8 research outputs found
A novel emaravirus comprising five RNA segments is associated with ringspot disease in oak
We report the complete nucleotide sequence of the genome of a novel virus in ringspot-diseased common oak (Quercus robur L.). The newly identified pathogen is associated with leaf symptoms such as mottle, chlorotic spots and ringspots on diseased trees. High-throughput sequencing (HTS, Illumina RNASeq) was used to explore the virome of a ringspot-diseased oak that had chlorotic ringspots of suspected viral origin on leaves for several years. Bioinformatic analysis of the HTS dataset followed by RT-PCR enabled us to determine complete sequences of four RNA genome segments of a novel virus. These sequences showed high similarity to members of the genus Emaravirus, which includes segmented negative-stranded RNA viruses of economic importance. To verify the ends of each RNA, we conducted rapid amplification of cDNA ends (RACE). We identified an additional genome segment (RNA 5) by RT-PCR using a genus-specific primer (PDAP213) to the conserved 3ÂŽ and 5ÂŽtermini in order to amplify full-length genome segments. RNA 5 encodes a 21-kDa protein that is homologous to the silencing suppressor P8 of High Plains wheat mosaic virus. The five viral RNAs were consistently detected by RT-PCR in ringspot-diseased oaks in Germany, Sweden, and Norway. We conclude that the virus represents a new member of the genus Emaravirus affecting oaks in Germany and in Scandinavia, and we propose the name âcommon oak ringspot-associated emaravirusâ (CORaV).FAZIT Stiftung
http://dx.doi.org/10.13039/501100003099Deutsche Forschungsgemeinschaft
http://dx.doi.org/10.13039/501100001659European Cooperation in Science and Technology
http://dx.doi.org/10.13039/501100000921Projekt DEALPeer Reviewe
Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)
55 PĂĄg.In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.This work was supported in part through the Laulima Government Solutions, LLC, prime contract with the U.S. National Institute of Allergy and Infec tious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. U.J.B. was supported by the Division of Intramural Resarch, NIAID. This work was also funded in part by Contract No. HSHQDC15-C-00064 awarded by DHS S and T for the management and operation of The National Biodefense Analysis and Countermeasures Centre, a federally funded research and development centre operated by the Battelle National Biodefense Institute (V.W.); and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowl edges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), USDA-ARS project 58-6066-9-033 and the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch Project, under Accession Number 1021494. The funders had no role in the design of the study; in the collection, analysis, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the U.S. Department of the Army, the U.S. Department of Defence, the U.S. Department of Health and Human Services, including the Centres for Disease Control and Prevention, the U.S. Department of Homeland Security (DHS) Science and Technology Directorate (S and T), or of the institutions and companies affiliated with the authors. In no event shall any of these entities have any responsibility or liability for any use, misuse, inability to use, or reliance upon the information contained herein. The U.S. departments do not endorse any products or commercial services mentioned in this publication. The U.S. Government retains and the publisher, by accepting the article for publication, acknowledges that the U.S.Government retains a non-exclusive, paid up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for U.S. Government purposes.Peer reviewe
Identification of an Emaravirus in a Common Oak (Quercus robur L.) Conservation Seed Orchard in Germany
We observed the health status of oak trees in a conservation seed orchard for over twenty years, focusing on characteristic virus-suspected symptoms. The orchard was established in 1992 in Kreuztal, North Rhine-Westphalia (Germany) with 1302 seedlings in 186 clusters. The number of seedlings showing chlorotic ringspots and mottle on leaves has fluctuated annually, but has increased from 3.3% to 12.1% in the last 20 years; the number of affected clusters has risen from 8% to 25.9%. A scientific breakthrough was the identification of a novel virus related to members of the genus Emaravirus in diseased oak by high-throughput sequencing (HTS). Screening of the oak seedlings in three consecutive years, using a newly established virus-specific diagnostic reverse transcription polymerase chain reaction (RT-PCR), confirmed the virus infection and revealed a close to 100% association between the observed leaf symptoms and the novel virus. As no other plant virus could be identified in the HTS-datasets, we assume the novel virus is primarily causing the symptoms. To reliably detect the novel virus in oaks, RT-PCR targeting the viral RNA3 or RNA4 should be applied in routine testing of symptomatic leaf tissue. It was obvious that most groups with virus-infected plants cluster, with only five out of the 42 affected groups being offside, not bordering on other affected groups of plants. There was no clear correlation between the detection of the virus and the overall vitality of the seedlings. There was no relation between seedling performance and presence or absence of viral infection. Forecasts on the future growth behavior of these virus-infected oak trees are therefore not possible.Deutsche ForschungsgemeinschaftEuropean Cooperation in Science and TechnologyFAZIT StiftungPeer Reviewe
