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Zhao L, Rosario K, Breitbart M, Duffy S. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. Adv Virus Res 2018; 103:71-133. [PMID: 30635078 DOI: 10.1016/bs.aivir.2018.10.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States.
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2
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Kraberger S, Saumtally S, Pande D, Khoodoo MHR, Dhayan S, Dookun-Saumtally A, Shepherd DN, Hartnady P, Atkinson R, Lakay FM, Hanson B, Redhi D, Monjane AL, Windram OP, Walters M, Oluwafemi S, Michel-Lett J, Lefeuvre P, Martin DP, Varsani A. Molecular diversity, geographic distribution and host range of monocot-infecting mastreviruses in Africa and surrounding islands. Virus Res 2017; 238:171-178. [PMID: 28687345 DOI: 10.1016/j.virusres.2017.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/28/2017] [Accepted: 07/01/2017] [Indexed: 10/19/2022]
Abstract
Maize streak virus (MSV), an important pathogen of maize in Africa, is the most extensively studied member of the Mastrevirus genus in the family Geminiviridae. Comparatively little is known about other monocot-infecting African mastreviruses, most of which infect uncultivated grasses. Here we determine the complete sequences of 134 full African mastrevirus genomes from predominantly uncultivated Poaceae species. Based on established taxonomic guidelines for the genus Mastrevirus, these genomes could be classified as belonging to the species Maize streak virus, Eragrostis minor streak virus, Maize streak Reunion virus, Panicum streak virus, Sugarcane streak Reunion virus and Sugarcane streak virus. Together with all other publicly available African monocot-infecting mastreviruses, the 134 new isolates extend the known geographical distributions of many of these species, including MSV which we found infecting Digitaria sp. on the island of Grand Canaria: the first definitive discovery of any African monocot-infecting mastreviruses north-west of the Saharan desert. These new isolates also extend the known host ranges of both African mastrevirus species and the strains within these. Most notable was the discovery of MSV-C isolates infecting maize which suggests that this MSV strain, which had previously only ever been found infecting uncultivated species, may be in the process of becoming adapted to this important staple crop.
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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; School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Salem Saumtally
- Mauritius Sugarcane Industry Research Institute, Réduit, Mauritius
| | - Daniel Pande
- Department of Botany, Maseno University, P.O. Box 333, Maseno, Kenya; Department of Biological and Biomedical Science and Technology, Laikipia University, P.O. Box 1100-20300, Nyahururu, Kenya
| | | | - Sonalall Dhayan
- Mauritius Sugarcane Industry Research Institute, Réduit, Mauritius
| | | | - Dionne N Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Penelope Hartnady
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Richard Atkinson
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Francisco M Lakay
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Britt Hanson
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Devasha Redhi
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Adérito L Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa; Department of Immunology, Norwegian Veterinary Institute, Pb 750 Sentrum, N-0106 Oslo, Norway
| | - Oliver P Windram
- Grand Challenges in Ecosystems & the Environment, Imperial College London, Silwood Park Campus, Buckhurst Road, SL5 7PY Ascot, Berks, UK
| | - Matthew Walters
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Sunday Oluwafemi
- Department of Crop Production, Soil and Environmental Management, Bowen University, P.M.B. 284, Iwo, Osun State, Nigeria
| | - Jean Michel-Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410 Saint-Pierre, Ile de La Réunion, France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410 Saint-Pierre, Ile de La Réunion, France
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, 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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3
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Pande D, Madzokere E, Hartnady P, Kraberger S, Hadfield J, Rosario K, Jäschke A, Monjane AL, Owor BE, Dida MM, Shepherd DN, Martin DP, Varsani A, Harkins GW. The role of Kenya in the trans-African spread of maize streak virus strain A. Virus Res 2017; 232:69-76. [PMID: 28192163 DOI: 10.1016/j.virusres.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 10/20/2022]
Abstract
