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Kuhn JH, Hughes HR. ICTV Virus Taxonomy Profile: Phasmaviridae 2024. J Gen Virol 2024; 105. [PMID: 38959049 DOI: 10.1099/jgv.0.002002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024] Open
Abstract
Phasmaviridae is a family for negative-sense RNA viruses with genomes of about 9.7-15.8 kb. These viruses are maintained in and/or transmitted by insects. Phasmavirids produce enveloped virions containing three single-stranded RNA segments that encode a nucleoprotein (N), a glycoprotein precursor (GPC), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Phasmaviridae, which is available at ictv.global/report/phasmaviridae.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Fort Collins, CO 80521, USA
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Mahillon M, Brodard J, Schoen R, Botermans M, Dubuis N, Groux R, Pannell JR, Blouin AG, Schumpp O. Revisiting a pollen-transmitted ilarvirus previously associated with angular mosaic of grapevine. Virus Res 2024; 344:199362. [PMID: 38508402 PMCID: PMC10979282 DOI: 10.1016/j.virusres.2024.199362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024]
Abstract
We report the characterization of a novel tri-segmented RNA virus infecting Mercurialis annua, a common crop weed and model species in plant science. The virus, named "Mercurialis latent virus" (MeLaV) was first identified in a mixed infection with the recently described Mercurialis orthotospovirus 1 (MerV1) on symptomatic plants grown in glasshouses in Lausanne (Switzerland). Both viruses were found to be transmitted by Thrips tabaci, which presumably help the inoculation of infected pollen in the case of MeLaV. Complete genome sequencing of the latter revealed a typical ilarviral architecture and close phylogenetic relationship with members of the Ilarvirus subgroup 1. Surprisingly, a short portion of MeLaV replicase was found to be identical to the partial sequence of grapevine angular mosaic virus (GAMV) reported in Greece in the early 1990s. However, we have compiled data that challenge the involvement of GAMV in angular mosaic of grapevine, and we propose alternative causal agents for this disorder. In parallel, three highly-conserved MeLaV isolates were identified in symptomatic leaf samples in The Netherlands, including a herbarium sample collected in 1991. The virus was also traced in diverse RNA sequencing datasets from 2013 to 2020, corresponding to transcriptomic analyses of M. annua and other plant species from five European countries, as well as metaviromics analyses of bees in Belgium. Additional hosts are thus expected for MeLaV, yet we argue that infected pollen grains have likely contaminated several sequencing datasets and may have caused the initial characterization of MeLaV as GAMV.
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Affiliation(s)
- Mathieu Mahillon
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Justine Brodard
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Ruben Schoen
- Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
| | - Nathalie Dubuis
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Raphaël Groux
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne (UNIL), Switzerland
| | - Arnaud G Blouin
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland.
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Weber F, Bouloy M, Lozach PY. An Introduction to Rift Valley Fever Virus. Methods Mol Biol 2024; 2824:1-14. [PMID: 39039402 DOI: 10.1007/978-1-0716-3926-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Rift Valley fever virus (RVFV) is a pathogen transmitted to humans and livestock via mosquito bites. This virus, which was discovered in Kenya in 1930, is considered by the World Health Organization (WHO) and the World Organisation for Animal Health (WOAH) to be associated with a high risk of causing large-scale epidemics. However, means dedicated to fighting RVFV have been limited, and despite recent research efforts, the virus remains poorly understood at both the molecular and cellular levels as well as at a broader scale of research in the field and in animal and human populations. In this introductory chapter of a methods book, we aim to provide readers with a concise overview of RVFV, from its ecology and transmission to the structural and genomic organization of virions and its life cycle in host cells.
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Affiliation(s)
- Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Michèle Bouloy
- Institut Pasteur, Université Paris Cité, Bunyavirus Molecular Genetics Unit, Paris, France
| | - Pierre-Yves Lozach
- IVPC UMR754, INRAE, Université Claude Bernard Lyon 1, EPHE, PSL Research University, Lyon, France.