Characterization of a Novel Emaravirus Affecting Ash Species (Fraxinus spp.) in Europe
We identified a novel virus in diseased European ash (Fraxinus excelsior) and manna ash (F. ornus) trees exhibiting chlorotic ringspots, mottle and leaf deformation such as curling and shoestring symptoms. High-throughput sequencing (HTS, Illumina RNASeq) of total RNA isolated from diseased leaf material in combination with RT-PCR-based amplification techniques and Sanger sequencing determined five complete genome segments, each encoding a single open reading frame. Sequence analyses of RNA1âRNA5 revealed a genome organization typical for emaraviruses, i.e., (i) conserved and complementary terminal 5âČ and 3âČ termini of each genome segment (ii) proteins showing significant homologies to the RNA-dependent RNA polymerase (RdRP) encoded by RNA1, the glycoprotein precursor (GPP) encoded by RNA2, the viral nucleocapsid protein (N, RNA3), the movement protein (MP, RNA4), and a protein of 26 kDA (P26, RNA5) highly similar to proteins of unknown function encoded by other emaraviruses. Furthermore, we identified spherical particles (double-membrane bodies, DMB) of different sizes (70â80 nm in diameter) which are typical for emaraviruses exclusively in virus-infected leaf tissue exhibiting mottle and leaf deformation. Sequence comparison and phylogenetic analyses confirmed the identified novel virus as a new member of the genus Emaravirus. We established a species-specific RT-PCR detection protocol and could associate the observed disease symptoms with the infection of the novel emaravirus in F. excelsior and F. ornus. Therefore, we propose the name ash shoestring-associated emaravirus (ASaV). Investigation of ASaV-infected sample trees originating from different locations in Switzerland, Germany, Italy and Sweden provided a wide geographical distribution of the virus in affected ash species. To our knowledge, this is the first confirmation of an emaravirus affecting ash tree species with shoestring symptoms of leaves in Europe
The Complex World of Emaraviruses—Challenges, Insights, and Prospects
Emaravirus (Order Bunyavirales; Family Fimoviridae) is a genus comprising over 20 emerging plant viruses with a worldwide distribution and economic impact. Emaraviruses infect a variety of host plants and have especially become prevalent in important long-living woody plants. These viruses are enveloped, with a segmented, single-stranded, negative-sense RNA genome and are transmitted by eriophyid mites or mechanical transmission. Emaraviruses have four core genome segments encoding an RNA-dependent RNA polymerase, a glycoprotein precursor, a nucleocapsid protein, and a movement protein. They also have additional genome segments, whose number varies widely. We report here that the proteins encoded by these segments form three main homology groups: a homolog of the sadwavirus Glu2 Pro glutamic protease; a protein involved in pathogenicity, which we named “ABC”; and a protein of unknown function, which we named “P55”. The distribution of these proteins parallels the emaravirus phylogeny and suggests, with other analyses, that emaraviruses should be split into at least two genera. Reliable diagnosis systems are urgently needed to detect emaraviruses, assess their economic and ecological importance, and take appropriate measures to prevent their spread (such as routine testing, hygiene measures, and control of mite vectors). Additional research needs include understanding the function of emaravirus proteins, breeding resistant plants, and clarifying transmission modes
Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)
