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Nogueira AM, Barbosa TMC, Quadros AFF, Orílio AF, Bigão MCJ, Xavier CAD, Ferro CG, Zerbini FM. Specific Nucleotides in the Common Region of the Begomovirus Tomato Rugose Mosaic Virus (ToRMV) Are Responsible for the Negative Interference over Tomato Severe Rugose Virus (ToSRV) in Mixed Infection. Viruses 2023; 15:2074. [PMID: 37896851 PMCID: PMC10611410 DOI: 10.3390/v15102074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Mixed infection between two or more begomoviruses is commonly found in tomato fields and can affect disease outcomes by increasing symptom severity and viral accumulation compared with single infection. Viruses that affect tomato include tomato severe rugose virus (ToSRV) and tomato rugose mosaic virus (ToRMV). Previous work showed that in mixed infection, ToRMV negatively affects the infectivity and accumulation of ToSRV. ToSRV and ToRMV share a high degree of sequence identity, including cis-elements in the common region (CR) and their specific recognition sites (iteron-related domain, IRD) within the Rep gene. Here, we investigated if divergent sites in the CR and IRD are involved in the interaction between these two begomoviruses. ToSRV clones were constructed containing the same nucleotides as ToRMV in the CR (ToSRV-A(ToR:CR)), IRD (ToSRV-A(ToR:IRD)) and in both regions (ToSRV-A(ToR:CR+IRD)). When plants were co-inoculated with ToRMV and ToSRV-A(ToR:IRD), the infectivity and accumulation of ToSRV were negatively affected. In mixed inoculation of ToRMV with ToSRV-A(ToR:CR), high infectivity of both viruses and high DNA accumulation of ToSRV-A(ToR:CR) were observed. A decrease in viral accumulation was observed in plants inoculated with ToSRV-A(ToR:CR+IRD). These results indicate that differences in the CR, but not the IRD, are responsible for the negative interference of ToRMV on ToSRV.
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Affiliation(s)
- Angélica M. Nogueira
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Departamento de Proteção Vegetal, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista (UNESP), Botucatu 18610-307, SP, Brazil
| | - Tarsiane M. C. Barbosa
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Departamento de Entomologia e Acarologia, ESALQ, Universidade de São Paulo, Piracicaba 13418-900, SP, Brazil
| | - Ayane F. F. Quadros
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Anelise F. Orílio
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Marcela C. J. Bigão
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - César A. D. Xavier
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Camila G. Ferro
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Departamento de Fitopatologia e Nematologia, ESALQ, Universidade de São Paulo, Piracicaba 13418-900, SP, Brazil
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
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Zerbini FM, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Hendrickson RC, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A. Correction to: Changes to virus taxonomy and the ICTV Statutes ratifed by the International Committee on Taxonomy of Viruses (2023). Arch Virol 2023; 168:269. [PMID: 37804442 DOI: 10.1007/s00705-023-05880-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Affiliation(s)
- Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570‑900, Brazil
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fürstengraben 1, 07743, Jena, Germany
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector‑Borne Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02‑106, Warsaw, Poland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710‑0046, Japan
| | - Koenraad Van Doorslaer
- Department of Immunobiology, School of Animal and Comparative Biomedical Sciences, BIO5 Institute, University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349‑008, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-4701, USA
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da Silva JPH, de Resende FMP, da Silva JCF, de Breuil S, Nome C, Bejerman N, Zerbini FM. Amesuviridae: a new family of plant-infecting viruses in the phylum Cressdnaviricota, realm Monodnaviria. Arch Virol 2023; 168:223. [PMID: 37561218 DOI: 10.1007/s00705-023-05852-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
The phylum Cressdnaviricota comprises viruses with single-stranded, circular DNA genomes that encode an HUH-type endonuclease (known as Rep). The phylum includes two classes, eight orders, and 11 families. Here, we report the creation of a twelfth family in the order Mulpavirales, class Arfiviricetes of the phylum Cressdnaviricota. The family Amesuviridae comprises viruses that infect plants and is divided into two genera: Temfrudevirus, including the species Temfrudevirus temperatum (with temperate fruit decay-associated virus as a member), and Yermavirus, including the species Yermavirus ilicis (with yerba mate-associated circular DNA virus as a member). Both viruses encode Rep proteins with HUH endonuclease and SH3 superfamily helicase domains. Phylogenetic analysis indicates that the replicative module of amesuviruses constitutes a well-supported monophyletic clade related to Rep proteins from viruses in the order Mulpavirales. Furthermore, both viruses encode a single capsid protein (CP) related to geminivirus CPs. Phylogenetic incongruence between the replicative and structural modules of amesuviruses suggests a chimeric origin resulting from remote recombination events between ancestral mulpavirales and geminivirids. The creation of the family Amesuviridae has been ratified by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
| | | | | | - Soledad de Breuil
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
| | - Claudia Nome
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
| | - Nicolas Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
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Zerbini FM, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Hendrickson RC, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A. Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023). Arch Virol 2023; 168:175. [PMID: 37296227 PMCID: PMC10861154 DOI: 10.1007/s00705-023-05797-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article reports changes to virus taxonomy and taxon nomenclature that were approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2023. The entire ICTV membership was invited to vote on 174 taxonomic proposals that had been approved by the ICTV Executive Committee in July 2022, as well as a proposed revision of the ICTV Statutes. All proposals and the revised ICTV Statutes were approved by a majority of the voting membership. Of note, the ICTV continued the process of renaming existing species in accordance with the recently mandated binomial format and included gene transfer agents (GTAs) in the classification framework by classifying them as viriforms. In total, one class, seven orders, 31 families, 214 genera, and 858 species were created.
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Affiliation(s)
- Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570‑900, Brazil
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fürstengraben 1, 07743, Jena, Germany
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector‑Borne Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02‑106, Warsaw, Poland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710‑0046, Japan
| | - Koenraad Van Doorslaer
- Department of Immunobiology, School of Animal and Comparative Biomedical Sciences, BIO5 Institute, University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349‑008, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-4701, USA
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Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Curtis Hendrickson R, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Orton RJ, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A, Zerbini FM. Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022). Arch Virol 2022; 167:2429-2440. [PMID: 35999326 PMCID: PMC10088433 DOI: 10.1007/s00705-022-05516-5] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2022. The entire ICTV was invited to vote on 174 taxonomic proposals approved by the ICTV Executive Committee at its annual meeting in July 2021. All proposals were ratified by an absolute majority of the ICTV members. Of note, the Study Groups have started to implement the new rule for uniform virus species naming that became effective in 2021 and mandates the binomial 'Genus_name species_epithet' format with or without Latinization. As a result of this ratification, the names of 6,481 virus species (more than 60 percent of all species names currently recognized by ICTV) now follow this format.
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Affiliation(s)
- Peter J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Stuart G Siddell
- Faculty of Life Sciences, School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA.
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Room Z-509, 3584 CH, Utrecht, The Netherlands.,Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fürstengraben 1, 07743, Jena, Germany
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET - UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité - Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit,, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- NIH/NIAID/DCR/Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Koenraad Van Doorslaer
- Department of Immunobiology, School of Animal and Comparative Biomedical Sciences, BIO5 Institute, University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and TransplantationClinical and Epidemiological VirologyInstitute for the Future, Rega Institute for Medical Research, 3000, Leuven, Belgium.,Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-4701, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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Fernandes PMB, Favaratto L, Fernandes AAR, Vicien C, Capalbo DMF, Zerbini FM. To become more sustainable organic agriculture needs genome editing technology. Front Bioeng Biotechnol 2022; 10:912793. [PMID: 36061445 PMCID: PMC9437244 DOI: 10.3389/fbioe.2022.912793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/27/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
| | - Luíza Favaratto
- Biotechnology Core, Federal University of Espírito Santo, Vitória, Brazil
| | | | - Carmen Vicien
- Faculty of Agronomy, University of Buenos Aires and Institute for Scientific Cooperation in Environment and Health, Buenos Aires, Argentina
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7
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Zerbini FM, Siddell SG, Mushegian AR, Walker PJ, Lefkowitz EJ, Adriaenssens EM, Alfenas-Zerbini P, Dutilh BE, García ML, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A. Differentiating between viruses and virus species by writing their names correctly. Arch Virol 2022; 167:1231-1234. [PMID: 35043230 PMCID: PMC9020231 DOI: 10.1007/s00705-021-05323-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Following the results of the International Committee on Taxonomy of Viruses (ICTV) Ratification Vote held in March 2021, a standard two-part "binomial nomenclature" is now the norm for naming virus species. Adoption of the new nomenclature is still in its infancy; thus, it is timely to reiterate the distinction between "virus" and "virus species" and to provide guidelines for naming and writing them correctly.