Maize streak virus (MSV), the causal agent of maize streak disease (MSD), is the most important viral pathogen of Africa's staple food crop, maize. Previous phylogeographic analyses have revealed that the most widely-distributed and common MSV variant, MSV-A1, has been repeatedly traversing Africa over the past fifty years with long-range movements departing from either the Lake Victoria region of East Africa, or the region around the convergence of Zimbabwe, South Africa and Mozambique in southern Africa. Despite Kenya being the second most important maize producing country in East Africa, little is known about the Kenyan MSV population and its contribution to the ongoing diversification and trans-continental dissemination of MSV-A1. We therefore undertook a sampling survey in this country between 2008 and 2011, collecting MSD prevalence data in 119 farmers' fields, symptom severity data for 170 maize plants and complete MSV genome sequence data for 159 MSV isolates. We then used phylogenetic and phylogeographic analyses to show that whereas the Kenyan MSV population is likely primarily derived from the MSV population in neighbouring Uganda, it displays considerably more geographical structure than the Ugandan population. Further, this geographical structure likely confounds apparent associations between virus genotypes and both symptom severity and MSD prevalence in Kenya. Finally, we find that Kenya is probably a sink rather than a source of MSV diversification and movement, and therefore, unlike Uganda, Kenya probably does not play a major role in the trans-continental dissemination of MSV-A1.
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Affiliation(s)
- Daniel Pande
- Department of Applied Plant Sciences, School of Agriculture and Food Security, Maseno, Kenya; Biological and Biomedical Science and Technology, Laikipia University, P.O. Box 1100-20300, Nyahururu, Kenya
| | - Eugene Madzokere
- South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
| | - Penelope Hartnady
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7001, South Africa
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - James Hadfield
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA
| | - Anja Jäschke
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Department of Infectious Diseases, University of Heidelberg, D-69120 Heidelberg, Germany
| | - Adérito L Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa; Department of Immunology, Norwegian Veterinary Institute, Pb 750 Sentrum, N-0106 Oslo, Norway
| | - Betty E Owor
- Department of Agricultural Production, School of Agricultural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Mathews M Dida
- Department of Applied Plant Sciences, School of Agriculture and Food Security, Maseno, Kenya
| | - Dionne N Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Darren P Martin
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7001, South Africa
| | - Arvind Varsani
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7001, South Africa; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; 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.
| | - Gordon W Harkins
- South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa.
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Identification of novel Bromus- and Trifolium-associated circular DNA viruses. Arch Virol 2015; 160:1303-11. [PMID: 25701210 DOI: 10.1007/s00705-015-2358-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/29/2015] [Indexed: 12/17/2022]
Abstract
The genomes of a large number of highly diverse novel circular DNA viruses from a wide range of sources have been characterised in recent years, including circular single-stranded DNA (ssDNA) viruses that share similarities with plant-infecting ssDNA viruses of the family Geminiviridae. Here, we describe six novel circular DNA viral genomes that encode replication-associated (Rep) proteins that are most closely related to those of either geminiviruses or gemycircularviruses (a new group of ssDNA viruses that are closely related to geminiviruses). Four possible viral genomes were recovered from Bromus hordeaceus sampled in New Zealand, and two were recovered from B. hordeaceus and Trifolium resupinatum sampled in France. Two of the viral genomes from New Zealand (one from the North Island and one from the South Island each) share >99 % sequence identity, and two genomes recovered from B. hordeaceus and T. resupinatum sampled in France share 74 % identity. All of the viral genomes that were recovered were found to have a major open reading frame on both their complementary and virion-sense strands, one of which likely encodes a Rep and the other a capsid protein. Although future infectivity studies are needed to identify the host range of these viruses, this is the first report of circular DNA viruses associated with grasses in New Zealand.