Laulima Government Solutions, LLC, prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. U.J.B. was supported by the Division of Intramural Resarch, NIAID. This work was also funded in part by Contract No. HSHQDC15-C-00064 awarded by DHS S and T for the management and operation of The National Biodefense Analysis and Countermeasures Centre, a federally funded research and development centre operated by the Battelle National Biodefense Institute (V.W.); and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowledges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), USDA-ARS project 58-6066-9-033 and the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch Project, under Accession Number 1â021â494.National Institutes of Health. National Institute of Allergy and Infectious Disease. Division of Clinical Research. Integrated Research Facility at Fort Detrick. Frederick, MD, USA.Hokkaido Research Organization. Agricultural Research Department. Ornamental Plants and Vegetables Research Center. Takikawa, Hokkaido, Japan.United States Department of Agriculture. Agricultural Research Service. US Horticultural Research Laboratory. Fort Pierce, FL, USA.D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation. Moscow, Russia.University of Ljubljana. Faculty of Medicine. Institute of Microbiology and Immunology. Ljubljana, Slovenia.Instituto Nacional de InvestigaciĂłn y TecnologĂa Agraria y Alimentaria - Campus de Montegancedo. Departamento de BiotecnologĂa-BiologĂa Vegetal. Centro de BiotecnologĂa y GenĂłmica de Plantas. Pozuelo de AlarcĂłn / Universidad PolitĂ©cnica de Madrid. Escuela TĂ©cnica Superior de IngenierĂa AgronĂłmica, Alimentaria y de Biosistemas. Madrid, Spain.University of Georgia. Insitute of Bioinformatics. Department of Infectious Diseases, Department of Epidemiology and Biostatistics. Center for Ecology of Infectious Diseases. Athens, GA, USA.Greifswald-Insel Riems. Institute of Novel and Emerging Infectious Diseases. Friedrich-Loeffler-Institut. Greifswald, Germany.Mississippi State University. Department of Biological Sciences. Mississippi State, MS, USA.ICAR-Indian Agricultural Research Institute. Division of Plant Pathology. New Delhi, India.Friedrich-Loeffler-Institut. Institute of Diagnostic Virology. Greifswald-Insel Riems, Germany.Instituto Nacional de TecnologĂa Agropecuaria-Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Unidad de Fitopatologia y Modelizacion Agricola. CĂłrdoba, Argentina.Centers for Disease Control and Prevention. Viral Special Pathogens Branch.
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Berlin, Germany.Ministry of Education. Jilin University. College of Veterinary Medicine. Key Laboratory of Zoonoses Research. State Key Laboratory for Zoonotic Diseases. Changchun, PR China / Georgetown University. School of Medicine. Division of Biomedical Graduate Research Organization. Department of Microbiology and Immunology. Washington, DC, USA.Institute of Vertebrate Biology of the Czech Academy of Sciences. Brno, CzechiaBoston University. National Emerging Infectious Diseases Laboratories. Chobanian and Avedisian School of Medicine. Department of Virology, Immunology and Microbiology. Boston, MA, USA.Friedrich-Loeffler-Institut. Institute of Novel and Emerging Infectious Diseases. Greifswald-Insel Riems, Germany.Bernhard-Nocht Institute for Tropical Medicine. WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research. Department of Virology. Hamburg, Germany.United States Department of Agriculture. 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Fayetteville, AR, USA.University Medical Centre Rotterdam. Erasmus MC. Department of Viroscience. Rotterdam, Netherlands.KU Leuven. Department of Microbiology, Immunology and Transplantation. Leuven, Belgium.The University of Texas Medical Branch at Galveston. Galveston, TX, USA.Wageningen University. Research, Biointeractions and Plant Health. Wageningen, Netherlands.National Biodefense Analysis and Countermeasures Center. Fort Detrick, Frederick, MD, USA.University of Queensland. School of Chemistry and Molecular Biosciences. St. Lucia, QLD, Australia.Washington State University. Department of Veterinary Microbiology and Pathology. Pullman, WA, USA.North Carolina State University. Department of Entomology and Plant Pathology. Raleigh, NC, USA.Chinese Academy of Sciences. Wuhan Institute of Virology. Key Laboratory of Special Pathogens and Biosafety. Wuhan, PR China.Agricultural University of Athens. School of Agricultural Production, Infrastructure and Environment. Department of Crop Science. Plant Pathology Laboratory. Votanikos, Athens, Greece.Yokohama Plant Protection Station. Yokohama, Kanagawa, Japan.Zhejiang University. Institute of Insect Sciences. Hangzhou, PR China.Universidade Federal de Viçosa. Dep. de Fitopatologia/BIOAGRO. Viçosa, MG, Brazil.Center for Disease Control and Prevention of Xinjiang Military Command Area. Xinjiang, PR China.Guangxi Academy of Specialty Crops. Guangxi, PR China / Fudan University. School of Life Sciences and Human Phenome Institute. Shanghai, PR China.University of Chinese Academy of Sciences. Beijing, PR China.Pharmaq Analytiq. Bergen, Norway.Francis Crick Institute. Worldwide Influenza Centre. London, UK.Navarro, BeatrizIn April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV
2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV
2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV