collected from symptomatic plants tentatively identified as Brevipalpus yothersi. Although phylogenetic analyses placed this virus between the higrevirus and cilevirus clades, we propose the tentative taxonomic placement of this virus, designated hibiscus yellow blotch virus (HYBV), within the genus Cilevirus.
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Affiliation(s)
- Alejandro Olmedo-Velarde
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, United States
| | - John Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, United States
| | - Michael J Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, United States
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14
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Chabi-Jesus C, Ramos-González PL, Postclam-Barro M, Fontenele RS, Harakava R, Bassanezi RB, Moreira AS, Kitajima EW, Varsani A, Freitas-Astúa J. Molecular Epidemiology of Citrus Leprosis Virus C: A New Viral Lineage and Phylodynamic of the Main Viral Subpopulations in the Americas. Front Microbiol 2021; 12:641252. [PMID: 33995302 PMCID: PMC8116597 DOI: 10.3389/fmicb.2021.641252] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Despite the importance of viral strains/variants as agents of emerging diseases, genetic and evolutionary processes affecting their ecology are not fully understood. To get insight into this topic, we assessed the population and spatial dynamic parameters of citrus leprosis virus C (CiLV-C, genus Cilevirus, family Kitaviridae). CiLV-C is the etiological agent of citrus leprosis disease, a non-systemic infection considered the main viral disorder affecting citrus orchards in Brazil. Overall, we obtained 18 complete or near-complete viral genomes, 123 complete nucleotide sequences of the open reading frame (ORF) encoding the putative coat protein, and 204 partial nucleotide sequences of the ORF encoding the movement protein, from 430 infected Citrus spp. samples collected between 1932 and 2020. A thorough examination of the collected dataset suggested that the CiLV-C population consists of the major lineages CRD and SJP, unevenly distributed, plus a third one called ASU identified in this work, which is represented by a single isolate found in an herbarium sample collected in Asuncion, Paraguay, in 1937. Viruses from the three lineages share about 85% nucleotide sequence identity and show signs of inter-clade recombination events. Members of the lineage CRD were identified both in commercial and non-commercial citrus orchards. However, those of the lineages SJP were exclusively detected in samples collected in the citrus belt of São Paulo and Minas Gerais, the leading Brazilian citrus production region, after 2015. The most recent common ancestor of viruses of the three lineages dates back to, at least, ∼1500 years ago. Since citrus plants were introduced in the Americas by the Portuguese around the 1520s, the Bayesian phylodynamic analysis suggested that the ancestors of the main CiLV-C lineages likely originated in contact with native vegetation of South America. The intensive expansion of CRD and SJP lineages in Brazil started probably linked to the beginning of the local citrus industry. The high prevalence of CiLV-C in the citrus belt of Brazil likely ensues from the intensive connectivity between orchards, which represents a potential risk toward pathogen saturation across the region.
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Affiliation(s)
- Camila Chabi-Jesus
- Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, São Paulo, Brazil.,Instituto Biológico/IB, São Paulo, Brazil
| | | | | | - Rafaela Salgado Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | | | | | - Alecio S Moreira
- Fundo de Defesa da Citricultura, Araraquara, Brazil.,Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Juliana Freitas-Astúa
- Instituto Biológico/IB, São Paulo, Brazil.,Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
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15
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Morozov SY, Lazareva EA, Solovyev AG. Sequence Relationships of RNA Helicases and Other Proteins Encoded by Blunervirus RNAs Highlight Recombinant Evolutionary Origin of Kitaviral Genomes. Front Microbiol 2020; 11:561092. [PMID: 33193144 PMCID: PMC7658314 DOI: 10.3389/fmicb.2020.561092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/28/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- Sergey Y Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.,Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia
| | - Ekaterina A Lazareva
- Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia
| | - Andrey G Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.,Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia.,Institute of Agricultural Biotechnology, Moscow, Russia
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16
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Discovery of Two Novel Negeviruses in a Dungfly Collected from the Arctic. Viruses 2020; 12:v12070692. [PMID: 32604989 PMCID: PMC7412485 DOI: 10.3390/v12070692] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/11/2022] Open
Abstract
Negeviruses are a proposed group of insect-specific viruses that can be separated into two distinct phylogenetic clades, Nelorpivirus and Sandewavirus. Negeviruses are well-known for their wide geographic distribution and broad host range among hematophagous insects. In this study, the full genomes of two novel negeviruses from each of these clades were identified by RNA extraction and sequencing from a single dungfly (Scathophaga furcata) collected from the Arctic Yellow River Station, where these genomes are the first negeviruses from cold zone regions to be discovered. Nelorpivirus dungfly1 (NVD1) and Sandewavirus dungfly1 (SVD1) have the typical negevirus genome organization and there was a very high coverage of viral transcripts. Small interfering RNAs derived from both viruses were readily detected in S. furcata, clearly showing that negeviruses are targeted by the host antiviral RNA interference (RNAi) pathway. These results and subsequent in silico analysis (studies) of public database and published virome data showed that the hosts of nege-like viruses include insects belonging to many orders as well as various non-insects in addition to the hematophagous insects previously reported. Phylogenetic analysis reveals at least three further groups of negeviruses, as well as several poorly resolved solitary branches, filling in the gaps within the two sub-groups of negeviruses and plant-associated viruses in the Kitaviridae. The results of this study will contribute to a better understanding of the geographic distribution, host range, evolution and host antiviral immune responses of negeviruses.