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Affiliation(s)
| | - Stuart G. Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA 22314, USA
| | - Peter J. Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia QLD 4072, Australia
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL 35294-2170, USA
| | | | | | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena 07743, Germany,Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris 75015, France
| | - Jens H. Kuhn
- NIH/NIAID/DCR/Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Amy J. Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, AZ 85721, USA
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Institute for the Future, 3000 Leuven, Belgium,Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ 85287-4701, USA
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8
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Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Davison AJ, Dempsey DM, Dutilh BE, García ML, Harrach B, Harrison RL, Hendrickson RC, Junglen S, Knowles NJ, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Nibert ML, Oksanen HM, Orton RJ, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Dooerslaer K, Vandamme AM, Varsani A, Zerbini FM. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Arch Virol 2021; 166:2633-2648. [PMID: 34231026 DOI: 10.1007/s00705-021-05156-1] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2021. The entire ICTV was invited to vote on 290 taxonomic proposals approved by the ICTV Executive Committee at its meeting in October 2020, as well as on the proposed revision of the International Code of Virus Classification and Nomenclature (ICVCN). All proposals and the revision were ratified by an absolute majority of the ICTV members. Of note, ICTV mandated a uniform rule for virus species naming, which will follow the binomial 'genus-species' format with or without Latinized species epithets. The Study Groups are requested to convert all previously established species names to the new format. ICTV has also abolished the notion of a type species, i.e., a species chosen to serve as a name-bearing type of a virus genus. The remit of ICTV has been clarified through an official definition of 'virus' and several other types of mobile genetic elements. The ICVCN and ICTV Statutes have been amended to reflect these changes.
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Affiliation(s)
- Peter J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA.
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Room Z-509, 3584 CH, Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - Balázs Harrach
- Veterinary Medical Research Institute, Hungária krt. 21, H-1143, Budapest, Hungary
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, 10300 Baltimore Avenue, Bldg 007 Barc-West, Beltsville, MD, 20705, USA
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Germany, Berlin, Germany
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, Surrey, UK
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- NIH/NIAID/DCR/Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Max L Nibert
- Department of Microbiology, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA, 02115, USA
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014, Helsinki, Finland
| | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Koenraad Van Dooerslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Institute for the Future, 3000, Leuven, Belgium.,Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008, Lisboa, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ, 85287-4701, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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9
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Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Dempsey DM, Dutilh BE, Harrach B, Harrison RL, Hendrickson RC, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert M, Orton RJ, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Varsani A, Zerbini FM, Davison AJ. Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020). Arch Virol 2020; 165:2737-2748. [PMID: 32816125 DOI: 10.1007/s00705-020-04752-x] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This article reports the changes to virus classification and taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2020. The entire ICTV was invited to vote on 206 taxonomic proposals approved by the ICTV Executive Committee at its meeting in July 2019, as well as on the proposed revision of the ICTV Statutes. All proposals and the revision of the Statutes were approved by an absolute majority of the ICTV voting membership. Of note, ICTV has approved a proposal that extends the previously established realm Riboviria to encompass nearly all RNA viruses and reverse-transcribing viruses, and approved three separate proposals to establish three realms for viruses with DNA genomes.
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Affiliation(s)
- Peter J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA.
| | | | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Room N-604, 3584 CH, Utrecht, The Netherlands
| | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, 10300 Baltimore Avenue, Bldg 007 Barc-West, Beltsville, MD, 20705, USA
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité, Universitätsmedizin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
| | - Andrew M Kropinski
- Departments of Food Science, and Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- NIH/NIAID/DCR Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Max Nibert
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA, 02115, USA
| | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Starkville, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Arvind Varsani
- School of Life Sciences, The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ, 85287-4701, USA
| | - Francisco Murilo Zerbini
- School of Life Sciences, The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ, 85287-4701, USA
| | - Andrew J Davison
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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10
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Siddell SG, Walker PJ, Lefkowitz EJ, Mushegian AR, Dutilh BE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert ML, Rubino L, Sabanadzovic S, Simmonds P, Varsani A, Zerbini FM, Davison AJ. Correction to: Binomial nomenclature for virus species: a consultation. Arch Virol 2020; 165:1263-1264. [PMID: 32065315 PMCID: PMC7160066 DOI: 10.1007/s00705-020-04555-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Peter J Walker
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, 4072, Australia
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Room N-604, 3584 CH, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center (Radboudumc), Geert Grooteplein 26, 6525 GA, Nijmegen, The Netherlands
| | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, Budapest, 1143, Hungary
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, 10300 Baltimore Avenue, Bldg 007 BARC-West, Beltsville, MD, 20705, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, Corporate Member of Free University Berlin, Humboldt-University Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
| | - Andrew M Kropinski
- Department of Food Science, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Division of Clinical Research, Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Max L Nibert
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA, 02115, USA
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, Sede Secondaria di Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Experimental Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3PS, UK
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ, 85287-4701, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK.
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11
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Calisher CH, Briese T, Brister JR, Charrel RN, Dürrwald R, Ebihara H, Fulhorst CF, Gāo GF, Groschup MH, Haddow AD, Hyndman TH, Junglen S, Klempa B, Klingström J, Kropinski AM, Krupovic M, LaBeaud AD, Maes P, Nowotny N, Nunes MRT, Payne SL, Radoshitzky SR, Rubbenstroth D, Sabanadzovic S, Sasaya T, Stenglein MD, Varsani A, Wahl V, Weaver SC, Zerbini FM, Vasilakis N, Kuhn JH. Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species. Syst Biol 2019; 68:828-839. [PMID: 30597118 PMCID: PMC6701456 DOI: 10.1093/sysbio/syy087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 12/16/2018] [Accepted: 11/19/2018] [Indexed: 01/09/2023] Open
Abstract
The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV's official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-devised taxa. Instead, these professionals look to the ICTV as an expert point source that provides the most current taxonomic affiliations of viruses of interests to facilitate document writing. These needs are currently unmet as an ICTV-supported, easily searchable database that includes all published virus names and abbreviations linked to their taxa is not available. In addition, in stark contrast to other biological taxonomic frameworks, virus taxonomy currently permits individual species to have several members. Consequently, confusion emerges among those who are not aware of the difference between taxa and viruses, and because certain well-known viruses cannot be located in ICTV publications or be linked to their species. In addition, the number of duplicate names and abbreviations has increased dramatically in the literature. To solve this conundrum, the ICTV could mandate listing all viruses of established species and all reported unclassified viruses in forthcoming online ICTV Reports and create a searchable webpage using this information. The International Union of Microbiology Societies could also consider changing the mandate of the ICTV to include the nomenclature of all viruses in addition to taxon considerations. With such a mandate expansion, official virus names and virus name abbreviations could be catalogued and virus nomenclature could be standardized. As a result, the ICTV would become an even more useful resource for all stakeholders in virology.
