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Bragard C, Baptista P, Chatzivassiliou E, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Stefani E, Thulke H, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Migheli Q, Vloutoglou I, Czwienczek E, Streissl F, Carluccio AV, Chiumenti M, Di Serio F, Rubino L, Reignault PL. Pest categorisation of chickpea chlorotic dwarf virus. EFSA J 2022; 20:e07625. [PMID: 36398295 PMCID: PMC9664252 DOI: 10.2903/j.efsa.2022.7625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The EFSA Panel on Plant Health conducted a pest categorisation of chickpea chlorotic dwarf virus (CpCDV) for the EU territory. The identity of CpCDV, a member of the genus Mastrevirus (family Geminiviridae) is established. Reliable detection and identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. CpCDV has been reported in Africa, Asia and Oceania. It has not been reported in the EU. CpCDV infects plant species in the family Fabaceae and several species of other families (Amaranthaceae, Brassicaceae, Caricaceae, Cucurbitaceae, Malvaceae and Solanaceae), including weeds. It may induce symptoms on its hosts, causing severe yield reduction. The virus is transmitted in a persistent, circulative and non‐propagative manner by the leafhopper species Orosius orientalis and O. albicinctus, which are not regulated. O. orientalis is known to be present in some EU member states. Plants for planting (other than seeds), parts of plants and cut flowers of CpCDV hosts and viruliferous leafhoppers were identified as the most relevant pathways for the entry of CpCDV into the EU. Cultivated and wild hosts of CpCDV are distributed across the EU. Would the pest enter and establish in the EU territory, impact on the production of cultivated hosts is expected. Phytosanitary measures are available to prevent entry and spread of the virus in the EU. CpCDV fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.
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Identification of New Chickpea Virus and Control of Chickpea Virus Disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:6465505. [PMID: 35668786 PMCID: PMC9167091 DOI: 10.1155/2022/6465505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 11/18/2022]
Abstract
Objective. The objective of the study was to discuss the classification, virus characteristics, detection methods, and control measures of chickpea virus, with an aim to provide a theoretical basis for identification of new chickpea virus and control of chickpea virus disease. Methods. The domestic and foreign studies were reviewed, and the virus coat protein or nucleic acid sequence was identified by immunological and molecular diagnostic techniques. Results. There were 14 main types of chickpea viruses attacking, and seven Luteoviridae viruses were reported, namely, chickpea chlorotic stunt virus (CpCSV), bean leafroll virus (BLRV), beet western yellows virus (BWYV), soybean dwarf virus (SbDV), cotton leafroll dwarf virus (CLRDV), cucurbit aphid-borne yellows virus (CABYV), and phasey bean mild yellows virus (PhBMYV). The family Geminiviridae includes chickpea chlorotic dwarf virus (CpCDV), chickpea chlorosis virus (CpCV), chickpea redleaf virus (CpRLV), chickpea yellows virus (CpYV), and mastrevirus. The family Nanoviridae is dominated by the faba bean necrotic yellows virus (FBNYV). The family Bromoviridae includes cucumber mosaic virus (CMV) and alfalfa mosaic virus (AMV). Conclusion. At present, there are mainly 12 types of viruses infecting chickpeas, which are transmitted by leafhoppers or aphids and are associated with symptoms such as yellowing, chlorosis, and stunted pod development, resulting in serious yield loss. Correct use of various molecular diagnostic tools to detect and identify chickpea virus can accurately assess chickpea virus infection and provide a basis for the prevention and treatment of chickpea virus disease.
