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Costa VA, Holmes EC. Diversity, evolution, and emergence of fish viruses. J Virol 2024; 98:e0011824. [PMID: 38785422 PMCID: PMC11237817 DOI: 10.1128/jvi.00118-24] [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] [Indexed: 05/25/2024] Open
Abstract
The production of aquatic animals has more than doubled over the last 50 years and is anticipated to continually increase. While fish are recognized as a valuable and sustainable source of nutrition, particularly in the context of human population growth and climate change, the rapid expansion of aquaculture coincides with the emergence of highly pathogenic viruses that often spread globally through aquacultural practices. Here, we provide an overview of the fish virome and its relevance for disease emergence, with a focus on the insights gained through metagenomic sequencing, noting potential areas for future study. In particular, we describe the diversity and evolution of fish viruses, for which the majority have no known disease associations, and demonstrate how viruses emerge in fish populations, most notably at an expanding domestic-wild interface. We also show how wild fish are a powerful and tractable model system to study virus ecology and evolution more broadly and can be used to identify the major factors that shape vertebrate viromes. Central to this is a process of virus-host co-divergence that proceeds over many millions of years, combined with ongoing cross-species virus transmission.
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Affiliation(s)
- Vincenzo A. Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
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2
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Buck CB, Welch N, Belford AK, Varsani A, Pastrana DV, Tisza MJ, Starrett GJ. Widespread Horizontal Gene Transfer Among Animal Viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586562. [PMID: 38712252 PMCID: PMC11071296 DOI: 10.1101/2024.03.25.586562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzing de novo assemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.
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Affiliation(s)
| | - Nicole Welch
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: L.E.K. Consulting, Boston, MA, USA
| | - Anna K. Belford
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: University of Pittsburgh, Pittsburgh, PA, USA
| | - Arvind Varsani
- Arizona State University, Tempe, AZ, USA
- University of Cape Town, South Africa
| | | | - Michael J. Tisza
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: Baylor College of Medicine, Houston, TX, USA
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3
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Grimwood RM, Fortune-Kelly G, Holmes EC, Ingram T, Geoghegan JL. Host specificity shapes fish viromes across lakes on an isolated remote island. Virology 2023; 587:109884. [PMID: 37757732 DOI: 10.1016/j.virol.2023.109884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Fish viromes often provide insights into the origin and evolution of viruses affecting tetrapods, including those associated with imporant human diseases. However, despite fish being the most diverse vertebrate group, their viruses are still understudied. We investigated the viromes of fish on Chatham Island (Rēkohu), a geographically isolated island housing 9% of New Zealand's threatened endemic fish species. Using metatranscriptomics, we analyzed samples from seven host species across 16 waterbodies. We identified 19 fish viruses, including 16 potentially novel species, expanding families such as the Coronaviridae, Hantaviridae, Poxviridae, and the recently proposed Tosoviridae. Surprisingly, virome composition was not influenced by the ecological factors measured and smelt (Retropinna retropinna) viromes were consistent across lakes despite differences in host life history, seawater influence, and community richness. Overall, fish viromes across Rēkohu were highly diverse and revealed a long history of co-divergence between host and virus despite their unique and geographically isolated ecosystem.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | | | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Travis Ingram
- Department of Zoology, University of Otago, Dunedin, 9016, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand; Institute of Environmental Science and Research, Wellington, 5018, New Zealand.