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Affiliation(s)
- Charles H Calisher
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, 3195 Rampart Rd., Delivery Code 1690, Foothills Campus, Fort Collins, CO 80523-1692, USA
| | - Thomas Briese
- Department of Epidemiology, Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 St., New York, NY 10032, USA
| | - J Rodney Brister
- National Center for Biotechnology, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 27102, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Faculté de Médecine, Université Aix-Marseille—IRD 190—Inserm 1207—IHU Méditerranée Infection), Marseille, France
| | - Ralf Dürrwald
- Department of Infectious Diseases, Robert Koch-Institut, Postfach 65 02 61, D-13302 Berlin, Germany
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Guggenheim Building, 18th Floor, 200 First St. SW, Rochester, MN 55905, USA
| | - Charles F Fulhorst
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0609, USA
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd., Changping District, Beijing 102206, China
| | - Martin H Groschup
- Institut für Virusdiagnostik, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Andrew D Haddow
- Department of Virology, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Timothy H Hyndman
- College of Veterinary Medicine, School of Veterinary and Life Sciences, Murdoch University, 90 South St., Murdoch, Western Australia 6150, Australia
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Germany
- Deutsches Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Boris Klempa
- Biomedicínske centrum, Virologický ústav, Slovenská Akadémia Vied, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - Jonas Klingström
- Centre for Infectious Medicine, Institutionen för Medicin, Huddinge, Karolinska Institutet, C2:94, Karolinska Universitetssjukhuset, 141 86 Stockholm, Sweden
| | - Andrew M Kropinski
- Department of Food Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department of Pathobiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Mart Krupovic
- Departement of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - A Desiree LaBeaud
- Division of Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Dr., G312, Stanford, CA, 94305 USA
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Zoonotic Infectious Diseases unit, Herestraat 49 box 1040, BE3000 Leuven, Belgium
| | - Norbert Nowotny
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Building 14, Dubai Healthcare City, P.O. Box 505055, Dubai, United Arab Emirates
| | - Márcio Roberto Teixeira Nunes
- Evandro Chagas Institute, Brazilian Ministry of Health, Rodovia Br-316, Km 7 s/n, Levilândia, Ananindeua, Pará, 67030-000, Brazil
| | - Susan L Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Veterinary Medical Sciences Building, 400 Raymond Stotzer Parkway, Texas A&M University 4467, College Station, TX 77843, USA
| | - Sheli R Radoshitzky
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Dennis Rubbenstroth
- Institut für Virusdiagnostik, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
- Institut für Virologie, Universitätsklinikum Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 402 Dorman Hall, Box 9655, Mississippi State, MS 39762, USA
| | - Takahide Sasaya
- Department of Planning and Coordination, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan
| | - Mark D Stenglein
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523 USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 727 E. Tyler St., P.O. Box 876101, Tempe, AZ 85287-6101, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, Frederick, MD 27102, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO and National Institute of Science and Technology for Plant-Pest Interactions, Universidade Federal de Viçosa, Av. P.H. Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Nikos Vasilakis
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, B-8200 Research Plaza, Fort Detrick, Frederick, MD 27102, USA
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12
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Abstract
Viruses constitute the largest group of emerging pathogens, and geminiviruses (plant viruses with circular, single-stranded DNA genomes) are the major group of emerging plant viruses. With their high potential for genetic variation due to mutation and recombination, their efficient spread by vectors, and their wide host range as a group, including both wild and cultivated hosts, geminiviruses are attractive models for the study of the evolutionary and ecological factors driving virus emergence. Studies on the epidemiological features of geminivirus diseases have traditionally focused primarily on crop plants. Nevertheless, knowledge of geminivirus infection in wild plants, and especially at the interface between wild and cultivated plants, is necessary to provide a complete view of their ecology, evolution, and emergence. In this review, we address the most relevant aspects of geminivirus variability and evolution in wild and crop plants and geminiviruses' potential to emerge in crops.
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Affiliation(s)
- Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain;
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), and National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil;
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13
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Siddell SG, Walker PJ, Lefkowitz EJ, Mushegian AR, Adams MJ, Dutilh BE, Gorbalenya AE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert M, Rubino L, Sabanadzovic S, Sanfaçon H, Simmonds P, Varsani A, Zerbini FM, Davison AJ. Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018). Arch Virol 2019; 164:943-946. [PMID: 30663020 DOI: 10.1007/s00705-018-04136-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in October 2018. Of note, the ICTV has approved, by an absolute majority, the creation of additional taxonomical ranks above those recognized previously. A total of 15 ranks (realm, subrealm, kingdom, subkingdom, phylum, subphylum, class, subclass, order, suborder, family, subfamily, genus, subgenus, and species) are now available to encompass the entire spectrum of virus diversity. Classification at ranks above genus is not obligatory but can be used by the authors of new taxonomic proposals when scientific justification is provided.
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Affiliation(s)
- Stuart G Siddell
- Faculty of Life Sciences, School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Peter J Walker
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA.
| | | | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Room Z-509, 3584 CH, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center (Radboudumc), Geert Grooteplein 26, 6525 GA, Nijmegen, The Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, E4-P, rm. E4-72, P. O. Box 9600, 2300 RC, Leiden, The Netherlands.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899, Moscow, Russia
| | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, 10300 Baltimore Avenue, Bldg 007 BARC-West, Beltsville, MD, 20705, USA
| | - Sandra Junglen
- Institute of Virology, Corporate Member of Free University Berlin, Charité-Universitätsmedizin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
| | - Andrew M Kropinski
- Departments of Food Science, and Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- NIH/NIAID/DCR Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Max Nibert
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA, 02115, USA
| | - Luisa Rubino
- Istituto di Protezione Sostenibile delle Piante, CNR, UOS Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Starkville, MS, 39762, USA
| | - Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, Summerland, British Columbia, V0H 1Z0, Canada
| | - Peter Simmonds
- Nuffield Department of Experimental Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3PS, UK
| | - Arvind Varsani
- School of Life Sciences, The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ, 85287-4701, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
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14
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Ferro MMM, Ramos-Sobrinho R, Xavier CAD, Zerbini FM, Lima GSA, Nagata T, Assunção IP. New approach for the construction of infectious clones of a circular DNA plant virus using Gibson Assembly. J Virol Methods 2018; 263:20-23. [PMID: 30366017 DOI: 10.1016/j.jviromet.2018.10.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/20/2018] [Accepted: 10/22/2018] [Indexed: 10/28/2022]
Abstract
Viruses belonging to the genus Begomovirus (family Geminiviridae) have circular single-strand DNA genomes encapsidated into quasi-icosahedral particles, and are transmitted by whiteflies of the Bemisia tabaci complex. Biological and molecular properties of begomoviruses have been studied efficiently with infectious clones containing dimeric genomic components. However, current approaches employing enzymatic digestion and ligation to binary vectors are laborious, mostly due to many cloning steps or partial digestion by restriction enzyme. Here, an infectious clone of the bipartite begomovirus Bean golden mosaic virus (BGMV) was obtained using PCR and Gibson Assembly (GA). Common bean (Phaseolus vulgaris) seedlings displayed severe yellow mosaic and stunt symptoms 15 days after agroinoculation with DNA-A and DNA-B of BGMV. The approach based on PCR-GA protocol is a fast and useful tool to obtain infectious clones of a circular DNA plant virus.
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Affiliation(s)
- M M M Ferro
- Setor de Fitossanidade/Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - R Ramos-Sobrinho
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil.
| | - C A D Xavier
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - F M Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - G S A Lima
- Setor de Fitossanidade/Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - T Nagata
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - I P Assunção
- Setor de Fitossanidade/Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
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15
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King AMQ, Lefkowitz EJ, Mushegian AR, Adams MJ, Dutilh BE, Gorbalenya AE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert ML, Rubino L, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Davison AJ. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018). Arch Virol 2018; 163:2601-2631. [PMID: 29754305 DOI: 10.1007/s00705-018-3847-1] [Citation(s) in RCA: 207] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 04/14/2018] [Indexed: 12/30/2022]
Abstract
This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2018. A total of 451 species, 69 genera, 11 subfamilies, 9 families and one new order were added to the taxonomy. The current totals at each taxonomic level now stand at 9 orders, 131 families, 46 subfamilies, 803 genera and 4853 species. A change was made to the International Code of Virus Classification and Nomenclature to allow the use of the names of people in taxon names under appropriate circumstances. An updated Master Species List incorporating the approved changes was released in March 2018 ( https://talk.ictvonline.org/taxonomy/ ).