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5
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Kraberger S, Argüello-Astorga GR, Greenfield LG, Galilee C, Law D, Martin DP, Varsani A. Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond. INFECTION GENETICS AND EVOLUTION 2015; 31:73-86. [PMID: 25583447 DOI: 10.1016/j.meegid.2015.01.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/23/2014] [Accepted: 01/02/2015] [Indexed: 12/20/2022]
Abstract
Our knowledge of circular replication-associated protein encoding single-stranded (CRESS) DNA virus diversity has increased dramatically in recent years, largely due to advances in high-throughput sequencing technologies. These viruses are apparently major virome components in most terrestrial and aquatic environments and it is therefore of interest to determine their diversity at the interfaces between these environments. Treated sewage water is a particularly interesting interface between terrestrial and aquatic viromes in that it is directly pumped into waterways and is likely to contain virus populations that have been strongly impacted by humans. We used a combination of high-throughput sequencing, full genome PCR amplification, cloning and Sanger sequencing to investigate the diversity of CRESS DNA viruses present in a sewage oxidation pond. Using this approach, we recovered 50 putatively complete novel CRESS viral genomes (it remains possible that some are components of multipartite viral genomes) and 11 putatively sub-genome-length circular DNA molecules which may be either defective genomes or components of multipartite genomes. Thirteen of the genomes have bidirectional genome organisations and share similar conserved replication-associated protein (Rep) motifs to those of the gemycircularviruses: a group that in turn is most closely related to the geminiviruses. The remaining 37 viral genomes share very low degrees of Rep similarity to those of all other known CRESS DNA viruses. This number of highly divergent CRESS DNA virus genomes within a single sewage treatment pond further reinforces the notion that there likely exist hundreds of completely unknown genus/family level CRESS DNA virus groupings.
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Affiliation(s)
- Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Gerardo R Argüello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216 San Luis Potosí, S.L.P., Mexico
| | - Laurence G Greenfield
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Craig Galilee
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Donald Law
- The Laboratories, Christchurch City Council, Christchurch, 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
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA; Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.
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6
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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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7
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Analysis of complete genomes of isolates of the Wheat dwarf virus from new geographical locations and descriptions of their defective forms. Virus Genes 2014; 48:133-9. [PMID: 24122067 DOI: 10.1007/s11262-013-0989-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/25/2013] [Indexed: 10/26/2022]
Abstract
Recently, the importance of the Geminiviruses infecting cereal crops has been appreciated, and they are now being studied in detail. Barley and wheat strains of Wheat dwarf virus are recorded in most European countries. Information on complete sequences of isolates from the United Kingdom, Spain, and Austria are reported here for the first time. Analysis revealed that their sequences are very stable. Recombination between strains was recorded only for the barley strain. We identified several defective forms of the barley strain from barley and wheat, which do not influence symptom expression. Sequences of barley isolates infecting wheat were obtained that did not differ from the isolates from barley. Based on specific features of the SIR of the barley strains, it is suggested that they are assigned to one of the two proposed new clusters, A1 or A2.
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8
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Shepherd DN, Dugdale B, Martin DP, Varsani A, Lakay FM, Bezuidenhout ME, Monjane AL, Thomson JA, Dale J, Rybicki EP. Inducible resistance to maize streak virus. PLoS One 2014; 9:e105932. [PMID: 25166274 PMCID: PMC4148390 DOI: 10.1371/journal.pone.0105932] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 07/28/2014] [Indexed: 11/18/2022] Open
Abstract
Maize streak virus (MSV), which causes maize streak disease (MSD), is the major viral pathogenic constraint on maize production in Africa. Type member of the Mastrevirus genus in the family Geminiviridae, MSV has a 2.7 kb, single-stranded circular DNA genome encoding a coat protein, movement protein, and the two replication-associated proteins Rep and RepA. While we have previously developed MSV-resistant transgenic maize lines constitutively expressing "dominant negative mutant" versions of the MSV Rep, the only transgenes we could use were those that caused no developmental defects during the regeneration of plants in tissue culture. A better transgene expression system would be an inducible one, where resistance-conferring transgenes are expressed only in MSV-infected cells. However, most known inducible transgene expression systems are hampered by background or "leaky" expression in the absence of the inducer. Here we describe an adaptation of the recently developed INPACT system to express MSV-derived resistance genes in cell culture. Split gene cassette constructs (SGCs) were developed containing three different transgenes in combination with three different promoter sequences. In each SGC, the transgene was split such that it would be translatable only in the presence of an infecting MSV's replication associated protein. We used a quantitative real-time PCR assay to show that one of these SGCs (pSPLITrepIII-Rb-Ubi) inducibly inhibits MSV replication as efficiently as does a constitutively expressed transgene that has previously proven effective in protecting transgenic maize from MSV. In addition, in our cell-culture based assay pSPLITrepIII-Rb-Ubi inhibited replication of diverse MSV strains, and even, albeit to a lesser extent, of a different mastrevirus species. The application of this new technology to MSV resistance in maize could allow a better, more acceptable product.