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Reddy MG, Baranwal VK, Sagar D, Rao GP. Molecular characterization of chickpea chlorotic dwarf virus and peanut witches' broom phytoplasma associated with chickpea stunt disease and identification of new host crops and leafhopper vectors in India. 3 Biotech 2021; 11:112. [PMID: 33598378 PMCID: PMC7859126 DOI: 10.1007/s13205-020-02613-7] [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: 11/07/2020] [Accepted: 12/23/2020] [Indexed: 11/02/2022] Open
Abstract
An investigation was carried out to identify and characterize the phytoplasma and viruses associated with the chickpea varieties showing severe stunting, leaf reddening, yellowing and phyllody symptoms during the summer season of 2018-2019 and 2019-2020 in eight states of India. The average disease incidence was recorded from 3 to 32% in different states. The presence of chickpea chlorotic dwarf virus (CpCDV) was confirmed in thirty-seven chickpea samples by amplification of CpCDV coat protein gene and sequence comparison analysis. No record of association of luteovirus, polerovirus and cucumovirus could be detected in any of the symptomatic chickpea samples by RT-PCR assay. Brassica nigra, B. juncea, Lens culinaris, two weeds (Heteropogan contartus, Aeschynomene virginica) and one leafhopper (Amarasca biguttula) were identified as new putative hosts for CpCDV. Association of peanut witches' broom phytoplasma was confirmed in twenty-eight chickpea samples, Sesamum indicum, five weeds hosts and two leafhopper species (Exitianus indicus, Empoasca motti) using nested PCR assays with primer pairs P1/P7 and R16F2n/R16Rn. The results of phytoplasma association in plants and leafhopper samples were further validated by using five multilocus genes (secA, rp, imp, tuf and secY) specific primers. Sequence comparison, phylogenetic and virtual RFLP analysis of 16S rRNA gene and five multilocus genes confirmed the identity of association of 16SrII-C and 16SrII-D subgroups of phytoplasmas strain with chickpea samples collected from Andhra Pradesh (AP), Telangana, Karnataka, Madhya Pradesh, Uttar Pradesh and New Delhi. Mixed infection of phytoplasma (16SrII-D) and CpCDV was also detected in symptomatic chickpea samples from AP and Telangana. The reports of association of 16SrII-C subgroup phytoplasma in chickpea and 16SrII-D subgroup phytoplasma in C. sparsiflora and C. roseus are the new host records in world and from India, respectively.
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Affiliation(s)
- Madem Gurivi Reddy
- Department of Plant Pathology, S.V. Agricultural College, Tirupati, Andhra Pradesh 517502 India
- Division of Plant Pathology, Indian Agriculture Research Institute, Pusa Campus, New Delhi, 110012 India
| | - Virendra Kumar Baranwal
- Division of Plant Pathology, Indian Agriculture Research Institute, Pusa Campus, New Delhi, 110012 India
| | - Doddachowdappa Sagar
- Division of Entomology, Indian Agriculture Research Institute, Pusa Campus, New Delhi, 110012 India
| | - Govind Pratap Rao
- Division of Plant Pathology, Indian Agriculture Research Institute, Pusa Campus, New Delhi, 110012 India
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Isolation of single-chain variable fragment (scFv) antibodies for detection of Chickpea chlorotic dwarf virus (CpCDV) by phage display. Arch Virol 2020; 165:2789-2798. [PMID: 32970278 DOI: 10.1007/s00705-020-04813-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/13/2020] [Indexed: 10/23/2022]
Abstract
Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus), has a wide host range and geographic distribution in many parts of the world, and it is one of the most important legume-infecting viruses. Detection of CpCDV-infected plants in the field and evaluation of viral resistance of plant cultivars are possible by conducting serological assays. Here, development and characterization of a specific recombinant monoclonal antibody for CpCDV as a diagnostic tool are described. For this purpose, the coat protein of CpCDV was expressed in Escherichia coli strain Rosetta (DE3) and used to screen a Tomlinson phage display antibody library to select a specific single-chain variable fragment (scFv). In each round of biopanning, the affinity of the phage for CpCDV-CP was tested by enzyme-linked immunosorbent assay (ELISA). The results showed that the specificity of the eluted phages increased after each round of panning. Testing of individual clones by ELISA showed that five clones of the monoclonal phage were more strongly reactive against CpCDV than the other clones. All selected positive clones contained the same sequence. The phage-displayed scFv antibody, which was named CpCDV-scFvB9, did not bind to other tested plant pathogens and showed high sensitivity in the detection of CpCDV. A Western blot assay demonstrated that CpCDV-scFvB9 reacted with the recombinant coat protein of CpCDV. Finally, the interaction CpCDV-scFvB9 and CpCDV-CP was analyzed in a molecular docking experiment. This is the first report on production of an scFv antibody against CpCDV, which could be useful for immunological detection of the virus.
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Samarfard S, McTaggart AR, Sharman M, Bejerman NE, Dietzgen RG. Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus. Pathogens 2020; 9:pathogens9030214. [PMID: 32183134 PMCID: PMC7157637 DOI: 10.3390/pathogens9030214] [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: 02/13/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/27/2022] Open
Abstract
Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1–3) of an Australian AMV isolate from alfalfa.