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Affiliation(s)
- Andrew M Q King
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, Surrey, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA.
| | | | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, P. O. Box 9600, E4-P, rm. E4-72, 2300 RC, Leiden, The Netherlands.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119899, Russia
| | - Balázs Harrach
- Centre for Agricultural Research, Hungarian Academy of Sciences, Institute for Veterinary Medical Research, Hungária krt. 21, Budapest, 1143, Hungary
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, 10300 Baltimore Avenue, Bldg 007 Barc-West, Beltsville, MD, 20705, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Rahel-Hirsch-Weg 3, Charitéplatz 1, 10117, Berlin, Germany.,German Center for Infection Research (DZIF), Berlin, Germany
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, Surrey, UK
| | - Andrew M Kropinski
- Departments of Food Science and Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- NIH/NIAID/DCR Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200, Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Max L Nibert
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Ave Louis, Pasteur, Boston, MA, 02115, USA
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, SS Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, Summerland, BC, V0H 1Z0, Canada
| | - Stuart G Siddell
- Faculty of Biomedical Sciences, School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Peter Simmonds
- Nuffield Department of Experimental Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ, 85287-4701, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
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16
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Bruckner FP, Xavier ADS, Cascardo RDS, Otoni WC, Zerbini FM, Alfenas‐Zerbini P. Translationally controlled tumour protein (TCTP) from tomato and Nicotiana benthamiana is necessary for successful infection by a potyvirus. Mol Plant Pathol 2017; 18:672-683. [PMID: 27159273 PMCID: PMC6638207 DOI: 10.1111/mpp.12426] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 05/20/2023]
Abstract
Translationally controlled tumour protein (TCTP) is a ubiquitously distributed protein in eukaryotes, involved in the regulation of several processes, including cell cycle progression, cell growth, stress protection, apoptosis and maintenance of genomic integrity. Its expression is induced during the early stages of tomato (Solanum lycopersicum) infection by the potyvirus Pepper yellow mosaic virus (PepYMV, a close relative of Potato virus Y). Tomato TCTP is a protein of 168 amino acids, which contains all the conserved domains of the TCTP family. To study the effects of TCTP silencing in PepYMV infection, Nicotiana benthamiana plants were silenced by virus-induced gene silencing (VIGS) and transgenic tomato plants silenced for TCTP were obtained. In the early stages of infection, both tomato and N. benthamiana silenced plants accumulated less virus than control plants. Transgenic tomato plants showed a drastic reduction in symptoms and no viral accumulation at 14 days post-inoculation. Subcellular localization of TCTP was determined in healthy and systemically infected N. benthamiana leaves. TCTP was observed in both the nuclei and cytoplasm of non-infected cells, but only in the cytoplasm of infected cells. Our results indicate that TCTP is a growth regulator necessary for successful PepYMV infection and that its localization is altered by the virus, probably to favour the establishment of virus infection. A network with putative interactions that may occur between TCTP and Arabidopsis thaliana proteins was built. This network brings together experimental data of interactions that occur in other eukaryotes and helps us to discuss the possibilities of TCTP involvement in viral infection.
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Affiliation(s)
- Fernanda Prieto Bruckner
- Departamento de Microbiologia/BIOAGRO/National Institute of Science and Technology in Plant‐Pest InteractionsUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
| | - André Da Silva Xavier
- Departamento de Fitopatologia/BIOAGRO/National Institute of Science and Technology in Plant‐Pest InteractionsUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
| | - Renan De Souza Cascardo
- Departamento de Microbiologia/BIOAGRO/National Institute of Science and Technology in Plant‐Pest InteractionsUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
| | - Wagner Campos Otoni
- Departamento de Biologia Vegetal/BIOAGROUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO/National Institute of Science and Technology in Plant‐Pest InteractionsUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
| | - Poliane Alfenas‐Zerbini
- Departamento de Microbiologia/BIOAGRO/National Institute of Science and Technology in Plant‐Pest InteractionsUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
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17
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Silva JCF, Carvalho TFM, Basso MF, Deguchi M, Pereira WA, Sobrinho RR, Vidigal PMP, Brustolini OJB, Silva FF, Dal-Bianco M, Fontes RLF, Santos AA, Zerbini FM, Cerqueira FR, Fontes EPB. Geminivirus data warehouse: a database enriched with machine learning approaches. BMC Bioinformatics 2017; 18:240. [PMID: 28476106 PMCID: PMC5420152 DOI: 10.1186/s12859-017-1646-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/25/2017] [Indexed: 03/28/2023] Open
Abstract
BACKGROUND The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible for significant economic losses worldwide. Geminiviruses are divided into nine genera, according to their insect vector, host range, genome organization, and phylogeny reconstruction. Using rolling-circle amplification approaches along with high-throughput sequencing technologies, thousands of full-length geminivirus and satellite genome sequences were amplified and have become available in public databases. As a consequence, many important challenges have emerged, namely, how to classify, store, and analyze massive datasets as well as how to extract information or new knowledge. Data mining approaches, mainly supported by machine learning (ML) techniques, are a natural means for high-throughput data analysis in the context of genomics, transcriptomics, proteomics, and metabolomics. RESULTS Here, we describe the development of a data warehouse enriched with ML approaches, designated geminivirus.org. We implemented search modules, bioinformatics tools, and ML methods to retrieve high precision information, demarcate species, and create classifiers for genera and open reading frames (ORFs) of geminivirus genomes. CONCLUSIONS The use of data mining techniques such as ETL (Extract, Transform, Load) to feed our database, as well as algorithms based on machine learning for knowledge extraction, allowed us to obtain a database with quality data and suitable tools for bioinformatics analysis. The Geminivirus Data Warehouse (geminivirus.org) offers a simple and user-friendly environment for information retrieval and knowledge discovery related to geminiviruses.
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Affiliation(s)
- Jose Cleydson F Silva
- Departamento de Informática, Universidade Federal de Viçosa, Viçosa, Brazil.,National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Marcos F Basso
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Michihito Deguchi
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Welison A Pereira
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Roberto R Sobrinho
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Pedro M P Vidigal
- Núcleo de Biomoléculas, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Otávio J B Brustolini
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Fabyano F Silva
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Maximiller Dal-Bianco
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Anésia A Santos
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Francisco Murilo Zerbini
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Fabio R Cerqueira
- Departamento de Informática, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Engenharia de Produção, Universidade Federal Fluminense, Petrópolis, Rio de Janeiro, Brazil
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil. .,Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil.
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18
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Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert ML, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Orton RJ, Smith DB, Gorbalenya AE, Davison AJ. 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. Arch Virol 2017; 162:1441-1446. [PMID: 28078475 DOI: 10.1007/s00705-016-3215-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/04/2016] [Indexed: 11/25/2022]
Abstract
We mark the 50th anniversary of the International Committee on Taxonomy of Viruses (ICTV) by presenting a brief history of the organization since its foundation, showing how it has adapted to advancements in our knowledge of virus diversity and the methods used to characterize it. We also outline recent developments, supported by a grant from the Wellcome Trust (UK), that are facilitating substantial changes in the operations of the ICTV and promoting dialogue with the virology community. These developments will generate improved online resources, including a freely available and regularly updated ICTV Virus Taxonomy Report. They also include a series of meetings between the ICTV and the broader community focused on some of the major challenges facing virus taxonomy, with the outcomes helping to inform the future policy and practice of the ICTV.