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4
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Abrantes J, Varsani A, Pereira P, Maia C, Farias I, Veríssimo A, Neves F. Identification and characterization of a polyomavirus in the thornback skate (Raja clavata). Virol J 2023; 20:190. [PMID: 37620878 PMCID: PMC10463871 DOI: 10.1186/s12985-023-02149-1] [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: 07/06/2023] [Accepted: 08/02/2023] [Indexed: 08/26/2023] Open
Abstract
Members of the family Polyomaviridae have a circular double-stranded DNA genome that have been identified in various hosts ranging from mammals to arachnids. Here we report the identification and analysis of a complete genome sequence of a novel polyomavirus, Raja clavata polyomavirus (RcPyV1), from a cartilaginous fish, the thornback skate (Raja clavata). The genome sequence was determined using a metagenomics approach with an aim to provide baseline viral data in cartilaginous fish in different ecosystems. The RcPyV1 genome (4,195 nucleotides) had typical organization of polyomavirus, including early antigens (small T; Large T) encoded on one strand and late viral proteins (VP1; VP2) on the complementary strand. Maximum-likelihood phylogenetic analysis of the large T-antigen revealed that RcPyV1 clusters with a polyomavirus obtained from another cartilaginous fish, the guitarfish polyomavirus 1 (GfPyV1). These two share ~ 56% pairwise identity in LT and VP1 protein sequences. These analyses support the hypothesis that cartilaginous fishes have a specific lineage of polyomaviruses.
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Affiliation(s)
- Joana Abrantes
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, 4169-007, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Integrative, Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Paulo Pereira
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
| | - Catarina Maia
- Portuguese Institute for Sea and Atmosphere, Division of Modelling and Management of Fisheries Resources, Alges, 1495-165, Portugal
| | - Inês Farias
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Portugal
| | - Ana Veríssimo
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
| | - Fabiana Neves
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal.
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5
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Harding EF, Russo AG, Yan GJH, Mercer LK, White PA. Revealing the uncharacterised diversity of amphibian and reptile viruses. ISME COMMUNICATIONS 2022; 2:95. [PMID: 37938670 PMCID: PMC9723728 DOI: 10.1038/s43705-022-00180-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/18/2022] [Accepted: 09/15/2022] [Indexed: 06/29/2023]
Abstract
Amphibians and non-avian reptiles represent a significant proportion of terrestrial vertebrates, however knowledge of their viruses is not proportional to their abundance. Many amphibians and reptiles have strict habitual environments and localised populations and are vulnerable to viral outbreaks and potential elimination as a result. We sought to identify viruses that were hidden in amphibian and reptile metatranscriptomic data by screening 235 RNA-sequencing datasets from a 122 species covering 25 countries. We identified 26 novel viruses and eight previously characterised viruses from fifteen different viral families. Twenty-five viruses had RNA genomes with identity to Arteriviridae, Tobaniviridae, Hantaviridae, Rhabdoviridae, Astroviridae, Arenaviridae, Hepeviridae, Picornaviridae, Orthomyxoviridae, Reoviridae, Flaviviridae and Caliciviridae. In addition to RNA viruses, we also screened datasets for DNA viral transcripts, which are commonly excluded from transcriptomic analysis. We identified ten DNA viruses with identity to Papillomaviridae, Parvoviridae, Circoviridae and Adomaviridae. With the addition of these viruses, we expand the global amphibian and reptile virome and identify new potentially pathogenic viruses that could challenge populations. We speculate that amphibian viruses often have simpler genomes than those in amniotes, as in the case of the Secondpapillomavirinae and Orthomyxoviridae viruses identified in this study. In addition, we find evidence of inter-family recombination in RNA viruses, and we also identify new members of the recombinant Adomaviridae family. Overall, we provide insights into the uncharacterised diversity of amphibian and reptile viruses with the aim of improving population management, treatment and conservation into the future.
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Affiliation(s)
- Emma F Harding
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Alice G Russo
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
- Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia
| | - Grace J H Yan
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Lewis K Mercer
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia.