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Kuhn JH, Adkins S, Brown K, de la Torre JC, Digiaro M, Hughes HR, Junglen S, Lambert AJ, Maes P, Marklewitz M, Palacios G, Sasaya T, Zhang YZ, Turina M. ICTV Virus Taxonomy Profile: Tulasviridae 2023. J Gen Virol 2023; 104:001933. [PMID: 38116934 PMCID: PMC10770928 DOI: 10.1099/jgv.0.001933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023] Open
Abstract
Tulasviridae is a family of ambisense RNA viruses with genomes of about 12.2 kb that have been found in fungi. The tulasvirid genome is nonsegmented and contains three open reading frames (ORFs) that encode a nucleoprotein (NP), a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain, and a protein of unknown function (X). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Tulasviridae, which is available at ictv.global/report/tulasviridae.
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Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick MD 21702, USA
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
| | - Katherine Brown
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge CB2 0QN, UK
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla CA 92037, USA
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, 70010 Valenzano, Italy
| | - Holly R. Hughes
- Centers for Disease Control and Prevention, Fort Collins CO 80521, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Amy J. Lambert
- Centers for Disease Control and Prevention, Fort Collins CO 80521, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases Unit, 3000 Leuven, Belgium
| | | | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8517, Japan
| | - Yong-Zhen Zhang
- School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 201052, PR China
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 10135 Torino, Italy
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Kuhn JH, Adkins S, Brown K, de la Torre JC, Digiaro M, Hughes HR, Junglen S, Lambert AJ, Maes P, Marklewitz M, Palacios G, Sasaya T, Turina M, Zhang YZ. ICTV Virus Taxonomy Profile: Wupedeviridae 2023. J Gen Virol 2023; 104:001932. [PMID: 38116933 PMCID: PMC10770926 DOI: 10.1099/jgv.0.001932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023] Open
Abstract
Wupedeviridae is a family of negative-sense RNA viruses with genomes of about 20.5 kb that have been found in myriapods. The wupedevirid genome consists of three monocistronic RNA segments with open reading frames (ORFs) that encode a nucleoprotein (NP), a glycoprotein (GP), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Wupedeviridae, which is available at ictv.global/report/wupedeviridae.
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Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick MD 21702, USA
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
| | - Katherine Brown
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge CB2 0QN, UK
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla CA 92037, USA
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, 70010 Valenzano, Italy
| | - Holly R. Hughes
- Centers for Disease Control and Prevention, Fort Collins CO 80521, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Amy J. Lambert
- Centers for Disease Control and Prevention, Fort Collins CO 80521, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases Unit, 3000 Leuven, Belgium
| | | | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8517, Japan
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 10135 Torino, Italy
| | - Yong-Zhen Zhang
- School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 201052, PR China
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Kuhn JH, Adkins S, Brown K, de la Torre JC, Digiaro M, Hughes HR, Junglen S, Lambert AJ, Maes P, Marklewitz M, Palacios G, Sasaya T, Turina M, Zhang YZ. ICTV Virus Taxonomy Profile: Cruliviridae 2023. J Gen Virol 2023; 104:001930. [PMID: 38117185 PMCID: PMC10770925 DOI: 10.1099/jgv.0.001930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023] Open
Abstract
Cruliviridae is a family of negative-sense RNA viruses with genomes of 10.8-11.5 kb that have been found in crustaceans. The crulivirid genome consists of three RNA segments with ORFs that encode a nucleoprotein (NP), a glycoprotein (GP), a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain, and in some family members, a zinc-finger (Z) protein of unknown function. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Cruliviridae, which is available at ictv.global/report/cruliviridae.
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Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick MD 21702, USA
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
| | - Katherine Brown
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge CB2 0QN, UK
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, 70010 Valenzano, Italy
| | - Holly R. Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Amy J. Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases Unit, 3000 Leuven, Belgium
| | | | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8517, Japan
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 10135 Torino, Italy
| | - Yong-Zhen Zhang
- School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 201052, PR China
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Kuhn JH, Adkins S, Brown K, de la Torre JC, Digiaro M, Hughes HR, Junglen S, Lambert AJ, Maes P, Marklewitz M, Palacios G, Sasaya T, Turina M, Zhang YZ. ICTV Virus Taxonomy Profile: Mypoviridae 2023. J Gen Virol 2023; 104:001931. [PMID: 38112172 PMCID: PMC10770932 DOI: 10.1099/jgv.0.001931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/20/2023] Open
Abstract
Mypoviridae is a family of negative-sense RNA viruses with genomes of about 16.0 kb that have been found in myriapods. The mypovirid genome consists of three monocistronic RNA segments that encode a nucleoprotein (NP), a glycoprotein (GP), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Mypoviridae, which is available at: ictv.global/report/mypoviridae.