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Affiliation(s)
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Andrew M Q King
- Sunfield, Dawney Hill, Pirbright, Woking, Surrey, GU24 0JB, UK
| | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, 1143, Budapest, Hungary
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, 10300 Baltimore Avenue, Bldg 007 Barc-West, Beltsville, MD, 20705, USA
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
| | - Andrew M Kropinski
- Departments of Food Science, Molecular and Cellular Biology and Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- NIH/NIAID/DCR Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Arlington, VA, 22230, USA
| | - Max L Nibert
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA, 02115, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Starkville, MS, 39762, USA
| | - Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, Summerland, BC, V0H 1Z0, Canada
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Biomedical Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Peter Simmonds
- Nuffield Department of Experimental Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3PS, UK
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ, 85287-4701, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Richard J Orton
- MRC, University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Donald B Smith
- Centre for Immunity, Infection and Evolution, Ashworth Laboratories, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, E4-P, rm. E4-72, P. O. Box 9600, 2300 RC, Leiden, The Netherlands
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899, Moscow, Russia
| | - Andrew J Davison
- MRC, University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
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19
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Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017). Arch Virol 2017; 162:2505-2538. [DOI: 10.1007/s00705-017-3358-5] [Citation(s) in RCA: 347] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
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20
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Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016). Arch Virol 2016; 161:2921-49. [PMID: 27424026 PMCID: PMC7086986 DOI: 10.1007/s00705-016-2977-6] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/08/2016] [Indexed: 10/25/2022]
Abstract
This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2016.Changes to virus taxonomy (the Universal Scheme of Virus Classification of the International Committee on Taxonomy of Viruses [ICTV]) now take place annually and are the result of a multi-stage process. In accordance with the ICTV Statutes ( http://www.ictvonline.org/statutes.asp ), proposals submitted to the ICTV Executive Committee (EC) undergo a review process that involves input from the ICTV Study Groups (SGs) and Subcommittees (SCs), other interested virologists, and the EC. After final approval by the EC, proposals are then presented for ratification to the full ICTV membership by publication on an ICTV web site ( http://www.ictvonline.org/ ) followed by an electronic vote. The latest set of proposals approved by the EC was made available on the ICTV website by January 2016 ( https://talk.ictvonline.org/files/proposals/ ). A list of these proposals was then emailed on 28 March 2016 to the 148 members of ICTV, namely the EC Members, Life Members, ICTV Subcommittee Members (including the SG chairs) and ICTV National Representatives. Members were then requested to vote on whether to ratify the taxonomic proposals (voting closed on 29 April 2016).
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Affiliation(s)
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL 35294-2170 USA
| | | | - Balázs Harrach
- Veterinary Medical Research Institute, Hungarian Academy of Sciences, Hungária krt. 21, 1143 Budapest, Hungary
| | - Robert L. Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, 10300 Baltimore Avenue, Bldg 007 Barc-West, Beltsville, MD 20705 USA
| | - Nick J. Knowles
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF UK
| | - Andrew M. Kropinski
- Departments of Food Science, Molecular and Cellular Biology and Pathobiology, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Jens H. Kuhn
- NIH/NIAID/DCR Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702 USA
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Arlington, VA USA
| | - Max Nibert
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA 02115 USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS 39762 USA
| | - Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, Summerland, BC V0H 1Z0 Canada
| | - Stuart G. Siddell
- Department of Cellular and Molecular Medicine, Faculty of Biomedical Sciences, University of Bristol, University Walk, Bristol, BS8 1TD UK
| | - Peter Simmonds
- Nuffield Department of Experimental Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3PS UK
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140 New Zealand
| | | | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, P. O. Box 9600, E4-P, rm. E4-72, 2300 RC Leiden, The Netherlands
| | - Andrew J. Davison
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH UK
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21
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Sá Antunes TF, Amaral RJV, Ventura JA, Godinho MT, Amaral JG, Souza FO, Zerbini PA, Zerbini FM, Fernandes PMB. The dsRNA Virus Papaya Meleira Virus and an ssRNA Virus Are Associated with Papaya Sticky Disease. PLoS One 2016; 11:e0155240. [PMID: 27166626 PMCID: PMC4863961 DOI: 10.1371/journal.pone.0155240] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/26/2016] [Indexed: 11/28/2022] Open
Abstract
Papaya sticky disease, or "meleira", is one of the major diseases of papaya in Brazil and Mexico, capable of causing complete crop loss. The causal agent of sticky disease was identified as an isometric virus with a double stranded RNA (dsRNA) genome, named papaya meleira virus (PMeV). In the present study, PMeV dsRNA and a second RNA band of approximately 4.5 kb, both isolated from latex of papaya plants with severe symptoms of sticky disease, were deep-sequenced. The nearly complete sequence obtained for PMeV dsRNA is 8,814 nucleotides long and contains two putative ORFs; the predicted ORF1 and ORF2 display similarity to capsid proteins and RdRp's, respectively, from mycoviruses tentatively classified in the family Totiviridae. The sequence obtained for the second RNA is 4,515 nucleotides long and contains two putative ORFs. The predicted ORFs 1 and 2 display 48% and 73% sequence identity, respectively, with the corresponding proteins of papaya virus Q, an umbravirus recently described infecting papaya in Ecuador. Viral purification in a sucrose gradient allowed separation of particles containing each RNA. Mass spectrometry analysis indicated that both PMeV and the second RNA virus (named papaya meleira virus 2, PMeV2) were encapsidated in particles formed by the protein encoded by PMeV ORF1. The presence of both PMeV and PMeV2 was confirmed in field plants showing typical symptoms of sticky disease. Interestingly, PMeV was detected alone in asymptomatic plants. Together, our results indicate that sticky disease is associated with double infection by PMeV and PMeV2.
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Affiliation(s)
| | | | - José Aires Ventura
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
- Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural, Vitória, Espírito Santo, Brazil
| | - Marcio Tadeu Godinho
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, 36570–900, Viçosa, Minas Gerais, Brazil
| | - Josiane G. Amaral
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, 36570–900, Viçosa, Minas Gerais, Brazil
| | - Flávia O. Souza
- Dep. de Microbiologia/BIOAGRO, Universidade Federal de Viçosa, 36570–900, Viçosa, Minas Gerais, Brazil
| | - Poliane Alfenas Zerbini
- Dep. de Microbiologia/BIOAGRO, Universidade Federal de Viçosa, 36570–900, Viçosa, Minas Gerais, Brazil
| | - Francisco Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, 36570–900, Viçosa, Minas Gerais, Brazil
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22
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Pinto VB, Silva JP, Fiallo-Olivé E, Navas-Castillo J, Zerbini FM. Novel begomoviruses recovered from Pavonia sp. in Brazil. Arch Virol 2015; 161:735-9. [PMID: 26660167 DOI: 10.1007/s00705-015-2708-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/30/2015] [Indexed: 11/29/2022]
Abstract
Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that cause serious infections in crop plants and are often also associated with non-cultivated plants. Here, we report the detection of two new begomoviruses in Pavonia sp. (Malvaceae). Sequence comparisons and phylogenetic analysis showed that these novel viruses are related to New World begomoviruses. The nucleotide sequences of the DNA-A of both viruses had the highest similarity to abutilon mosaic Bolivia virus (AbMBoV). Based on symptoms observed in the field and considering the host, we propose the names pavonia mosaic virus (PavMV) and pavonia yellow mosaic virus (PavYMV) for these two new begomoviruses.
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Affiliation(s)
- Vitor Batista Pinto
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.,National Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - João Paulo Silva
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.,National Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Elvira Fiallo-Olivé
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.,National Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29750, Algarrobo-Costa, Málaga, Spain
| | - Jésus Navas-Castillo
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.,National Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29750, Algarrobo-Costa, Málaga, Spain
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil. .,National Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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23
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Sobrinho RR, Xavier CAD, Pereira HMDB, Lima GSDA, Assunção IP, Mizubuti ESG, Duffy S, Zerbini FM. Contrasting genetic structure between two begomoviruses infecting the same leguminous hosts. J Gen Virol 2014; 95:2540-2552. [DOI: 10.1099/vir.0.067009-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Begomoviruses are whitefly-transmitted, ssDNA plant viruses and are among the most damaging pathogens causing epidemics in economically important crops worldwide. Wild/non-cultivated plants play a crucial epidemiological role, acting as begomovirus reservoirs and as ‘mixing vessels' where recombination can occur. Previous work suggests a higher degree of genetic variability in begomovirus populations from non-cultivated hosts compared with cultivated hosts. To assess this supposed host effect on the genetic variability of begomovirus populations, cultivated (common bean, Phaseolus vulgaris, and lima bean, Phaseolus lunatus) and non-cultivated (Macroptilium lathyroides) legume hosts were sampled from two regions of Brazil. A total of 212 full-length DNA-A genome segments were sequenced from samples collected between 2005 and 2012, and populations of the begomoviruses Bean golden mosaic virus (BGMV) and Macroptilium yellow spot virus (MaYSV) were obtained. We found, for each begomovirus species, similar genetic variation between populations infecting cultivated and non-cultivated hosts, indicating that the presumed genetic variability of the host did not a priori affect viral variability. We observed a higher degree of genetic variation in isolates from MaYSV populations than BGMV populations, which was explained by numerous recombination events in MaYSV. MaYSV and BGMV showed distinct distributions of genetic variation, with the BGMV population (but not MaYSV) being structured by both host and geography.