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6
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Armwood AR, Stilwell JM, Ng TFF, Clauss TM, Leary JH, Mader D, Camus AC. A novel herpes-like virus inducing branchial lesions in a tiger shark ( Galeocerdo cuvier). Vet Pathol 2021; 59:348-352. [PMID: 34794368 DOI: 10.1177/03009858211052662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A juvenile, male tiger shark (Galeocerdo cuvier) developed illness after capture in Florida waters and was euthanized. Gross lesions included mild skin abrasions, hepatic atrophy, and coelomic fluid. Histologically, gills contained multifocal lamellar epithelial cell necrosis and thromboses. Scattered gill and esophageal epithelial cells had large, basophilic, intracytoplasmic, and intranuclear inclusions. Ultrastructurally, lamellar epithelial cells contained arrays of intracytoplasmic viral particles and scattered intranuclear nucleocapsids. Capsulated virions were 148 ± 11 nm with an 84 ± 8 nm icosahedral nucleocapsid and an electron-dense core. Next-generation sequencing, quantitative polymerase chain reaction, and in situ hybridization performed on formalin-fixed tissue confirmed a herpes-like viral infection. The viral polymerase shared 24% to 31% protein homology with other alloherpesviruses of fish, indicating a divergent virus. This report documents the pathologic findings associated with a molecularly confirmed novel herpes-like virus in an elasmobranch.
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Affiliation(s)
| | | | | | | | | | - Doug Mader
- Tropical Veterinary Services, Big Pine Key, FL, USA
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7
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Yang JX, Chen X, Li YY, Song TY, Ge JQ. Isolation of a novel adomavirus from cultured American eels, Anguilla rostrata, with haemorrhagic gill necrosis disease. JOURNAL OF FISH DISEASES 2021; 44:1811-1818. [PMID: 34324718 DOI: 10.1111/jfd.13500] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/10/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Recently, the culture of American eels (Anguilla rostrate) in China has been impacted by emergence of a disease with signs of haemorrhagic gill necrosis. The gills of diseased eels are covered with petecchia and they bleed when the operculum is pressed. In this study, a novel American eel adomavirus (AEAdoV) was isolated from the diseased eels using the eel ovary cell line (EO). The virus proliferated in the EO cells with a maximum TCID50 /ml of 106.29 ± 0.23 at 6 days post-infection. The virions were non-enveloped with a diameter of 75-85 nm and shown to be a DNA virus upon 5-iodo-2'-deoxyuridine (IDU) treatment. PCR assays showed that AEAdoV encodes a superfamily 3 helicases (S3H) replicase and shared high similarities with Anguilla marmorata adomavirus (MEAdoV). Although no clinical signs or mortality was observed among the eels injected with AEAdoV, the virus was reisolated from livers, kidneys and gills of injected eels at 35 days post-injection. Our results suggested that AEAdoV exhibited a latent infection in A. rostrata. The pathogenicity of the AEAdoV needs to be confirmed further.
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Affiliation(s)
- Jin-Xian Yang
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xi Chen
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Ying-Ying Li
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Tie-Ying Song
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jun-Qing Ge
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
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8
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Starrett GJ, Tisza MJ, Welch NL, Belford AK, Peretti A, Pastrana DV, Buck CB. Adintoviruses: a proposed animal-tropic family of midsize eukaryotic linear dsDNA (MELD) viruses. Virus Evol 2021; 7:veaa055. [PMID: 34646575 PMCID: PMC8502044 DOI: 10.1093/ve/veaa055] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA viruses. This supports the inference that at least some polintons are actually viruses capable of cell-to-cell spread. At present, there are no polinton-associated capsid protein genes annotated in public sequence databases. To rectify this deficiency, we used a data-mining approach to investigate the distribution and gene content of polinton-like elements and related DNA viruses in animal genomic and metagenomic sequence datasets. The results define a discrete family-like clade of viruses with two genus-level divisions. We propose the family name Adintoviridae, connoting similarities to adenovirus virion proteins and the presence of a retrovirus-like integrase gene. Although adintovirus-class PolB sequences were detected in datasets for fungi and various unicellular eukaryotes, sequences resembling adintovirus virion proteins and accessory genes appear to be restricted to animals. Degraded adintovirus sequences are endogenized into the germlines of a wide range of animals, including humans.
