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Walker PJ, Bigarré L, Kurath G, Dacheux L, Pallandre L. Revised Taxonomy of Rhabdoviruses Infecting Fish and Marine Mammals. Animals (Basel) 2022; 12:ani12111363. [PMID: 35681827 PMCID: PMC9179924 DOI: 10.3390/ani12111363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The Rhabdoviridae is a family of viruses that includes some important pathogens of fish and marine mammals. Aspects of the taxonomic classification of fish viruses assigned to this family have recently been reviewed by the International Committee on Taxonomy of Viruses (ICTV). This paper describes the newly approved taxonomy, including the assignment of new subfamilies and new virus species. The paper also considers a taxonomic conundrum presented by viruses assigned to one group of fish rhabdoviruses (genus Novirhabdovirus) for which assignment to the family Rhabdoviridae may not be appropriate. Abstract The Rhabdoviridae is a large family of negative-sense (-) RNA viruses that includes important pathogens of ray-finned fish and marine mammals. As for all viruses, the taxonomic assignment of rhabdoviruses occurs through a process implemented by the International Committee on Taxonomy of Viruses (ICTV). A recent revision of taxonomy conducted in conjunction with the ICTV Rhabdoviridae Study Group has resulted in the establishment of three new subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae) within the Rhabdoviridae, as well as three new genera (Cetarhavirus, Siniperhavirus, and Scophrhavirus) and seven new species for viruses infecting fish or marine mammals. All rhabdovirus species have also now been named or renamed to comply with the binomial format adopted by the ICTV in 2021, comprising the genus name followed by a species epithet. Phylogenetic analyses of L protein (RNA-dependent RNA polymerase) sequences of (-) RNA viruses indicate that members of the genus Novirhabdovirus (subfamily Gammarhabdovirinae) do not cluster within the Rhabdoviridae, suggesting the need for a review of their current classification.
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Affiliation(s)
- Peter J. Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4067, Australia
- Correspondence:
| | - Laurent Bigarré
- Laboratory of Ploufragan-Plouzané-Niort, Technopole Brest Iroise, ANSES, 29280 Plouzané, France; (L.B.); (L.P.)
| | - Gael Kurath
- Western Fisheries Research Center, US Geological Survey, 6505 NE 65th Street, Seattle, WA 98115, USA;
| | - Laurent Dacheux
- Unit Lyssavirus Epidemiology and Neuropathology, Université Paris Cité, Institut Pasteur, 28 Rue du Docteur Roux, CEDEX 15, 75724 Paris, France;
| | - Laurane Pallandre
- Laboratory of Ploufragan-Plouzané-Niort, Technopole Brest Iroise, ANSES, 29280 Plouzané, France; (L.B.); (L.P.)
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Emelianchik A, Rodrigues TCS, Subramaniam K, Nielsen O, Burek-Huntington KA, Rotstein D, Popov VL, Stone D, Waltzek TB. Characterization of a novel rhabdovirus isolated from a stranded harbour porpoise (Phocoena phocoena). Virus Res 2019; 273:197742. [PMID: 31499088 DOI: 10.1016/j.virusres.2019.197742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 11/28/2022]
Abstract
An adult male harbour porpoise (Phocoena phocoena) stranded off the coast of Alaska displaying poor body condition, scattered mild ulcerative dermatitis, and necrotizing balanoposthitis. Necropsy findings included severe verminous panniculitis, pneumonia, hepatitis, and enteritis. Histopathological examination of skin lesions revealed a pustular epidermitis and dermatitis, with ballooning degeneration of keratinocytes and occasional amphophilic intracytoplasmic inclusion bodies. A swab sample collected from the ulcerative penile lesions was processed for virus isolation resulting in cytopathic effects observed in primary beluga whale kidney (BWK) cells. Transmission electron microscopy revealed bullet-shaped virions budding from the cell surface of infected BWK cells consistent with a rhabdovirus. A cDNA library was prepared using RNA extracted from infected cell culture supernatant and sequenced on an Illumina MiSeq sequencer. The near-complete genome of a novel rhabdovirus was recovered. Genetic and phylogenetic analyses based on the complete L gene supported the harbour porpoise rhabdovirus (HPRV) as a new species. HPRV clustered phylogenetically with dolphin rhabdovirus (DRV) and this cetacean rhabdovirus clade was found to be the sister group to members of the genus Perhabdovirus that infect fish. A specific nested RT-PCR assay detected HPRV RNA in the epaxial musculature of the harbour porpoise. Our results are consistent with a previous hypothesis that cetacean rhabdoviruses may have arisen following a host jump from fish and suggest that DRV and HPRV represent separate species belonging in a new genus within the family Rhabdoviridae. Further research is needed to determine the health impact of HPRV in harbour porpoise populations, its prevalence, and route of transmission.