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Affiliation(s)
- Roberto Ramos Sobrinho
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | | | | | | | - Iraíldes Pereira Assunção
- Departamento de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL 57100-000, Brazil
| | | | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University Of New Jersey, New Brunswick, NJ 08901, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
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24
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Zanardo LG, Silva FN, Lima ATM, Milanesi DF, Castilho-Urquiza GP, Almeida AMR, Zerbini FM, Carvalho CM. Molecular variability of cowpea mild mottle virus infecting soybean in Brazil. Arch Virol 2014; 159:727-37. [PMID: 24142270 DOI: 10.1007/s00705-013-1879-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 10/03/2013] [Indexed: 11/26/2022]
Abstract
Molecular variability was assessed for 18 isolates of cowpea mild mottle virus (CPMMV, genus Carlavirus, family Betaflexiviridae) found infecting soybean in various Brazilian states (Bahia, Goiás, Maranhão, Mato Grosso, Minas Gerais, Pará) in 2001 and 2010. A variety of symptoms was expressed in soybean cv. CD206, ranging from mild (crinkle/blistering leaves, mosaic and vein clearing) to severe (bud blight, dwarfing, leaf and stem necrosis). Recombination analysis revealed only one CPMMV isolate to be recombinant. Pairwise comparisons and phylogenetic analysis were performed for partial genomes (ORF 2 to the 3' terminus) and for each ORF individually (ORFs 2 to 6), showing the isolates to be distinct. The topology of the phylogenetic tree could be related to symptoms, but not to the year of collection or geographical origin. Additionally, the phylogenetic analysis supported the existence of two distinct strains of the virus, designated CPMMV-BR1 and CPMMV-BR2, with molecular variations between them.
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Affiliation(s)
- L G Zanardo
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
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Fernandes FR, Cruz ARR, Faria JC, Zerbini FM, Aragão FJL. Three distinct begomoviruses associated with soybean in central Brazil. Arch Virol 2009; 154:1567-70. [PMID: 19636495 DOI: 10.1007/s00705-009-0463-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Accepted: 06/26/2009] [Indexed: 10/20/2022]
Abstract
We report the complete nucleotide sequences of geminiviruses of the genus Begomovirus infecting soybean (Glycine max) in central Brazil. Samples obtained from soybean plants collected at Santo Antonio de Goiás, Goiás State, showing typical symptoms of viral infection, were analyzed. Infection was confirmed by PCR-based amplification of a DNA-A fragment with universal begomovirus primers. Total DNA from infected plants was then subjected to rolling-circle amplification (RCA), and 2.6-kb molecules were cloned into plasmid vectors. Sequencing of the three DNA-A and two DNA-B clones thus obtained confirmed infection by three distinct begomoviruses: bean golden mosaic virus, Sida micrantha mosaic virus and okra mottle virus, the last of which was reported recently to be a novel virus infecting okra plants in Brazil. Begomovirus infection of soybean plants has been reported sporadically in Brazil and has generally not been considered to be of economic relevance.
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Affiliation(s)
- Fernanda R Fernandes
- Embrapa Recursos Genéticos e Biotecnologia, Laboratório de Transferência de Genes, PqEB W5 Norte, Brasília, DF, 70770-900, Brazil
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26
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Alfenas-Zerbini P, Maia IG, Fávaro RD, Cascardo JCM, Brommonschenkel SH, Zerbini FM. Genome-wide analysis of differentially expressed genes during the early stages of tomato infection by a potyvirus. Mol Plant Microbe Interact 2009; 22:352-61. [PMID: 19245329 DOI: 10.1094/mpmi-22-3-0352] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plant responses against pathogens cause up- and downward shifts in gene expression. To identify differentially expressed genes in a plant-virus interaction, susceptible tomato plants were inoculated with the potyvirus Pepper yellow mosaic virus (PepYMV) and a subtractive library was constructed from inoculated leaves at 72 h after inoculation. Several genes were identified as upregulated, including genes involved in plant defense responses (e.g., pathogenesis-related protein 5), regulation of the cell cycle (e.g., cytokinin-repressed proteins), signal transduction (e.g., CAX-interacting protein 4, SNF1 kinase), transcriptional regulators (e.g., WRKY and SCARECROW transcription factors), stress response proteins (e.g., Hsp90, DNA-J, 20S proteasome alpha subunit B, translationally controlled tumor protein), ubiquitins (e.g., polyubiquitin, ubiquitin activating enzyme 2), among others. Downregulated genes were also identified, which likewise display identity with genes involved in several metabolic pathways. Differential expression of selected genes was validated by macroarray analysis and quantitative real-time polymerase chain reaction. The possible roles played by some of these genes in the viral infection cycle are discussed.
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Affiliation(s)
- Poliane Alfenas-Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil.
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27
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Carvalho CM, Machado JPB, Zerbini FM, Fontes EP. NSP-interacting GTPase: A cytosolic protein as cofactor for nuclear shuttle proteins. Plant Signal Behav 2008; 3:752-4. [PMID: 19704847 PMCID: PMC2634578 DOI: 10.4161/psb.3.9.6641] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2008] [Accepted: 07/21/2008] [Indexed: 05/07/2023]
Abstract
Despite the significant progress in the identification of essential components of the nuclear transport machinery, some events of this process are still unclear. Particularly, functional information about the release of nuclear-exported macromolecules at the cytoplasmic side of the nuclear pore complex and their subsequent trans-cytoplasmic movement is lacking. Recently, we identified a cytoplasmic GTPase, designated NIG (NSP-interacting GTPase), which may play a relevant role in these processes. NIG interacts in vivo with the geminivirus NSP and promotes the translocation of the viral protein from the nucleus to the cytoplasm where it is redirected to the cell surface to interact with the viral movement protein, MP. Here we position the NIG function into the mechanistic model for the intracellular trafficking of viral DNA and discuss the putative role of NIG in general cellular nucleocytoplasmic transport of nucleic acid-protein complexes.
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Affiliation(s)
- Claudine M Carvalho
- Departamento de Fitopatologia; BIOAGRO; Universidade Federal de Viçosa; Viçosa, Minas Gerais Brazil
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28
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Jadão AS, Krause-Sakate R, Liberti D, Pavan MA, Echer MM, Svanella-Dumas L, Zerbini FM, Candresse T, Le Gall O. Further characterization of two sequiviruses infecting lettuce and development of specific RT-PCR primers. Arch Virol 2007; 152:999-1007. [PMID: 17238013 DOI: 10.1007/s00705-006-0895-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 11/06/2006] [Indexed: 10/23/2022]
Abstract
Lettuce mottle virus (LeMoV) and dandelion yellow mosaic virus (DaYMV) infect lettuce in South America and Europe, respectively. LeMoV and DaYMV possess isometric particles, occur at low concentrations in plants and have narrow host ranges. Partial genome sequences of both viruses were obtained using purified viral preparations and universal primers for members of the family Sequiviridae. DaYMV and LeMoV sequences were analyzed and showed identity with other members of the family. Universal primers that detect both viruses and specific primers for LeMoV and DaYMV were designed and used in RT-PCR-based diagnostic assays. These results provide the first molecular data on the LeMoV and DaYMV genomes and suggest that LeMoV is a member of the genus Sequivirus, probably distinct from DaYMV.