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Affiliation(s)
- Dionne N. Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
- * E-mail:
| | - Benjamin Dugdale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Darren P. Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
- Centre for High-Performance Computing, Rosebank, 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, Cape Town, South Africa
| | - Francisco M. Lakay
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Marion E. Bezuidenhout
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Adérito L. Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Jennifer A. Thomson
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - James Dale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Edward P. Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
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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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10
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Kraberger S, Harkins GW, Kumari SG, Thomas JE, Schwinghamer MW, Sharman M, Collings DA, Briddon RW, Martin DP, Varsani A. Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East. Virology 2013; 444:282-91. [PMID: 23886492 DOI: 10.1016/j.virol.2013.06.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 06/08/2013] [Accepted: 06/24/2013] [Indexed: 11/25/2022]
Abstract
Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.
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Affiliation(s)
- Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
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11
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A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 2013; 158:1411-24. [DOI: 10.1007/s00705-012-1601-7] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 12/01/2012] [Indexed: 10/27/2022]
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12
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Rosario K, Padilla-Rodriguez M, Kraberger S, Stainton D, Martin DP, Breitbart M, Varsani A. Discovery of a novel mastrevirus and alphasatellite-like circular DNA in dragonflies (Epiprocta) from Puerto Rico. Virus Res 2013; 171:231-7. [DOI: 10.1016/j.virusres.2012.10.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/14/2012] [Accepted: 10/18/2012] [Indexed: 11/28/2022]
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13
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Kraberger S, Thomas JE, Geering AD, Dayaram A, Stainton D, Hadfield J, Walters M, Parmenter KS, van Brunschot S, Collings DA, Martin DP, Varsani A. Australian monocot-infecting mastrevirus diversity rivals that in Africa. Virus Res 2012; 169:127-36. [DOI: 10.1016/j.virusres.2012.07.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 07/14/2012] [Accepted: 07/17/2012] [Indexed: 11/26/2022]
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14
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Hadfield J, Thomas JE, Schwinghamer MW, Kraberger S, Stainton D, Dayaram A, Parry JN, Pande D, Martin DP, Varsani A. Molecular characterisation of dicot-infecting mastreviruses from Australia. Virus Res 2012; 166:13-22. [PMID: 22406325 DOI: 10.1016/j.virusres.2012.02.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/16/2012] [Accepted: 02/20/2012] [Indexed: 11/24/2022]
Abstract
Monocotyledonous and dicotyledonous plant infecting mastreviruses threaten various agricultural systems throughout Africa, Eurasia and Australasia. In Australia three distinct mastrevirus species are known to infect dicotyledonous hosts such as chickpea, bean and tobacco. Amongst 34 new "dicot-infecting" mastrevirus full genome sequences obtained from these hosts we discovered one new species, four new strains, and various variants of previously described mastrevirus species. Besides providing additional support for the hypothesis that evolutionary processes operating during dicot-infecting mastrevirus evolution (such as patterns of pervasive homologous and non-homologous recombination, and strong purifying selection acting on all genes) have mostly mirrored those found in their monocot-infecting counterparts, we find that the Australian dicot-infecting viruses display patterns of phylogeographic clustering reminiscent of those displayed by monocot infecting mastrevirus species such as Panicum streak virus and Maize streak virus.