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Affiliation(s)
- Samira Samarfard
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia;
| | - Alistair R. McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia;
| | - Murray Sharman
- Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia;
| | - Nicolás E. Bejerman
- Instituto de Patología Vegetal–Centro de Investigaciones Agropecuarias–Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba 5020, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Unidad de Fitopatología y Modelización Agrícola, Córdoba 5020, Argentina
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia;
- Correspondence: ; Tel.: +61-7-334-66503
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6
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Makkouk KM. Plant Pathogens which Threaten Food Security: Viruses of Chickpea and Other Cool Season Legumes in West Asia and North Africa. Food Secur 2020. [DOI: 10.1007/s12571-020-01017-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Complete Genome Sequence of a New Chickpea Chlorotic Dwarf Virus Strain Isolated from Tomato in Kenya, Obtained from Illumina Sequencing. Microbiol Resour Announc 2020; 9:9/5/e01344-19. [PMID: 32001561 PMCID: PMC6992865 DOI: 10.1128/mra.01344-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High-throughput sequence analysis revealed the complete genome sequence of a novel, hitherto uncharacterized strain of Chickpea chlorotic dwarf virus (CpCDV) from tomato plants in Kenya. The sequence shared its highest nucleotide similarity (88.7%) with two CpCDV isolates from Burkina Faso. High-throughput sequence analysis revealed the complete genome sequence of a novel, hitherto uncharacterized strain of Chickpea chlorotic dwarf virus (CpCDV) from tomato plants in Kenya. The sequence shared its highest nucleotide similarity (88.7%) with two CpCDV isolates from Burkina Faso.
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Complete Genome Sequence of a New Mastrevirus, Chickpea Redleaf Virus 2, from Australia. Microbiol Resour Announc 2019; 8:8/36/e00602-19. [PMID: 31488527 PMCID: PMC6728637 DOI: 10.1128/mra.00602-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present here the complete genome sequence of a novel mastrevirus isolated from
Cicer arietinum
(chickpea) from Australia. We propose the name chickpea redleaf virus 2.
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Diamos AG, Crawford JM, Mason HS. Fine-tuning expression of begomoviral movement and nuclear shuttle proteins confers cell-to-cell movement to mastreviral replicons in Nicotiana benthamiana leaves. J Gen Virol 2019; 100:1038-1051. [PMID: 31107197 DOI: 10.1099/jgv.0.001275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Geminiviruses are a group of small plant viruses responsible for devastating crop damage worldwide. The emergence of agricultural diseases caused by geminiviruses is attributed in part to their high rates of recombination, leading to complementary function between viral components across species and genera. We have developed a mastreviral reporter system based on bean yellow dwarf virus (BeYDV) that replicates to high levels in the plant nucleus, expressing very high levels of GFP. To investigate the potential for complementation of movement function by other geminivirus genera, the movement protein (MP) and nuclear shuttle protein (NSP) from the bipartite begomovirus Bean dwarf mosaic virus (BDMV) were produced and characterized in Nicotiana benthamiana leaves. While overexpression of MP and NSP strongly inhibited GFP expression from the mastreviral reporter and caused adverse plant symptoms, optimizing the expression levels of MP and NSP allowed functional cell-to-cell movement. Hybrid virus vectors were created that express BDMV MP and NSP from mastreviral replicons, allowing efficient cell-to-cell movement comparable to native BDMV replicons. We find that the expression levels of MP and NSP must be fine-tuned to provide sufficient MP/NSP for movement without eliciting the plant hypersensitive response or adversely impacting gene expression from viral replicons. The ability to confer cell-to-cell movement to mastrevirus replicons depended strongly on replicon size: 2.1-2.7 kb replicons were efficiently moved, while 3 kb replicons were inhibited, and 3.9 kb replicons were very strongly inhibited. Optimized expression of MP/NSP from the normally phloem-limited Abutilon mosaic virus (AbMV) allows efficient movement in non-phloem cells.