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Affiliation(s)
- A S Jadão
- UMR GDPP INRA-Bordeaux 2, IBVM, Villenave d'Ornon Cedex, France
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29
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Andrade EC, Manhani GG, Alfenas PF, Calegario RF, Fontes EPB, Zerbini FM. Tomato yellow spot virus, a tomato-infecting begomovirus from Brazil with a closer relationship to viruses from Sida sp., forms pseudorecombinants with begomoviruses from tomato but not from Sida. J Gen Virol 2006; 87:3687-3696. [PMID: 17098986 DOI: 10.1099/vir.0.82279-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Geminiviruses are characterized by a circular, single-stranded DNA genome and twinned icosahedral particles. Begomoviruses (whitefly-transmitted geminiviruses) are a major constraint to crop production worldwide. In Brazil, tomato-infecting begomoviruses emerged as serious pathogens over the last 10 years, due to the introduction of a new biotype of the insect vector. Tomato yellow spot virus (ToYSV) is a newly described begomovirus originally isolated from tomato, but phylogenetically closer to viruses from Sida sp. A study was performed to determine the viability of pseudorecombinants formed between the DNA components of ToYSV and other weed- and tomato-infecting begomoviruses from Brazil. Despite its closer relationship to weed-infecting viruses, ToYSV was only capable of forming viable pseudorecombinants with tomato viruses. An infectious pseudorecombinant formed between ToYSV DNA-A and tomato crinkle leaf yellows virus (TCrLYV) DNA-B induced severe symptoms in Nicotiana benthamiana. This was attributed, at least in part, to the fact that the origins of replication of both components had identical Rep-binding sequences. However, this was not the case for another infectious pseudorecombinant formed between tomato golden mosaic virus (TGMV) DNA-A and ToYSV DNA-B, which have different Rep-binding sequences. These results reinforce the notion that pseudorecombinant formation cannot be explained solely on the basis of phylogenetic relationships and conserved iteron sequences, and suggest that the TGMV Rep protein may be more versatile in terms of recognizing heterologous DNA components than that of ToYSV.
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Affiliation(s)
- E C Andrade
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - G G Manhani
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - P F Alfenas
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - R F Calegario
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - E P B Fontes
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - F M Zerbini
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
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30
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Krause-Sakate R, Jadão AS, Firmino AC, Pavan MA, Zerbini FM, Rosales IM, Bustamante P, Gall OL. First Report of a Lettuce-Infecting Sequivirus in Chile. Plant Dis 2005; 89:1129. [PMID: 30791287 DOI: 10.1094/pd-89-1129a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sequiviruses are isometric aphidborne plant viruses. Dandelion yellow mosaic virus (DaYMV), genus Sequivirus, was isolated from dandelion and lettuce in Europe. Lettuce mottle virus (LeMoV), a putative sequivirus, is often found in mixed infections with Lettuce mosaic virus (LMV) in Brazil (3). DaYMV, LeMoV and LMV cause similar mosaics in field-grown lettuce. Differences in biology and sequence suggest that DaYMV and LeMoV are distinct species (2). Forty-two and 101 lettuce samples with mosaic symptoms collected from two locations near Santiago during a survey of lettuce viruses in Chile in 2002 and 2003, respectively, were analyzed for the presence of LeMoV using reverse transcription polymerase chain reaction (RT-PCR). Total RNA was extracted (1) and used for RT-PCR with the specific LeMoV primers pairs Lmo3 (5' ACATGAGCACTAGTGAGG 3') and Lmo4 (5' AGATAGAGCCGTCT GGCG 3') (2). One of the 42 and three of the 101 samples produced the expected 300-bp fragment. Isometric particles of 30 nm diameter, typical of a sequivirus, were visualized by transmission electron microscopy. These samples were tested using RT-PCR for the presence of LMV and Cucumber mosaic virus (CMV), but no mixed infections were observed. One isolate, Ch36, was reamplified with the degenerate primer pairs DALE 1 (5' GARTTCAACATGCACGCCAG 3') and DALE 2 (5' TTTTTCTCCCCATYCGTCAT 3') which amplify part of the putative replicase gene (2) and produced a 563-bp fragment that was cloned on pGEM-T Easy (Promega, Madison, WI) and sequenced. The Ch36 product (EMBL Accession No. AM039965) showed 97% amino acid identity with LeMoV from Brazil, 79% with DaYMV, 72% with the sequivirus Parsnip yellow fleck virus, and 34% with the waikavirus Maize chlorotic dwarf virus. To our knowledge, this is the first report of a sequivirus in field lettuce in Chile, and although the virus was found at low incidence, this report extends the range of LeMoV to the western side of the Cordillera de Los Andes. The impact of LeMoV needs to be further analyzed in Chile, Brazil, and possibly other South American countries. References: (1) Y. D. Bertheau et al. DNA amplification by polymerase chain reaction (PCR) 1998. In: Methods for the Detection and Quantification of Erwinia carotovora subsp. atroseptica on potatoes. M. C. N. Perombelon and J. M. van der Wolff, eds. Scott. Crop Res. Inst. Occasional Publ., Dundee, 1998. (2) A. S. Jadão. Caracterização parcial e desenvolvimento de oligonucleotídeos específicos para detecção de sequivirus infectando alface. Ph.D. thesis. FCA-UNESP-Botucatu, Brazil, 2004. (3) O. Stangarlin et al. Plant Dis. 84:490, 2000.
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Affiliation(s)
- R Krause-Sakate
- FCA/UNESP, Departamento Produção Vegetal, CP237, 18603-970, Botucatu-SP, Brazil
| | - A S Jadão
- FCA/UNESP, Departamento Produção Vegetal, CP237, 18603-970, Botucatu-SP, Brazil
| | - A C Firmino
- FCA/UNESP, Departamento Produção Vegetal, CP237, 18603-970, Botucatu-SP, Brazil
| | - M A Pavan
- FCA/UNESP, Departamento Produção Vegetal, CP237, 18603-970, Botucatu-SP, Brazil
| | | | - I M Rosales
- INIA La Platina, Casilla 439/3 Santiago, Chile
| | - P Bustamante
- Roche Applied Science, Quilin 375, Santiago, Chile
| | - O Le Gall
- IBVM, INRA, BP81, 33883 Villenave d'Ornon, France
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Krause-Sakate R, Fakhfakh H, Peypelut M, Pavan MA, Zerbini FM, Marrakchi M, Candresse T, Le Gall O. A naturally occurring recombinant isolate of Lettuce mosaic virus. Arch Virol 2004; 149:191-7. [PMID: 14689284 DOI: 10.1007/s00705-003-0201-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2002] [Revised: 01/01/2003] [Accepted: 07/11/2003] [Indexed: 10/26/2022]
Abstract
LMV-Common and LMV-Most are two seed-borne types of Lettuce mosaic virus (LMV), genus Potyvirus. LMV-Most, but not LMV-Common, overcomes the resistance afforded to lettuce by two recessive genes, mo11 and mo12. An RT-PCR-based assay thought to be specific for LMV-Most also amplified LMV-Tn2, previously typified as LMV-Common. The sequence of selected regions along the genome indicated that LMV-Tn2 is a natural recombinant between LMV-Most and LMV-Common isolates, with a putative recombination site located within the P3 coding region. This is the first evidence of a naturally occurring LMV recombinant isolate.