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Affiliation(s)
| | - Michael J Tisza
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Nicole L Welch
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Anna K Belford
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Alberto Peretti
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
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9
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First Isolation of a Novel Aquatic Flavivirus from Chinook Salmon (Oncorhynchus tshawytscha) and Its In Vivo Replication in a Piscine Animal Model. J Virol 2020; 94:JVI.00337-20. [PMID: 32434883 DOI: 10.1128/jvi.00337-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/12/2020] [Indexed: 01/17/2023] Open
Abstract
The first isolation of a flavivirus from fish was made from moribund Chinook salmon (Oncorhynchus tshawytscha) from the Eel River, California, USA. Following the observation of cytopathic effect in a striped-snakehead fish cell line, 35-nm virions with flaviviral morphology were visualized using electron microcopy. Next-generation sequencing and rapid amplification of cDNA ends obtained the complete genome. Reverse transcriptase quantitative PCR (RT-qPCR) confirmed the presence of viral RNA in formalin-fixed tissues from the wild salmon. For the first time, in vivo replication of an aquatic flavivirus was demonstrated following intracoelomic injection in a Chinook salmon model of infection. RT-qPCR demonstrated viral replication in salmon brains up to 15 days postinjection. Infectious virus was then reisolated in culture, fulfilling Rivers' postulates. Only limited replication occurred in the kidneys of Chinook salmon or in tissues of rainbow trout (Oncorhynchus mykiss). The proposed salmon flavivirus (SFV) has a 10.3-kb genome that encodes a rare dual open reading frame, a feature uncharacteristic of classical flaviviruses. Phylogenetic analysis places SFV in a basal position among a new subgroup of recently recognized aquatic and bat flaviviruses distinct from the established mosquito-borne, tick-borne, insect-only, and unknown-vector flavivirus groups. While the pathogenic potential of the virus remains to be fully elucidated, its basal phylogeny and the in vivo infection model will allow SFV to serve as a prototype for aquatic flaviviruses. Ongoing field and laboratory studies will facilitate better understanding of the potential impacts of SFV infection on ecologically and economically important salmonid species.IMPORTANCE Chinook salmon are a keystone fish species of great ecological and commercial significance in their native northern Pacific range and in regions to which they have been introduced. Threats to salmon populations include habitat degradation, climate change, and infectious agents, including viruses. While the first isolation of a flavivirus from wild migrating salmon may indicate an emerging disease threat, characterization of the genome provides insights into the ecology and long evolutionary history of this important group of viruses affecting humans and other animals and into an expanding group of recently discovered aquatic flaviviruses.
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10
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Blazer VS, Young KT, Smith GD, Sperry AJ, Iwanowicz LR. Hyperpigmented melanistic skin lesions of smallmouth bass Micropterus dolomieu from the Chesapeake Bay watershed. DISEASES OF AQUATIC ORGANISMS 2020; 139:199-212. [PMID: 32495746 DOI: 10.3354/dao03480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hyperpigmented melanistic skin lesions (HPMLs) of smallmouth bass Micropterus dolomieu are observed in the Potomac and Susquehanna rivers, Chesapeake Bay watershed, USA. Routine, nonlethal population surveys were conducted at 8 sites on the mainstem Susquehanna River and 9 on the Juniata River, a tributary of the Susquehanna River, between 2012 and 2018, and the prevalence of HPMLs was documented. A total of 4078 smallmouth bass were collected from the mainstem Susquehanna River and 6478 from the Juniata River. Lesions were primarily seen in bass greater than 200 mm, and prevalence in the Susquehanna River (8%) was higher (p < 0.001) than in the Juniata River (2%). As part of ongoing fish health monitoring projects, smallmouth bass were collected at additional sites, primarily tributaries of the Susquehanna (n = 758) and Potomac (n = 545) rivers between 2013 and 2018. Prevalence in the Susquehanna River (13%) was higher (p < 0.001) than the Potomac (3%). Microscopically, HPMLs were characterized by an increased number of melanocytes in the epidermis or within the dermis and epidermis. RNAseq analyses of normal and melanistic skin identified 3 unique sequences in HPMLs. Two were unidentified and the third was a viral helicase (E1). Transcript abundance in 16 normal skin samples and 16 HPMLs showed upregulation of genes associated with melanogenesis and cell proliferation in HPMLs. The E1 transcript was detected in 12 of the 16 melanistic areas but in no samples from normal skin. Further research will be necessary to identify the putative new virus and determine its role in melanocyte proliferation.