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Affiliation(s)
- Andrew G Diamos
- 1 Center for Immunology, Virology, and Vaccinology, Biodesign Institute at ASU, and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - John M Crawford
- 1 Center for Immunology, Virology, and Vaccinology, Biodesign Institute at ASU, and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Hugh S Mason
- 1 Center for Immunology, Virology, and Vaccinology, Biodesign Institute at ASU, and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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10
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Hameed U, Zia-Ur-Rehman M, Ali SA, Haider MS, Brown JK. Invasion of previously unreported dicot plant hosts by chickpea chlorotic dwarf virus in Pakistan. Virusdisease 2019; 30:95-100. [DOI: 10.1007/s13337-018-0454-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 04/18/2018] [Indexed: 10/16/2022] Open
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Kanakala S, Kuria P. Chickpea chlorotic dwarf virus: An Emerging Monopartite Dicot Infecting Mastrevirus. Viruses 2018; 11:E5. [PMID: 30577666 PMCID: PMC6357115 DOI: 10.3390/v11010005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/26/2018] [Accepted: 12/04/2018] [Indexed: 12/25/2022] Open
Abstract
Chickpea stunt disease (CSD), caused by Chickpea chlorotic dwarf virus (CpCDV) is a threat to chickpea production leading to yield losses of 75⁻95%. Chickpea chlorotic dwarf virus is a monopartite, single-stranded circular DNA virus in the genus Mastrevirus and family Geminiviridae. It is transmitted by Orosius albicinctus in a circulative (persistent) and nonpropagative manner. Symptoms of CSD include very small leaves, intense discoloration (yellowing (kabuli type) and reddening (desi type)), and bushy stunted appearance of the plant. Presently, CpCDVs occurs in Africa, Asia, Australia, and the Middle East, causing extensive losses on economically important crops in in the families Fabaceae, Asteraceae, Amaranthaceae, Brassicaceae, Cucurbitaceae, Caricaceae, Chenopodiaceae, Leguminosae, Malvaceae, Pedaliaceae, and Solanaceae. High frequency of recombinations has played a significant role in the wide host range, diversification, and rapid evolution of CpCDVs. This review highlights the extensive research on the CpCDV genome diversity, host range, plant⁻virus⁻insect interactions, and RNA interference-based resistance of CpCDV, providing new insights into the host adaptation and virus evolution.
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Affiliation(s)
- Surapathrudu Kanakala
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50010, USA.
| | - Paul Kuria
- Kenya Agricultural and Livestock Research Organization, Nairobi 00200, Kenya.
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Hamza M, Tahir MN, Mustafa R, Kamal H, Khan MZ, Mansoor S, Briddon RW, Amin I. Identification of a dicot infecting mastrevirus along with alpha- and betasatellite associated with leaf curl disease of spinach (Spinacia oleracea) in Pakistan. Virus Res 2018; 256:174-182. [PMID: 30149045 DOI: 10.1016/j.virusres.2018.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/16/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022]
Abstract
Spinach is a common vegetable crop and very little data is available about its virus infection. Symptomatic leaves of spinach were collected during field survey. Circular DNA molecules were amplified from symptomatic samples using rolling circle amplification (RCA). After restriction analysis, presumed bands of virus and satellites were cloned, sequenced and analyzed. Analysis of sequenced RCA product revealed the presence of chickpea chlorotic dwarf virus (CpCDV; Mastrevirus). Further analyses of the cloned virus showed that strain "C" of CpCDV was present in symptomatic samples of spinach collected from field associated with vein darkening, curling and enations on leaves. Amplification of alpha- and betasatellites with universal primers was performed. CpCDV showed association with cotton leaf curl Multan betasatellite (CLCuMB) and cotton leaf curl Multan alphasatellites (CLCuMA). Infectivity analysis of CpCDV and CpCDV/CLCuMB were done in N. benthamiana using particle bombardment method and the results showed that CpCDV was able to transreplicates CLCuMB in this host. To our knowledge, this is the first report of a dicot infecting mastrevirus (CpCDV) along with CLCuMB and CLCuMA associated with leaf curl disease of spinach in Pakistan. The significance of the results is discussed.
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Affiliation(s)
- Muhammad Hamza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Nouman Tahir
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan; Department of Plant Pathology, Bahauddin Zakariya University, Multan, Pakistan
| | - Roma Mustafa
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Hira Kamal
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Zuhaib Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
| | - Rob W Briddon
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan.
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Molecular characterization of faba bean necrotic yellows viruses in Tunisia. Arch Virol 2017; 163:687-694. [PMID: 29147784 DOI: 10.1007/s00705-017-3651-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/06/2017] [Indexed: 10/18/2022]
Abstract
Faba bean necrotic yellows virus (FBNYV) (genus Nanovirus; family Nanoviridae) has a genome comprising eight individually encapsidated circular single-stranded DNA components. It has frequently been found infecting faba bean (Vicia faba L.) and chickpea (Cicer arietinum L.) in association with satellite molecules (alphasatellites). Genome sequences of FBNYV from Azerbaijan, Egypt, Iran, Morocco, Spain and Syria have been determined previously and we now report the first five genome sequences of FBNYV and associated alphasatellites from faba bean sampled in Tunisia. In addition, we have determined the genome sequences of two additional FBNYV isolates from chickpea plants sampled in Syria and Iran. All individual FBNYV genome component sequences that were determined here share > 84% nucleotide sequence identity with FBNYV sequences available in public databases, with the DNA-M component displaying the highest degree of diversity. As with other studied nanoviruses, recombination and genome component reassortment occurs frequently both between FBNYV genomes and between genomes of nanoviruses belonging to other species.