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Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
| | - Katherine Brown
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge CB2 0QN, UK
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, 70010 Valenzano, Italy
| | - Holly R. Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Amy J. Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases Unit, 3000 Leuven, Belgium
| | | | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8517, Japan
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 10135 Torino, Italy
| | - Yong-Zhen Zhang
- School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 201052, PR China
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Adkins S, Brown K, de la Torre JC, Digiaro M, Hughes HR, Junglen S, Lambert AJ, Maes P, Marklewitz M, Palacios G, Sasaya (笹谷孝英) T, Turina M, Zhang (张永振) YZ, Kuhn JH. ICTV Virus Taxonomy Profile: Leishbuviridae 2023. J Gen Virol 2023; 104:001934. [PMID: 38064269 PMCID: PMC10770927 DOI: 10.1099/jgv.0.001934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Leishbuviridae is a family of negative-sense RNA viruses with genomes of about 8.0 kb that have been found in protists. The leishbuvirid genome consists of three monocistronic RNA segments with open reading frames (ORFs) that encode a nucleoprotein (NP), a glycoprotein (GP), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Leishbuviridae, which is available at ictv.global/report/leishbuviridae.
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Affiliation(s)
- Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
| | - Katherine Brown
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge CB2 0QN, UK
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, 70010 Valenzano, Italy
| | - Holly R. Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Amy J. Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases Unit, 3000 Leuven, Belgium
| | | | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Takahide Sasaya (笹谷孝英)
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8517, Japan
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 10135 Torino, Italy
| | - Yong-Zhen Zhang (张永振)
- School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 201052, PR China
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
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Nourinejhad Zarghani S, Al Kubrusli R, Iancev S, Jalkanen R, Büttner C, von Bargen S. Molecular Population Genetics of Aspen Mosaic-Associated Virus in Finland and Sweden. Viruses 2023; 15:1678. [PMID: 37632020 PMCID: PMC10460043 DOI: 10.3390/v15081678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Aspen mosaic-associated virus (AsMaV) is a newly identified Emaravirus, in the family Fimoviridae, Bunyavirales, associated with mosaic symptoms in aspen trees (Populus tremula). Aspen trees are widely distributed in Europe and understanding the population structure of AsMaV may aid in the development of better management strategies. The virus genome consists of five negative-sense single-stranded RNA (-ssRNA) molecules. To investigate the genetic diversity and population parameters of AsMaV, different regions of the genome were amplified and analyzed and full-length sequence of the divergent isolates were cloned and sequenced. The results show that RNA3 or nucleoprotein is a good representative for studying genetic diversity in AsMaV. Developed RT-PCR-RFLP was able to identify areas with a higher number of haplotypes and could be applied for screening the large number of samples. In general, AsMaV has a conserved genome and based on the phylogenetic studies, geographical structuring was observed in AsMaV isolates from Sweden and Finland, which could be attributed to founder effects. The genome of AsMaV is under purifying selection but not distributed uniformly on genomic RNAs. Distant AsMaV isolates displayed amino acid sequence variations compared to other isolates, and bioinformatic analysis predicted potential post-translational modification sites in some viral proteins.
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Affiliation(s)
- Shaheen Nourinejhad Zarghani
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Serghei Iancev
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | | | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
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Zhao YJ, Shirouzu T, Chiba Y, Hosaka K, Moriyama H, Urayama SI, Hagiwara D. Identification of novel RNA mycoviruses from wild mushroom isolates in Japan. Virus Res 2023; 325:199045. [PMID: 36681193 DOI: 10.1016/j.virusres.2023.199045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
The characterization of viruses from environmental samples could aid in our understanding of their ecological significance and potential for biotechnological exploitation. While there has been much focus on pathogenic fungi or commercially cultivated mushrooms, attention to viruses from wild Basidiomycota mushrooms is lacking. Therefore, in this study, we conducted viral screening of fungal mycelia isolated from wild basidiocarps using agarose gel electrophoresis (AGE) and fragmented and primer-ligated dsRNA sequencing (FLDS). Among the 51 isolates, seven isolates were detected with virus-like bands during the initial screening with AGE, but only five isolates were detected with viruses after long-term storage. Using the FLDS method, we obtained seven viral genome sequences, including five double-stranded RNA (dsRNA) viruses belonging to Partitiviridae and Curvulaviridae, one positive-sense single-stranded RNA (ssRNA) virus belonging to Endornaviridae and one negative-sense ssRNA virus belonging to Tulasviridae (Bunyavirales). All viruses characterized in this study are novel species. These findings greatly expanded our knowledge of the diversity of RNA viruses from environmental samples.