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Affiliation(s)
- R Krause-Sakate
- Equipe de Virologie, IBVM, INRA Bordeaux-Aquitaine, Villenave d'Ornon, France
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Ribeiro SG, Ambrozevícius LP, Avila AC, Bezerra IC, Calegario RF, Fernandes JJ, Lima MF, de Mello RN, Rocha H, Zerbini FM. Distribution and genetic diversity of tomato-infecting begomoviruses in Brazil. Arch Virol 2003; 148:281-95. [PMID: 12556993 DOI: 10.1007/s00705-002-0917-0] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Tomato-infecting begomoviruses have been reported throughout Brazil since the introduction of the B biotype of Bemisia tabaci. Here, we report a large scale survey on the distribution and genetic diversity of tomato-infecting begomoviruses. Tomato samples with typical begomovirus symptoms were collected in seven different states, comprising the major tomato growing areas of the country. Viruses were detected by polymerase chain reaction (PCR) using universal primers for the genus Begomovirus. PCR-amplified fragments were cloned and sequenced. Based on sequence comparisons and phylogenetic analyses, at least seven previously undescribed species of begomoviruses were found. Four of the new viruses were found exclusively in the Southeastern states, two exclusively in the Northeastern states, and one was found in both regions. Sequence comparisons reveal strong evidence of recombination among the Brazilian begomoviruses. Together, the results indicate the existence of a high degree of pre-existing genetic diversity among tomato-infecting begomoviruses in Brazil and suggest that these viruses have emerged after being transferred from natural hosts to tomatoes, due to the introduction into Brazil of a novel polyfagous biotype of the whitefly vector.
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Affiliation(s)
- S G Ribeiro
- EMBRAPA Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, Brazil
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Ribeiro SG, de Ávila AC, Bezerra IC, Fernandes JJ, Faria JC, Lima MF, Gilbertson RL, Maciel-Zambolim E, Zerbini FM. Widespread Occurrence of Tomato Geminiviruses in Brazil, Associated with the New Biotype of the Whitefly Vector. Plant Dis 1998; 82:830. [PMID: 30856961 DOI: 10.1094/pdis.1998.82.7.830c] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Although tomato golden mosaic virus (TGMV) was reported in Brazil more than 20 years ago (3), tomato-infecting geminiviruses have not been of economic significance in the country until recently. However, a sharp increase in the incidence of geminivirus-like symptoms in tomatoes has been reported in several areas of Brazil since 1994. This has coincided with the appearance of the B biotype of Bemisia tabaci, which, as opposed to the A biotype, readily colonizes solanaceous plants (2). We have isolated geminiviruses from symptomatic tomato plants in the Federal District, in two different areas of the state of Minas Gerais, and in the state of Pernambuco. Tomato plants in these areas showed a variety of symptoms, including yellow mosaic, severe leaf distortion, down-cupping, and epinasty. Whitefly infestation was high in all fields sampled, and in some fields, particularly in Pernambuco, incidence of virus-like symptoms was close to 100%, and no tomatoes of commercial value were harvested (1). Using primer pairs PAL1v1978/PAR1c496 and PCRc1/PBL1v2040 (4), DNA-A and -B fragments were polymerase chain reaction (PCR)-amplified from total DNA extracted from diseased plants, cloned, and sequenced. Sequence comparisons of the PCR fragments indicated the existence of at least six different geminiviruses. The nucleotide sequence homologies for DNA-A fragments ranged from 67 to 80% for the 5' end of the cp gene, and from 44 to 80% for the 5' end of the rep gene. Data base comparisons indicated the viruses are most closely related to TGMV, bean golden mosaic virus from Brazil (BGMV-Br), and tomato yellow vein streak virus (ToYVSV), although homologies were less than 80% for the fragments compared. A similar lack of a close relationship with each other and other geminiviruses was obtained with two DNA-B component PCR products compared, corresponding to the 5' end of the BC1 open reading frame. Infectious, full-length genomic clones from the tomato viruses are being generated for biological and molecular characterization. References: (1) I. C. Bezerra et al. Fitopatol. Bras. 22:331, 1997. (2) F. H. França et al., Ann. Soc. Entomol. Bras. 25:369, 1996. (3) J. C. Matyis et al. Summa Phytopathol. 1:267, 1975. (4) M. R. Rojas et al. Plant Dis. 77:340, 1993.
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Affiliation(s)
- S G Ribeiro
- Embrapa-Biotecnologia, Cx. Postal 2372, Brasília, DF, 70770-900, Brazil
| | - A C de Ávila
- EMBRAPA-Hortaliças, Cx. Postal 218, Brasília, DF, 70359-970, Brazil
| | - I C Bezerra
- EMBRAPA-Hortaliças, Cx. Postal 218, Brasília, DF, 70359-970, Brazil
| | - J J Fernandes
- Dep. de Agronomia, UF Uberlândia, MG, 38400-902, Brazil
| | - J C Faria
- EMBRAPA-Arroz e Feijão, Cx. Postal 179, Goiânia, GO, 74100-000, Brazil
| | - M F Lima
- EMBRAPA-Semi-Árido, Cx. Postal 23, Petrolina, PE, 56300-000, Brazil
| | - R L Gilbertson
- Department of Plant Pathology, University of California, Davis, 95616
| | | | - F M Zerbini
- Dep. de Fitopatologia, UF Viçosa, MG, 36571-000, Brazil
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Rojas MR, Zerbini FM, Allison RF, Gilbertson RL, Lucas WJ. Capsid protein and helper component-proteinase function as potyvirus cell-to-cell movement proteins. Virology 1997; 237:283-95. [PMID: 9356340 DOI: 10.1006/viro.1997.8777] [Citation(s) in RCA: 149] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The role of bean common mosaic necrosis potyvirus (BCMNV) and lettuce mosaic potyvirus (LMV) proteins was investigated in terms of their capacity to function as viral movement proteins (MPs). Using Escherichia coli-expressed proteins and microinjection techniques, direct evidence was obtained that both the potyviral capsid protein (CP) and helper component- proteinase (HC-Pro) function in this capacity, in that both proteins (a) trafficked from cell to cell, (b) induced an increase in plasmodesmal size exclusion limit, and (c) facilitated cell-to-cell movement of viral RNA. CP and HC-Pro mutants were also produced and used in microinjection experiments. Mutations in the core region of the CP either impaired (single and double amino acid substitution mutants) or abolished (triple amino acid substitution mutant) cell-to-cell movement, as did C-terminal deletion mutants in HC-Pro. The BCMNV P1, CI, NIa, and NIb proteins did not exhibit viral MP properties, but NIa and NIb proteins were found to accumulate within the nuclei of injected cells. These results further establish the multifunctional nature of the potyvirus CP and HC-Pro.
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Affiliation(s)
- M R Rojas
- Division of Biological Sciences, University of California, Davis, California 95616, USA
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Zerbini FM, Koike ST, Gilbertson RL. Gazania spp.: A New Host of Lettuce Mosaic Potyvirus, and a Potential Inoculum Source for Recent Lettuce Mosaic Outbreaks in the Salinas Valley of California. Plant Dis 1997; 81:641-646. [PMID: 30861850 DOI: 10.1094/pdis.1997.81.6.641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lettuce mosaic potyvirus (LMV) outbreaks in the Salinas Valley of California have increased in recent years despite a comprehensive lettuce mosaic management program. In a previous study, it was established that new serologically and/or genetically distinct LMV strains were not responsible for these outbreaks. Therefore, the role of alternate hosts was investigated. Here we provide evidence that the ornamental plant, Gazania spp., is an alternate host of LMV. A number of lines of evidence were used to establish that gazanias were infected by LMV, including indirect enzyme-linked immunosorbent assay, dot blot hybridization with an LMV coat protein (CP) probe, and sap- and aphid-transmission of LMV from gazania to lettuce and Nicotiana benthamiana. Additionally, an LMV CP fragment was amplified from an infected gazania plant by reverse transcription-polymerase chain reaction, and the nucleotide sequence of this fragment was 99% identical to the CP sequence of an LMV isolate from the Salinas Valley. We further show that LMV-infected gazanias are widely distributed in the Salinas Valley, and are present near areas where LMV outbreaks have occurred. Field experiments demonstrated that LMV could be transmitted from infected gazania to lettuce. LMV-infected gazanias also were found in local nurseries, suggesting that infection of gazania with LMV had occurred prior to planting in the Salinas Valley (i.e., lettuce was not serving as the source of inoculum for infection of gazania in the Salinas Valley). These results establish that gazania is an alternate host of LMV, and suggest that gazanias may be a primary inoculum source for recent lettuce mosaic outbreaks in the Salinas Valley.
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Affiliation(s)
| | - Steven T Koike
- University of California Cooperative Extension, Salinas 93901
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