1
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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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Louboutin L, Dheilly NM, Cabon J, Picon Camacho S, Leroux A, Lucas P, Le Breton A, Blanchard Y, Morin T. Characterization of a novel picornavirus isolated from moribund gilthead seabream (Sparus aurata) larvae. JOURNAL OF FISH DISEASES 2022; 45:707-716. [PMID: 35172021 DOI: 10.1111/jfd.13596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Gilthead seabream represents a species of importance in Mediterranean aquaculture. The larval stage is particularly sensitive and frequently impacted in suboptimal environmental or sanitary conditions. In the present study, investigations were carried out in a seabream hatchery following an unusual mortality reaching 70% among 50-day post-hatching. Anorexia, loss of appetite and abnormal swimming behaviour were observed in absence of parasites or pathogenic bacteria. Proliferation of rod-shaped bacteria in the gut lumen was associated with focal degeneration in the intestinal mucosa. Cytopathic effects on an EK-1 cell line after 21 days of culture at 14°C and 20°C in contact with homogenized affected larvae revealed the presence of a viral agent. Molecular characterization by high-throughput sequencing showed a typical picornavirus genome organization with a polyprotein precursor of 2276 amino acids sharing 46.3% identity with that of the Eel Picornavirus-1. A specific real-time PCR confirmed the presence of the viral genome in affected larval homogenate and corresponding cell culture supernatant. We propose the name Potamipivirus daurada for this novel species within the genus Potamipivirus. The etiological role of this virus remains uncertain at this time, and future studies will be necessary to investigate its prevalence in natural and aquaculture-reared populations as well as its ability to cause diseases in gilthead seabream.
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Affiliation(s)
- Lénaïg Louboutin
- ANSES, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail-Laboratoire de Ploufragan-Plouzané-Niort, Unité Virologie, Plouzané, France
| | - Nolwenn M Dheilly
- ANSES, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail-Laboratoire de Ploufragan-Plouzané-Niort, Unité Génétique virale et biosécurité, Ploufragan, France
| | - Joëlle Cabon
- ANSES, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail-Laboratoire de Ploufragan-Plouzané-Niort, Unité Virologie, Plouzané, France
| | | | - Aurélie Leroux
- ANSES, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail-Laboratoire de Ploufragan-Plouzané-Niort, Unité Génétique virale et biosécurité, Ploufragan, France
| | - Pierrick Lucas
- ANSES, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail-Laboratoire de Ploufragan-Plouzané-Niort, Unité Génétique virale et biosécurité, Ploufragan, France
| | - Alain Le Breton
- Vet'eau- Selarl Dr Alain Le Breton, Grenade-sur-Garonne, France
| | - Yannick Blanchard
- ANSES, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail-Laboratoire de Ploufragan-Plouzané-Niort, Unité Génétique virale et biosécurité, Ploufragan, France
| | - Thierry Morin
- ANSES, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail-Laboratoire de Ploufragan-Plouzané-Niort, Unité Virologie, Plouzané, France
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3
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Zell R, Groth M, Selinka L, Selinka HC. Picorna-Like Viruses of the Havel River, Germany. Front Microbiol 2022; 13:865287. [PMID: 35444619 PMCID: PMC9013969 DOI: 10.3389/fmicb.2022.865287] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
To improve the understanding of the virome diversity of riverine ecosystems in metropolitan areas, a metagenome analysis was performed with water collected in June 2018 from the river Havel in Berlin, Germany. After enrichment of virus particles and RNA extraction, paired-end Illumina sequencing was conducted and assignment to virus groups and families was performed. This paper focuses on picorna-like viruses, the most diverse and abundant group of viruses with impact on human, animal, and environmental health. Here, we describe altogether 166 viral sequences ranging in size from 1 to 11.5 kb. The 71 almost complete genomes are comprised of one candidate iflavirus, one picornavirus, two polycipiviruses, 27 marnaviruses, 27 dicistro-like viruses, and 13 untypeable viruses. Many partial picorna-like virus sequences up to 10.2 kb were also investigated. The sequences of the Havel picorna-like viruses represent genomes of seven of eight so far known Picornavirales families. Detection of numerous distantly related dicistroviruses suggests the existence of additional, yet unexplored virus groups with dicistronic genomes, including few viruses with unusual genome layout. Of special interest is a clade of dicistronic viruses with capsid protein-encoding sequences at the 5′-end of the genome. Also, monocistronic viruses with similarity of their polymerase and capsid proteins to those of dicistroviruses are interesting. A second protein with NTP-binding site present in the polyprotein of solinviviruses and related viruses needs further attention. The results underline the importance to study the viromes of fluvial ecosystems. So far acknowledged marnaviruses have been isolated from marine organisms. However, the present study and available sequence data suggest that rivers and limnic habitats are relevant ecosystems with circulation of marnaviruses as well as a plethora of unknown picorna-like viruses.