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Affiliation(s)
- Yan-Jie Zhao
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Takashi Shirouzu
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
| | - Yuto Chiba
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Syun-Ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
| | - Daisuke Hagiwara
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
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Ayllón MA, Vainio EJ. Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle. Adv Virus Res 2023; 115:1-86. [PMID: 37173063 DOI: 10.1016/bs.aivir.2023.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.
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Affiliation(s)
- María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain; Departamento Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
| | - Eeva J Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Helsinki, Finland
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Chao S, Wang H, Zhang S, Chen G, Mao C, Hu Y, Yu F, Wang S, Lv L, Chen L, Feng G. Novel RNA Viruses Discovered in Weeds in Rice Fields. Viruses 2022; 14:2489. [PMID: 36366587 PMCID: PMC9717734 DOI: 10.3390/v14112489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/03/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022] Open
Abstract
Weeds often grow alongside crop plants. In addition to competing with crops for nutrients, water and space, weeds host insect vectors or act as reservoirs for viral diversity. However, little is known about viruses infecting rice weeds. In this work, we used metatranscriptomic deep sequencing to identify RNA viruses from 29 weed samples representing 23 weed species. A total of 224 RNA viruses were identified: 39 newly identified viruses are sufficiently divergent to comprise new families and genera. The newly identified RNA viruses clustered within 18 viral families. Of the identified viruses, 196 are positive-sense single-stranded RNA viruses, 24 are negative-sense single-stranded RNA viruses and 4 are double-stranded RNA viruses. We found that some novel RNA viruses clustered within the families or genera of several plant virus species and have the potential to infect plants. Collectively, these results expand our understanding of viral diversity in rice weeds. Our work will contribute to developing effective strategies with which to manage the spread and epidemiology of plant viruses.
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Affiliation(s)
- Shufen Chao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Haoran Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Shu Zhang
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430000, China
| | - Guoqing Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Chonghui Mao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Yang Hu
- Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550000, China
| | - Fengquan Yu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110000, China
| | - Shuo Wang
- Sanya Agricultural Technology Extension and Service Centre, Sanya 572000, China
| | - Liang Lv
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430000, China
| | - Long Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Guozhong Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
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13
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Urrutia CD, Romay G, Shaw BD, Verchot J. Advancing the Rose Rosette Virus Minireplicon and Encapsidation System by Incorporating GFP, Mutations, and the CMV 2b Silencing Suppressor. Viruses 2022; 14:836. [PMID: 35458566 PMCID: PMC9031449 DOI: 10.3390/v14040836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/01/2022] [Accepted: 04/13/2022] [Indexed: 11/26/2022] Open
Abstract
Plant infecting emaraviruses have segmented negative strand RNA genomes and little is known about their infection cycles due to the lack of molecular tools for reverse genetic studies. Therefore, we innovated a rose rosette virus (RRV) minireplicon containing the green fluorescent protein (GFP) gene to study the molecular requirements for virus replication and encapsidation. Sequence comparisons among RRV isolates and structural modeling of the RNA dependent RNA polymerase (RdRp) and nucleocapsid (N) revealed three natural mutations of the type species isolate that we reverted to the common species sequences: (a) twenty-one amino acid truncations near the endonuclease domain (named delA), (b) five amino acid substitutions near the putative viral RNA binding loop (subT), and (c) four amino acid substitutions in N (NISE). The delA and subT in the RdRp influenced the levels of GFP, gRNA, and agRNA at 3 but not 5 days post inoculation (dpi), suggesting these sequences are essential for initiating RNA synthesis and replication. The NISE mutation led to sustained GFP, gRNA, and agRNA at 3 and 5 dpi indicating that the N supports continuous replication and GFP expression. Next, we showed that the cucumber mosaic virus (CMV strain FNY) 2b singularly enhanced GFP expression and RRV replication. Including agRNA2 with the RRV replicon produced observable virions. In this study we developed a robust reverse genetic system for investigations into RRV replication and virion assembly that could be a model for other emaravirus species.