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Zaagueri T, Miozzi L, Mnari-Hattab M, Noris E, Accotto GP, Vaira AM. Deep Sequencing Data and Infectivity Assays Indicate that Chickpea Chlorotic Dwarf Virus is the Etiological Agent of the "Hard Fruit Syndrome" of Watermelon. Viruses 2017; 9:E311. [PMID: 29068372 PMCID: PMC5707518 DOI: 10.3390/v9110311] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/13/2017] [Accepted: 10/21/2017] [Indexed: 11/25/2022] Open
Abstract
Chickpea chlorotic dwarf virus (CpCDV), a polyphagous mastrevirus, family Geminiviridae, has been recently linked to the onset of the "hard fruit syndrome" of watermelon, first described in Tunisia, that makes fruits unmarketable due to the presence of white hard portions in the flesh, chlorotic mottling on the rind, and an unpleasant taste. To investigate the etiological agent of this disease, total RNA extracted from symptomatic watermelon fruits was subjected to small RNA sequencing through next generation sequencing (NGS) techniques. Data obtained showed the presence of CpCDV and two other viral species. However, following validation through polymerase chain reaction (PCR), CpCDV was the only viral species consistently detected in all samples. Watermelon seedlings were then challenged by an agroinfectious CpCDV clone; several plants proved to be CpCDV-infected, and were able to produce fruits. CpCDV infected and replicated in watermelon fruits and leaves, leading to abnormality in fruits and in seed production, similar to those described in field. These results indicate that CpCDV is the etiological agent of the "hard fruit syndrome" of watermelon.
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Affiliation(s)
- Takoua Zaagueri
- Laboratoire de Biotechnologie Appliquée à l'Agriculture, Institut National de la Recherche Agronomique de Tunisie (INRAT), Université de Carthage, El Rue Hedi Karray Menzah, 1004 Tunis, Tunisia.
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Laura Miozzi
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Monia Mnari-Hattab
- Laboratoire de Biotechnologie Appliquée à l'Agriculture, Institut National de la Recherche Agronomique de Tunisie (INRAT), Université de Carthage, El Rue Hedi Karray Menzah, 1004 Tunis, Tunisia.
| | - Emanuela Noris
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
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Picard C, Dallot S, Brunker K, Berthier K, Roumagnac P, Soubeyrand S, Jacquot E, Thébaud G. Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:139-160. [PMID: 28525307 DOI: 10.1146/annurev-phyto-080516-035616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.
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Affiliation(s)
- Coralie Picard
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Sylvie Dallot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | - Philippe Roumagnac
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | | | - Emmanuel Jacquot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Gaël Thébaud
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
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16
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Kraberger S, Geering ADW, Walters M, Martin DP, Varsani A. Novel mastreviruses identified in Australian wild rice. Virus Res 2017; 238:193-197. [PMID: 28684155 DOI: 10.1016/j.virusres.2017.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/29/2017] [Accepted: 07/02/2017] [Indexed: 11/15/2022]
Abstract
Most known mastreviruses (family Geminiviridae) infect members of the grass family, Poaceae. Although the greatest number of grass-infecting mastrevirus species have been discovered in Africa, it is apparent that the ten grass-infecting mastrevirus species that have so far only been discovered in south-east Queensland have a degree of diversity that rivals that observed in Africa. In this study, we have used a deep sequencing approach to identify two new mastrevirus species, tentatively named rice latent virus 1 and 2 (RLV 1 and 2), from two, undescribed wild rice species (Oryza AA genome group) in Cape York Peninsula, Queensland. The sequences of these new viruses had less than 70% identity with any previously identified mastrevirus, and therefore their discovery vastly expands the known diversity of monocot-infecting mastreviruses in Australia. This study also highlights the potential risks of novel crop pathogens emerging from uncultivated grass species, as the wild rice hosts are very closely related to domesticated rice.
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Andrew D W Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Matthew Walters
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA; School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa.