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Affiliation(s)
- Vicki S Blazer
- US Geological Survey, National Fish Health Research Laboratory, Leetown Science Center, Kearneysville, WV 25430, USA
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11
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Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini FM, Kuhn JH. Global Organization and Proposed Megataxonomy of the Virus World. Microbiol Mol Biol Rev 2020; 84:e00061-19. [PMID: 32132243 PMCID: PMC7062200 DOI: 10.1128/mmbr.00061-19] [Citation(s) in RCA: 324] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Institut Pasteur, Archaeal Virology Unit, Department of Microbiology, Paris, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia/Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
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12
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Draft Genome Sequence of an Adomavirus Associated with Raised Mucoid Skin Lesions on Smallmouth Bass (Micropterus dolomieu). Microbiol Resour Announc 2020; 9:9/14/e01479-19. [PMID: 32241864 PMCID: PMC7118190 DOI: 10.1128/mra.01479-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Raised mucoid skin lesions have been observed on smallmouth bass (Micropterus dolomieu) for years. Here, we report the draft genome of a novel adomavirus (Micropterus dolomieu adomavirus 2) associated with this disease. The circular genome is 17,561 bp and most similar to that of alpha-adomaviruses. Raised mucoid skin lesions have been observed on smallmouth bass (Micropterus dolomieu) for years. Here, we report the draft genome of a novel adomavirus (Micropterus dolomieu adomavirus 2) associated with this disease. The circular genome is 17,561 bp and most similar to that of alpha-adomaviruses.
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13
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Pao HY, Wu CY, Wen CM. Persistent development of adomavirus and aquareovirus in a novel cell line from marbled eel with petechial skin haemorrhage. JOURNAL OF FISH DISEASES 2019; 42:345-355. [PMID: 30632177 DOI: 10.1111/jfd.12939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 06/09/2023]
Abstract
In Taiwan, a petechial haemorrhage disease associated with mortality has affected marbled eels (Anguilla marmorata). The eels were revealed to be infected with adomavirus (MEAdoV, previously recognized as a polyoma-like virus). In this study, cell line DMEPF-5 was established from the pectoral fin of a diseased eel. DMEPF-5 was passaged >70 times and thoroughly proliferated in L-15 medium containing 2%-15% foetal bovine serum at 20-30°C. Transcripts of neural cell adhesion molecule 1 and nestin genes, and nucleic acids of MEAdoV and a novel reovirus (MERV) in the cells were demonstrated by reverse transcription-polymerase chain reaction analysis. Phylogenetic analysis revealed that the AdoV LO8 proteins mostly relate to adenovirus adenain, whereas MERV is close to American grass carp reovirus in Aquareovirus G, based on a partial VP2 nucleotide sequence. DMEPF-5 cells are susceptible to additional viral infection. Taken together, the marbled eels with the haemorrhagic disease have coinfection with MEAdoV and MERV, and the pathogenic role of MEAdoV and MERV warrants research. DMEPF-5 has gene expression associated with mesenchymal stem and progenitor cells and is the first cell line persistently infected with adomavirus and aquareovirus. DMEPF-5 can facilitate studies of such viruses and haemorrhagic disease.
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Affiliation(s)
- Hui-Yu Pao
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Cheng-Yu Wu
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Chiu Ming Wen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
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