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Affiliation(s)
| | | | | | - Ole Nielsen
- Department of Fisheries & Oceans Canada, 501 University Crescent, Winnipeg, Manitoba, Canada
| | | | - David Rotstein
- Marine Mammal Pathology Services, 19117 Bloomfield Road, 20832, Olney, Maryland, USA
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard, 77555-0609, Galveston, Texas, USA
| | - David Stone
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, DT4 8UB, UK
| | - Thomas B Waltzek
- University of Florida, 2187 Mowry Road, 32611, Gainesville, Florida, USA.
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Munang'andu HM, Mugimba KK, Byarugaba DK, Mutoloki S, Evensen Ø. Current Advances on Virus Discovery and Diagnostic Role of Viral Metagenomics in Aquatic Organisms. Front Microbiol 2017; 8:406. [PMID: 28382024 PMCID: PMC5360701 DOI: 10.3389/fmicb.2017.00406] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022] Open
Abstract
The global expansion of the aquaculture industry has brought with it a corresponding increase of novel viruses infecting different aquatic organisms. These emerging viral pathogens have proved to be a challenge to the use of traditional cell-cultures and immunoassays for identification of new viruses especially in situations where the novel viruses are unculturable and no antibodies exist for their identification. Viral metagenomics has the potential to identify novel viruses without prior knowledge of their genomic sequence data and may provide a solution for the study of unculturable viruses. This review provides a synopsis on the contribution of viral metagenomics to the discovery of viruses infecting different aquatic organisms as well as its potential role in viral diagnostics. High throughput Next Generation sequencing (NGS) and library construction used in metagenomic projects have simplified the task of generating complete viral genomes unlike the challenge faced in traditional methods that use multiple primers targeted at different segments and VPs to generate the entire genome of a novel virus. In terms of diagnostics, studies carried out this far show that viral metagenomics has the potential to serve as a multifaceted tool able to study and identify etiological agents of single infections, co-infections, tissue tropism, profiling viral infections of different aquatic organisms, epidemiological monitoring of disease prevalence, evolutionary phylogenetic analyses, and the study of genomic diversity in quasispecies viruses. With sequencing technologies and bioinformatics analytical tools becoming cheaper and easier, we anticipate that metagenomics will soon become a routine tool for the discovery, study, and identification of novel pathogens including viruses to enable timely disease control for emerging diseases in aquaculture.
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Affiliation(s)
- Hetron M. Munang'andu
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
| | - Kizito K. Mugimba
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere UniversityKampala, Uganda
| | - Denis K. Byarugaba
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere UniversityKampala, Uganda
| | - Stephen Mutoloki
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
| | - Øystein Evensen
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
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Smits SL, Bodewes R, Ruiz-González A, Baumgärtner W, Koopmans MP, Osterhaus ADME, Schürch AC. Recovering full-length viral genomes from metagenomes. Front Microbiol 2015; 6:1069. [PMID: 26483782 PMCID: PMC4589665 DOI: 10.3389/fmicb.2015.01069] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 09/17/2015] [Indexed: 12/17/2022] Open
Abstract
Infectious disease metagenomics is driven by the question: “what is causing the disease?” in contrast to classical metagenome studies which are guided by “what is out there?” In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.
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Affiliation(s)
- Saskia L Smits
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Aritz Ruiz-González
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Conservation Genetics Laboratory, National Institute for Environmental Protection and Research Bologna, Italy
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover Hannover, Germany
| | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment Bilthoven, Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Center for Infection Medicine and Zoonoses Research Hannover, Germany
| | - Anita C Schürch
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
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Smits SL, Bodewes R, Ruiz-Gonzalez A, Baumgärtner W, Koopmans MP, Osterhaus ADME, Schürch AC. Assembly of viral genomes from metagenomes. Front Microbiol 2014; 5:714. [PMID: 25566226 PMCID: PMC4270193 DOI: 10.3389/fmicb.2014.00714] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 11/30/2014] [Indexed: 11/20/2022] Open
Abstract
Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity are, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.
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Affiliation(s)
- Saskia L. Smits
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Viroclinics BiosciencesRotterdam, Netherlands
| | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
| | - Aritz Ruiz-Gonzalez
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU)Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU)Vitoria-Gasteiz, Spain
- Conservation Genetics Laboratory, National Institute for Environmental Protection and Research (ISPRA)Bologna, Italy
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine HannoverHannover, Germany
| | - Marion P. Koopmans
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | - Albert D. M. E. Osterhaus
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Viroclinics BiosciencesRotterdam, Netherlands
- Center for Infection Medicine and Zoonoses ResearchHannover, Germany
| | - Anita C. Schürch
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
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