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17
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New strains of chickpea chlorotic dwarf virus discovered on diseased papaya and tomato plants in Burkina Faso. Arch Virol 2017; 162:1791-1794. [DOI: 10.1007/s00705-017-3262-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/11/2017] [Indexed: 11/27/2022]
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18
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Stainton D, Martin DP, Muhire BM, Lolohea S, Halafihi M, Lepoint P, Blomme G, Crew KS, Sharman M, Kraberger S, Dayaram A, Walters M, Collings DA, Mabvakure B, Lemey P, Harkins GW, Thomas JE, Varsani A. The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events. Virus Evol 2015; 1:vev009. [PMID: 27774281 PMCID: PMC5014477 DOI: 10.1093/ve/vev009] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component single-stranded DNA virus, which infects banana plants in many regions of the world, often resulting in large-scale crop losses. We analyzed 171 banana leaf samples from fourteen countries and recovered, cloned, and sequenced 855 complete BBTV components including ninety-four full genomes. Importantly, full genomes were determined from eight countries, where previously no full genomes were available (Samoa, Burundi, Republic of Congo, Democratic Republic of Congo, Egypt, Indonesia, the Philippines, and the USA [HI]). Accounting for recombination and genome component reassortment, we examined the geographic structuring of global BBTV populations to reveal that BBTV likely originated in Southeast Asia, that the current global hotspots of BBTV diversity are Southeast Asia/Far East and India, and that BBTV populations circulating elsewhere in the world have all potentially originated from infrequent introductions. Most importantly, we find that rather than the current global BBTV distribution being due to increases in human-mediated movements of bananas over the past few decades, it is more consistent with a pattern of infrequent introductions of the virus to different parts of the world over the past 1,000 years.
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Affiliation(s)
- Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Darren P Martin
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Brejnev M Muhire
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Mana'ia Halafihi
- Ministry of Agriculture and Food, Forests and Fisheries, Kingdom of Tonga
| | | | - Guy Blomme
- Bioversity International Uganda Office, Naguru, Kampala, Uganda
| | - Kathleen S Crew
- Queensland Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Murray Sharman
- Queensland Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Anisha Dayaram
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Matthew Walters
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - David A Collings
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Batsirai Mabvakure
- South African National Bioinformatics Institute, MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Bellville, 7535, South Africa
| | - Philippe Lemey
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Gordon W Harkins
- South African National Bioinformatics Institute, MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Bellville, 7535, South Africa
| | - John E Thomas
- The University of Queensland, Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, Ecosciences Precinct, PO Box 46, Brisbane, QLD, 4001, Australia
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand; Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
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19
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Fahmy IF, Taha O, El-Ashry AN. First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash. Virusdisease 2015; 26:33-41. [PMID: 26436119 PMCID: PMC4585055 DOI: 10.1007/s13337-014-0246-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/29/2014] [Indexed: 10/24/2022] Open
Abstract
This study aims to identifying and characterizing some molecular properties of geminiviruses co-infection in squash field crop cultivated in Egypt. Squash crops observed to be heavily infected with several insect vectors, also severe chlorosis and stunting was observed. Electron microscopic analysis has revealed geminate capsid particles which indicate the infection of Geminiviruses, especially SqLCV which represent an economic problem to squash filed crop in Egypt. We have investigated possible mixed infections with different plant viruses associated with chlorotic stunt diseases and or other genus groups of geminiviruses. The main objective of this study is to investigate the recombination events, possible recombinants and variants among these genera in the same family differing in vector transmission. This is the first report of the molecular characterization, phylogenetic analysis and putative recombination events of the full length genome of the Chickpea Chlorotic Dwarf Mastrevirus in Egypt. And the first report of co-infection with another begomovirus infecting squash plants. A full length clone of both viruses were isolated and characterized at the molecular level. The complete nucleotide sequence of DNA-A was determined (2,572 bp) and submitted to the genbank under accession no. KF692356. The isolate from Egypt has about 97.8 % homology with the Chickpea chlorotic dwarf virus (CpCDV) isolate from Syria DNA-A isolate FR687959, a 83.2 % homology with the Sudan isolate AM933134 and a 82.7 % homology with Pakistan isolate FR687960. To best of our knowledge this is the first report of complete genome of CpCDV that infect squash plants in Egypt and worldwide.