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Affiliation(s)
- James Hadfield
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch 8140, New Zealand
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15
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Geering ADW, Thomas JE, Holton T, Hadfield J, Varsani A. Paspalum striate mosaic virus: an Australian mastrevirus from Paspalum dilatatum. Arch Virol 2011; 157:193-7. [DOI: 10.1007/s00705-011-1129-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 09/18/2011] [Indexed: 10/16/2022]
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16
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Monjane AL, Harkins GW, Martin DP, Lemey P, Lefeuvre P, Shepherd DN, Oluwafemi S, Simuyandi M, Zinga I, Komba EK, Lakoutene DP, Mandakombo N, Mboukoulida J, Semballa S, Tagne A, Tiendrébéogo F, Erdmann JB, van Antwerpen T, Owor BE, Flett B, Ramusi M, Windram OP, Syed R, Lett JM, Briddon RW, Markham PG, Rybicki EP, Varsani A. Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa. J Virol 2011; 85:9623-36. [PMID: 21715477 PMCID: PMC3165777 DOI: 10.1128/jvi.00640-11] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 06/21/2011] [Indexed: 01/11/2023] Open
Abstract
Maize streak virus strain A (MSV-A), the causal agent of maize streak disease, is today one of the most serious biotic threats to African food security. Determining where MSV-A originated and how it spread transcontinentally could yield valuable insights into its historical emergence as a crop pathogen. Similarly, determining where the major extant MSV-A lineages arose could identify geographical hot spots of MSV evolution. Here, we use model-based phylogeographic analyses of 353 fully sequenced MSV-A isolates to reconstruct a plausible history of MSV-A movements over the past 150 years. We show that since the probable emergence of MSV-A in southern Africa around 1863, the virus spread transcontinentally at an average rate of 32.5 km/year (95% highest probability density interval, 15.6 to 51.6 km/year). Using distinctive patterns of nucleotide variation caused by 20 unique intra-MSV-A recombination events, we tentatively classified the MSV-A isolates into 24 easily discernible lineages. Despite many of these lineages displaying distinct geographical distributions, it is apparent that almost all have emerged within the past 4 decades from either southern or east-central Africa. Collectively, our results suggest that regular analysis of MSV-A genomes within these diversification hot spots could be used to monitor the emergence of future MSV-A lineages that could affect maize cultivation in Africa.
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Affiliation(s)
- Adérito L. Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Gordon W. Harkins
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Darren P. Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
- Centre for High-Performance Computing, Rosebank, Cape Town, South Africa
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Leuven, Belgium
| | - Pierre Lefeuvre
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 97410, Saint Pierre, La Réunion, France
| | - Dionne N. Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Sunday Oluwafemi
- Department of Crop Production, Soil and Environmental Management, Bowen University, Iwo, Osun State, P.M.B. 284, Nigeria
| | | | - Innocent Zinga
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Ephrem K. Komba
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Didier P. Lakoutene
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Noella Mandakombo
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Joseph Mboukoulida
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Silla Semballa
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Appolinaire Tagne
- Cereals Research Program, Institute of Agricultural Research for Development, Box 2067 Messa, Yaounde, Cameroon
| | - Fidèle Tiendrébéogo
- Centre de Recherche en Sciences Biologiques Alimentaires et Nutritionnelles (CRSBAN), UFR/SVT Université de Ouagadougou, 03 BP 7131 Ouagadougou 03, Burkina Faso
| | - Julia B. Erdmann
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Institute of Biology, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Tania van Antwerpen
- South African Sugarcane Research Institute, Mount Edgecombe, KwaZulu Natal, South Africa
| | - Betty E. Owor
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom, CB2 3EA
| | - Bradley Flett
- Crop Protection, ARC-Grain Crops Institute, Potchefstroom 2520, South Africa
| | - Moses Ramusi
- Crop Protection, ARC-Grain Crops Institute, Potchefstroom 2520, South Africa
| | - Oliver P. Windram
- Warwick HRI Biology Centre, University of Warwick, Wellesbourne, CV35 9EF, England
| | - Rizwan Syed
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Jean-Michel Lett
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 97410, Saint Pierre, La Réunion, France
| | - Rob W. Briddon
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, P.O. Box 577, Faisalabad, Pakistan
| | - Peter G. Markham
- Department of Disease and Stress Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Edward P. Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Arvind Varsani
- Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
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17
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Martin DP, Biagini P, Lefeuvre P, Golden M, Roumagnac P, Varsani A. Recombination in eukaryotic single stranded DNA viruses. Viruses 2011; 3:1699-738. [PMID: 21994803 PMCID: PMC3187698 DOI: 10.3390/v3091699] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/18/2011] [Accepted: 09/05/2011] [Indexed: 12/23/2022] Open
Abstract
Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.
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Affiliation(s)
- Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa; E-Mail:
| | - Philippe Biagini
- UMR CNRS 6578 Anthropologie Bioculturelle, Equipe “Emergence et co-évolution virale”, Etablissement Français du Sang Alpes-Méditerranée, Université de la Méditerranée, 27 Bd. Jean Moulin, 13005 Marseille, France; E-Mail:
| | - Pierre Lefeuvre
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Ligne Paradis, 97410, Saint Pierre, La Réunion, France; E-Mail:
| | - Michael Golden
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa; E-Mail:
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, TA A-54/K, Campus International de Montferrier-Baillarguet, 34398 Montpellier, France; E-Mail:
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa; E-Mail:
- Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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18
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Martin DP, Briddon RW, Varsani A. Recombination patterns in dicot-infecting mastreviruses mirror those found in monocot-infecting mastreviruses. Arch Virol 2011; 156:1463-9. [PMID: 21484422 DOI: 10.1007/s00705-011-0994-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 03/28/2011] [Indexed: 11/28/2022]
Abstract
Recombination has profoundly shaped the evolution of viruses in the family Geminiviridae and has been studied extensively in the two best characterised geminivirus lineages: the dicotyledonous plant infecting begomoviruses and the monocotyledonous plant infecting mastreviruses. Here, we demonstrate that the sizes and distributions of recombination events detectable within the members of a third major geminivirus lineage--the dicotyledonous plant infecting mastreviruses--are very similar to those of the monocot-infecting mastreviruses. This suggests that, despite host range differences, very similar biochemical, ecological and evolutionary factors must underlie recombination patterns in the dicot- and monocot-infecting mastreviruses.
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Affiliation(s)
- Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa
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19
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Hosseini A, Massumi H, Heydarnejad J, Hosseini Pour A, Varsani A. Characterisation of potato virus Y isolates from Iran. Virus Genes 2011; 42:128-40. [PMID: 21082231 DOI: 10.1007/s11262-010-0546-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Accepted: 10/18/2010] [Indexed: 11/24/2022]
Abstract
A survey of Potato virus Y (PVY) was conducted in cultivated fields in six Iranian provinces between January 2005 to July 2007. Two hundred samples from potato and tomato were collected and analyzed by enzyme-linked immunosorbent assay (ELISA) for potyviruses. Almost one fourth of the samples were found to be infected by PVY. Analysis of these PVY-positive samples using three monoclonal antibodies (MAbs) facilitating the simultaneous detection of three main strains namely the ordinary (PVY(O)), strain (PVY(N)) and C (PVY(C)) strains. However, the fourth strain (PVY(NTN)) and some others recombinant isolates were also identified by molecular methods. Host range and symptoms analysis using sap inoculation of four different strains of PVY onto a range of plants revealed that the four strains showed biological properties that seemed to be consistent with their molecular grouping. Fourteen isolates of PVY were chosen based on the host and geographical location, primer specificity and serology for further biological and molecular characterisation. The coat protein (CP) and P1 genes and 3'-non-translated region (3'NTR) from 14 representative isolates were sequenced and analysed with the sequences available in GenBank. Composite analysis of the P1, CP and 3'-UTR sequences with all full genome sequences of PVY revealed that there are three potential strains of PVY in Iran, PVY(O), PVY(N)-W and PVY(NTN). Isolate KER.SA(N) was the most divergent of all the 14 isolates reacted with PVY(N) specific MAbs but grouped with PVY(O) strains in maximum likelihood phylogentic analysis. The PVY(NTN) isolates from Iran more closely related to the European than North American PVY(NTN) isolates.