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Affiliation(s)
| | | | | | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77845, USA; (C.D.U.); (G.R.); (B.D.S.)
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14
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Highly adaptive
Phenuiviridae
with biomedical importance in multiple fields. J Med Virol 2022; 94:2388-2401. [DOI: 10.1002/jmv.27618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/24/2021] [Accepted: 01/21/2022] [Indexed: 11/07/2022]
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15
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Kormelink R, Verchot J, Tao X, Desbiez C. The Bunyavirales: The Plant-Infecting Counterparts. Viruses 2021; 13:v13050842. [PMID: 34066457 PMCID: PMC8148189 DOI: 10.3390/v13050842] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/18/2022] Open
Abstract
Negative-strand (-) RNA viruses (NSVs) comprise a large and diverse group of viruses that are generally divided in those with non-segmented and those with segmented genomes. Whereas most NSVs infect animals and humans, the smaller group of the plant-infecting counterparts is expanding, with many causing devastating diseases worldwide, affecting a large number of major bulk and high-value food crops. In 2018, the taxonomy of segmented NSVs faced a major reorganization with the establishment of the order Bunyavirales. This article overviews the major plant viruses that are part of the order, i.e., orthospoviruses (Tospoviridae), tenuiviruses (Phenuiviridae), and emaraviruses (Fimoviridae), and provides updates on the more recent ongoing research. Features shared with the animal-infecting counterparts are mentioned, however, special attention is given to their adaptation to plant hosts and vector transmission, including intra/intercellular trafficking and viral counter defense to antiviral RNAi.
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Affiliation(s)
- Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Xiaorong Tao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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A Look into Bunyavirales Genomes: Functions of Non-Structural (NS) Proteins. Viruses 2021; 13:v13020314. [PMID: 33670641 PMCID: PMC7922539 DOI: 10.3390/v13020314] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/12/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
In 2016, the Bunyavirales order was established by the International Committee on Taxonomy of Viruses (ICTV) to incorporate the increasing number of related viruses across 13 viral families. While diverse, four of the families (Peribunyaviridae, Nairoviridae, Hantaviridae, and Phenuiviridae) contain known human pathogens and share a similar tri-segmented, negative-sense RNA genomic organization. In addition to the nucleoprotein and envelope glycoproteins encoded by the small and medium segments, respectively, many of the viruses in these families also encode for non-structural (NS) NSs and NSm proteins. The NSs of Phenuiviridae is the most extensively studied as a host interferon antagonist, functioning through a variety of mechanisms seen throughout the other three families. In addition, functions impacting cellular apoptosis, chromatin organization, and transcriptional activities, to name a few, are possessed by NSs across the families. Peribunyaviridae, Nairoviridae, and Phenuiviridae also encode an NSm, although less extensively studied than NSs, that has roles in antagonizing immune responses, promoting viral assembly and infectivity, and even maintenance of infection in host mosquito vectors. Overall, the similar and divergent roles of NS proteins of these human pathogenic Bunyavirales are of particular interest in understanding disease progression, viral pathogenesis, and developing strategies for interventions and treatments.
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Goodin M, Verchot J. Introduction to Special Issue of Plant Virus Emergence. Viruses 2021; 13:v13010055. [PMID: 33401517 PMCID: PMC7824620 DOI: 10.3390/v13010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 12/30/2020] [Indexed: 11/16/2022] Open
Abstract
We are pleased to present in this Special Issue a series of reviews and research studies on the topic of "Plant Virus Emergence" [...].
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Affiliation(s)
- Michael Goodin
- Plant Pathology Department, University of Kentucky, Lexington, KY 40546, USA
- Correspondence: (M.G.); (J.V.); Tel.: +1-979-845-1788 (J.V.)
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77802, USA
- Correspondence: (M.G.); (J.V.); Tel.: +1-979-845-1788 (J.V.)
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