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Affiliation(s)
- Inas Farouk Fahmy
- />Phytopathogen Vector Interaction Lab, Department of Microbiology, Agricultural Research Center (ARC), Agricultural Genetic Engineering Research Institute, Giza, Egypt
| | - Omnia Taha
- />Phytopathogen Vector Interaction Lab, Department of Microbiology, Agricultural Research Center (ARC), Agricultural Genetic Engineering Research Institute, Giza, Egypt
| | - Abdel Nasser El-Ashry
- />Department of Plant Pathology, Faculty of Agriculture, Institute fuer Nutzpflanzenwissenschaften und Ressourcen Schutz, University of Bonn, Bonn, Germany
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20
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Krupovic M, Zhi N, Li J, Hu G, Koonin EV, Wong S, Shevchenko S, Zhao K, Young NS. Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing. Genome Biol Evol 2015; 7:993-1001. [PMID: 25840414 PMCID: PMC4419787 DOI: 10.1093/gbe/evv034] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viruses with single-stranded (ss) DNA genomes infect hosts in all three domains of life and include many medically, ecologically, and economically important pathogens. Recently, a new group of ssDNA viruses with chimeric genomes has been discovered through viral metagenomics. These chimeric viruses combine capsid protein genes and replicative protein genes that, respectively, appear to have been inherited from viruses with positive-strand RNA genomes, such as tombusviruses, and ssDNA genomes, such as circoviruses, nanoviruses or geminiviruses. Here, we describe the genome sequence of a new representative of this virus group and reveal an additional layer of chimerism among ssDNA viruses. We show that not only do these viruses encompass genes for capsid proteins and replicative proteins that have distinct evolutionary histories, but also the replicative genes themselves are chimeras of functional domains inherited from viruses of different families. Our results underscore the importance of horizontal gene transfer in the evolution of ssDNA viruses and the role of genetic recombination in the emergence of novel virus groups.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Institut Pasteur, Paris, France
| | - Ning Zhi
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Jungang Li
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Gangqing Hu
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Susan Wong
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Sofiya Shevchenko
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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21
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Identification of an Australian-like dicot-infecting mastrevirus in Pakistan. Arch Virol 2014; 160:825-30. [DOI: 10.1007/s00705-014-2299-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 11/28/2014] [Indexed: 10/24/2022]
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22
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Kraberger S, Kumari SG, Hamed AA, Gronenborn B, Thomas JE, Sharman M, Harkins GW, Muhire BM, Martin DP, Varsani A. Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains. INFECTION GENETICS AND EVOLUTION 2014; 29:203-15. [PMID: 25444941 DOI: 10.1016/j.meegid.2014.11.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
Abstract
In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.
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Affiliation(s)
- Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
| | - Safaa G Kumari
- Virology Laboratory, International Centre for Agricultural Research in the Dry Areas (ICARDA), Tunis, Tunisia.
| | - Abdelmagid A Hamed
- Plant Pathology Research Program, Agricultural Research Corporation, P.O. Box 126, Wadmedani, Sudan
| | - Bruno Gronenborn
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | - John E Thomas
- Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Murray Sharman
- Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Gordon W Harkins
- South African National Bioinformatics Institute, SA Medical Research Unit for Bioinformatics Capacity Development, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Brejnev M Muhire
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
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23
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Candresse T, Filloux D, Muhire B, Julian C, Galzi S, Fort G, Bernardo P, Daugrois JH, Fernandez E, Martin DP, Varsani A, Roumagnac P. Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context. PLoS One 2014; 9:e102945. [PMID: 25061967 PMCID: PMC4111361 DOI: 10.1371/journal.pone.0102945] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/24/2014] [Indexed: 12/21/2022] Open
Abstract
Comprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, which are only suited to the detection and characterisation of specific, well characterised pathogens. Here, we demonstrate the utility of sequence-independent next generation sequencing (NGS) of both virus-derived small interfering RNAs (siRNAs) and virion-associated nucleic acids (VANA) for the detailed identification and characterisation of viruses infecting two quarantined sugarcane plants. Both plants originated from Egypt and were known to be infected with Sugarcane streak Egypt Virus (SSEV; Genus Mastrevirus, Family Geminiviridae), but were revealed by the NGS approaches to also be infected by a second highly divergent mastrevirus, here named Sugarcane white streak Virus (SWSV). This novel virus had escaped detection by all routine quarantine detection assays and was found to also be present in sugarcane plants originating from Sudan. Complete SWSV genomes were cloned and sequenced from six plants and all were found to share >91% genome-wide identity. With the exception of two SWSV variants, which potentially express unusually large RepA proteins, the SWSV isolates display genome characteristics very typical to those of all other previously described mastreviruses. An analysis of virus-derived siRNAs for SWSV and SSEV showed them to be strongly influenced by secondary structures within both genomic single stranded DNA and mRNA transcripts. In addition, the distribution of siRNA size frequencies indicates that these mastreviruses are likely subject to both transcriptional and post-transcriptional gene silencing. Our study stresses the potential advantages of NGS-based virus metagenomic screening in a plant quarantine setting and indicates that such techniques could dramatically reduce the numbers of non-intercepted virus pathogens passing through plant quarantine stations.