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Affiliation(s)
- Atefe Hosseini
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
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20
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Varsani A, Regnard GL, Bragg R, Hitzeroth II, Rybicki EP. Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates. J Gen Virol 2010; 92:752-67. [PMID: 21177924 DOI: 10.1099/vir.0.028126-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Psittacine beak and feather disease (PBFD) has a broad host range and is widespread in wild and captive psittacine populations in Asia, Africa, the Americas, Europe and Australasia. Beak and feather disease circovirus (BFDV) is the causative agent. BFDV has an ∼2 kb single stranded circular DNA genome encoding just two proteins (Rep and CP). In this study we provide support for demarcation of BFDV strains by phylogenetic analysis of 65 complete genomes from databases and 22 new BFDV sequences isolated from infected psittacines in South Africa. We propose 94% genome-wide sequence identity as a strain demarcation threshold, with isolates sharing >94% identity belonging to the same strain, and strain subtypes sharing >98% identity. Currently, BFDV diversity falls within 14 strains, with five highly divergent isolates from budgerigars probably representing a new species of circovirus with three strains (budgerigar circovirus; BCV-A, -B and -C). The geographical distribution of BFDV and BCV strains is strongly linked to the international trade in exotic birds; strains with more than one host are generally located in the same geographical area. Lastly, we examined BFDV and BCV sequences for evidence of recombination, and determined that recombination had occurred in most BFDV and BCV strains. We established that there were two globally significant recombination hotspots in the viral genome: the first is along the entire intergenic region and the second is in the C-terminal portion of the CP ORF. The implications of our results for the taxonomy and classification of circoviruses are discussed.
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Affiliation(s)
- Arvind Varsani
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
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21
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Hadfield J, Martin DP, Stainton D, Kraberger S, Owor BE, Shepherd DN, Lakay F, Markham PG, Greber RS, Briddon RW, Varsani A. Bromus catharticus striate mosaic virus: a new mastrevirus infecting Bromus catharticus from Australia. Arch Virol 2010; 156:335-41. [DOI: 10.1007/s00705-010-0872-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 11/20/2010] [Indexed: 10/18/2022]
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22
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A novel species of mastrevirus (family Geminiviridae) isolated from Digitaria didactyla grass from Australia. Arch Virol 2010; 155:1529-34. [DOI: 10.1007/s00705-010-0759-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 07/12/2010] [Indexed: 11/26/2022]
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23
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Duffy S, Seah YM. 98% identical, 100% wrong: per cent nucleotide identity can lead plant virus epidemiology astray. Philos Trans R Soc Lond B Biol Sci 2010; 365:1891-7. [PMID: 20478884 PMCID: PMC2880110 DOI: 10.1098/rstb.2010.0056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Short-form publications such as Plant Disease reports serve essential functions: the rapid dissemination of information on the geography of established plant pathogens, incidence and symptomology of pathogens in new hosts, and the discovery of novel pathogens. Many of these sentinel publications include viral sequence data, but most use that information only to confirm the virus' species. When researchers use the standard technique of per cent nucleotide identity to determine that the new sequence is closely related to another sequence, potentially erroneous conclusions can be drawn from the results. Multiple introductions of the same pathogen into a country are being ignored because researchers know fast-evolving plant viruses can accumulate substantial sequence divergence over time, even from a single introduction. An increased use of phylogenetic methods in short-form publications could speed our understanding of these cryptic second introductions and aid in control of epidemics.
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Affiliation(s)
- Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
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