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Kondo H, Fujita M, Hisano H, Hyodo K, Andika IB, Suzuki N. Virome Analysis of Aphid Populations That Infest the Barley Field: The Discovery of Two Novel Groups of Nege/Kita-Like Viruses and Other Novel RNA Viruses. Front Microbiol 2020; 11:509. [PMID: 32318034 PMCID: PMC7154061 DOI: 10.3389/fmicb.2020.00509] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Aphids (order Hemiptera) are important insect pests of crops and are also vectors of many plant viruses. However, little is known about aphid-infecting viruses, particularly their diversity and relationship to plant viruses. To investigate the aphid viromes, we performed deep sequencing analyses of the aphid transcriptomes from infested barley plants in a field in Japan. We discovered virus-like sequences related to nege/kita-, flavi-, tombus-, phenui-, mononega-, narna-, chryso-, partiti-, and luteoviruses. Using RT-PCR and sequence analyses, we determined almost complete sequences of seven nege/kitavirus-like virus genomes; one of which was a variant of the Wuhan house centipede virus (WHCV-1). The other six seem to belong to four novel viruses distantly related to Wuhan insect virus 9 (WhIV-9) or Hubei nege-like virus 4 (HVLV-4). We designated the four viruses as barley aphid RNA virus 1 to 4 (BARV-1 to -4). Moreover, some nege/kitavirus-like sequences were found by searches on the transcriptome shotgun assembly (TSA) libraries of arthropods and plants. Phylogenetic analyses showed that BARV-1 forms a clade with WHCV-1 and HVLV-4, whereas BARV-2 to -4 clustered with WhIV-9 and an aphid virus, Aphis glycines virus 3. Both virus groups (tentatively designated as Centivirus and Aphiglyvirus, respectively), together with arthropod virus-like TSAs, fill the phylogenetic gaps between the negeviruses and kitaviruses lineages. We also characterized the flavi/jingmen-like and tombus-like virus sequences as well as other RNA viruses, including six putative novel viruses, designated as barley aphid RNA viruses 5 to 10. Interestingly, we also discovered that some aphid-associated viruses, including nege/kita-like viruses, were present in different aphid species, raising a speculation that these viruses might be distributed across different aphid species with plants being the reservoirs. This study provides novel information on the diversity and spread of nege/kitavirus-related viruses and other RNA viruses that are associated with aphids.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Miki Fujita
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Hiroshi Hisano
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
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Arena GD, Ramos-González PL, Falk BW, Casteel CL, Freitas-Astúa J, Machado MA. Plant Immune System Activation Upon Citrus Leprosis Virus C Infection Is Mimicked by the Ectopic Expression of the P61 Viral Protein. FRONTIERS IN PLANT SCIENCE 2020; 11:1188. [PMID: 32849736 PMCID: PMC7427430 DOI: 10.3389/fpls.2020.01188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/22/2020] [Indexed: 05/04/2023]
Abstract
Citrus leprosis virus C (CiLV-C, genus Cilevirus, family Kitaviridae) is an atypical virus that does not spread systemically in its plant hosts. Upon its inoculation by Brevipalpus mites, only localized lesions occur, and the infection remains limited to cells around mite feeding sites. Here, we aimed to gain insights into the putative causes of viral unfitness in plants by expanding the limited knowledge of the molecular mechanisms underlying plant/kitavirid interactions. Firstly, we quantified the CiLV-C viral RNAs during the infection in Arabidopsis thaliana plants using RT-qPCR and systematized it by defining three stages of distinguishing subgenomic and genomic RNA accumulation: i) 0-24 h after infestation, ii) 2-4 days after infestation (dai), and iii) 6-10 dai. Accordingly, the global plant response to CiLV-C infection was assessed by RNA-Seq at each period. Results indicated a progressive reprogramming of the plant transcriptome in parallel to the increasing viral loads. Gene ontology enrichment analysis revealed the induction of cell growth-related processes at the early stages of the infection and the triggering of the SA-mediated pathway, ROS burst and hypersensitive response (HR) at the presymptomatic stage. Conversely, infected plants downregulated JA/ET-mediated pathways and processes involved in the primary metabolism including photosynthesis. Marker genes of unfolded protein response were also induced, suggesting a contribution of the endoplasmic reticulum stress to the cell death caused by the viral infection. Finally, we transiently expressed CiLV-C proteins in Nicotiana benthamiana plants to undertake their roles in the elicited plant responses. Expression of the CiLV-C P61 protein consistently triggered ROS burst, upregulated SA- and HR-related genes, increased SA levels, reduced JA levels, and caused cell death. Mimicry of responses typically observed during CiLV-C-plant interaction indicates P61 as a putative viral effector causing the HR-like symptoms associated with the infection. Our data strengthen the hypothesis that symptoms of CiLV-C infection might be the outcome of a hypersensitive-like response during an incompatible interaction. Consequently, the locally restricted infection of CiLV-C, commonly observed across infections by kitavirids, supports the thesis that these viruses, likely arising from an ancestral arthropod-infecting virus, are unable to fully circumvent plant defenses.
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Affiliation(s)
- Gabriella D. Arena
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, Brazil
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, São Paulo, Brazil
| | - Pedro Luis Ramos-González
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, São Paulo, Brazil
- *Correspondence: Pedro Luis Ramos-González, ; Juliana Freitas-Astúa,
| | - Bryce W. Falk
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Clare L. Casteel
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Juliana Freitas-Astúa
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, São Paulo, Brazil
- Laboratório de Virologia Vegetal, Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
- *Correspondence: Pedro Luis Ramos-González, ; Juliana Freitas-Astúa,
| | - Marcos A. Machado
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, Brazil
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