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Affiliation(s)
- Thierry Candresse
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882 Villenave d'Ornon Cedex, France
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882 Villenave d'Ornon Cedex, France
| | - Denis Filloux
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Brejnev Muhire
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Charlotte Julian
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Serge Galzi
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Guillaume Fort
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Pauline Bernardo
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Jean-Heindrich Daugrois
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Emmanuel Fernandez
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, South Africa
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
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24
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Grigoras I, Ginzo AIDC, Martin DP, Varsani A, Romero J, Mammadov AC, Huseynova IM, Aliyev JA, Kheyr-Pour A, Huss H, Ziebell H, Timchenko T, Vetten HJ, Gronenborn B. Genome diversity and evidence of recombination and reassortment in nanoviruses from Europe. J Gen Virol 2014; 95:1178-1191. [DOI: 10.1099/vir.0.063115-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The recent identification of a new nanovirus, pea necrotic yellow dwarf virus, from pea in Germany prompted us to survey wild and cultivated legumes for nanovirus infections in several European countries. This led to the identification of two new nanoviruses: black medic leaf roll virus (BMLRV) and pea yellow stunt virus (PYSV), each considered a putative new species. The complete genomes of a PYSV isolate from Austria and three BMLRV isolates from Austria, Azerbaijan and Sweden were sequenced. In addition, the genomes of five isolates of faba bean necrotic yellows virus (FBNYV) from Azerbaijan and Spain and those of four faba bean necrotic stunt virus (FBNSV) isolates from Azerbaijan were completely sequenced, leading to the first identification of FBNSV occurring in Europe. Sequence analyses uncovered evolutionary relationships, extensive reassortment and potential remnants of mixed nanovirus infections, as well as intra- and intercomponent recombination events within the nanovirus genomes. In some virus isolates, diverse types of the same genome component (paralogues) were observed, a type of genome complexity not described previously for any member of the family Nanoviridae. Moreover, infectious and aphid-transmissible nanoviruses from cloned genomic DNAs of FBNYV and BMLRV were reconstituted that, for the first time, allow experimental reassortments for studying the genome functions and evolution of these nanoviruses.
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Affiliation(s)
- Ioana Grigoras
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | - Ana Isabel del Cueto Ginzo
- Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Carretera de La Coruna Km. 7.0, Madrid 28040, Spain
| | - Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8140, New Zealand
| | - Javier Romero
- Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Carretera de La Coruna Km. 7.0, Madrid 28040, Spain
| | - Alamdar Ch. Mammadov
- Department of Fundamental Problems of Biological Productivity, Institute of Botany, Azerbaijan National Academy of Sciences, 40 Badamdar Highway, Baku AZ 1073, Azerbaijan
| | - Irada M. Huseynova
- Department of Fundamental Problems of Biological Productivity, Institute of Botany, Azerbaijan National Academy of Sciences, 40 Badamdar Highway, Baku AZ 1073, Azerbaijan
| | - Jalal A. Aliyev
- Department of Fundamental Problems of Biological Productivity, Institute of Botany, Azerbaijan National Academy of Sciences, 40 Badamdar Highway, Baku AZ 1073, Azerbaijan
| | | | - Herbert Huss
- Lehr- und Forschungszentrum für Landwirtschaft (LFZ) Raumberg-Gumpenstein, Versuchsstation Lambach/Stadl-Paura, 4651 Stadl-Paura, Austria
| | - Heiko Ziebell
- Julius Kühn Institut, Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, 38104 Braunschweig, Germany
| | - Tatiana Timchenko
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | - Heinrich-Josef Vetten
- Julius Kühn Institut, Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, 38104 Braunschweig, Germany
| | - Bruno Gronenborn
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
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25
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Manzoor MT, Ilyas M, Shafiq M, Haider MS, Shahid AA, Briddon RW. A distinct strain of chickpea chlorotic dwarf virus (genus Mastrevirus, family Geminiviridae) identified in cotton plants affected by leaf curl disease. Arch Virol 2013; 159:1217-21. [PMID: 24212888 DOI: 10.1007/s00705-013-1911-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/27/2013] [Indexed: 11/26/2022]
Abstract
As part of a study to determine the diversity of whitefly-transmitted viruses (genus Begomovirus, family Geminiviridae) associated with cotton leaf curl disease in Pakistan, leaf samples from cotton plants showing typical leaf curl disease symptoms were collected in various locations of Punjab province. Sequence analysis of full-length virus clones (~2.7 kb) showed plants to be infected with the begomovirus cotton leaf curl Burewala virus, the only virus identified in cotton in the Punjab since 2001. Surprisingly, a second virus, the leafhopper-transmitted chickpea chlorotic dwarf virus (CpCDV) of the genus Mastrevirus (family Geminiviridae), was identified in a small number of plants. The sequences of four CpCDV isolates from cotton originating from geographically distinct areas in Punjab were obtained. Analysis of the sequences showed them to represent a distinct, newly identified strain of CpCDV with the highest levels of nucleotide sequence identity to isolates of CpCDV strains C and D that have been identified previously in Pakistan. CpCDV has not been identified previously in cotton. The significance of this finding is discussed.
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