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Affiliation(s)
- Roland Zell
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Marco Groth
- CF DNA Sequencing, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Lukas Selinka
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Hans-Christoph Selinka
- Section II 1.4 Microbiological Risks, Department of Environmental Hygiene, German Environment Agency, Berlin, Germany
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4
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Wang G, Luan Y, Wei J, Li Y, Shi H, Cheng H, Bai A, Xie J, Xu W, Qin P. Genetic and Pathogenic Characterization of a New Iridovirus Isolated from Cage-Cultured Large Yellow Croaker (Larimichthys crocea) in China. Viruses 2022; 14:v14020208. [PMID: 35215802 PMCID: PMC8879442 DOI: 10.3390/v14020208] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 12/18/2022] Open
Abstract
Iridoviruses are an important pathogen of ectothermic vertebrates and are considered a significant threat to aquacultural fish production. Recently, one of the most economically important marine species in China, the large yellow croaker (Larimichthys crocea), has been increasingly reported to be the victim of iridovirus disease. In this study, we isolated and identified a novel iridovirus, LYCIV-ZS-2020, from cage-cultured large yellow croaker farms in Zhoushan island, China. Genome sequencing and subsequent phylogenetic analyses showed that LYCIV-ZS-2020 belongs to the genus Megalocytivirus and is closely related to the Pompano iridoviruses isolated in the Dominican Republic. LYCIV-ZS-2020 enriched from selected tissues of naturally infected large yellow croaker was used in an artificial infection trial and the results proved its pathogenicity in large yellow croaker. This is the first systematic research on the genetic and pathogenic characterization of iridovirus in large yellow croakers, which expanded our knowledge of the iridovirus.
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Affiliation(s)
- Gengshen Wang
- Key Laboratory of Mariculture and Enhancement of Zhejiang Province, Marine Fisheries Research Institute of Zhejiang, Zhoushan 316100, China; (G.W.); (H.S.); (H.C.); (J.X.); (W.X.)
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316100, China
| | - Yingjia Luan
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (J.W.); (Y.L.)
| | - Jinping Wei
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (J.W.); (Y.L.)
| | - Yunfeng Li
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (J.W.); (Y.L.)
| | - Hui Shi
- Key Laboratory of Mariculture and Enhancement of Zhejiang Province, Marine Fisheries Research Institute of Zhejiang, Zhoushan 316100, China; (G.W.); (H.S.); (H.C.); (J.X.); (W.X.)
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316100, China
| | - Haoxue Cheng
- Key Laboratory of Mariculture and Enhancement of Zhejiang Province, Marine Fisheries Research Institute of Zhejiang, Zhoushan 316100, China; (G.W.); (H.S.); (H.C.); (J.X.); (W.X.)
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316100, China
| | - Aixu Bai
- Huaian Customs District, Huaian 223001, China;
| | - Jianjun Xie
- Key Laboratory of Mariculture and Enhancement of Zhejiang Province, Marine Fisheries Research Institute of Zhejiang, Zhoushan 316100, China; (G.W.); (H.S.); (H.C.); (J.X.); (W.X.)
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316100, China
| | - Wenjun Xu
- Key Laboratory of Mariculture and Enhancement of Zhejiang Province, Marine Fisheries Research Institute of Zhejiang, Zhoushan 316100, China; (G.W.); (H.S.); (H.C.); (J.X.); (W.X.)
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316100, China
| | - Pan Qin
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (J.W.); (Y.L.)
- Correspondence:
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5
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Danne L, Horn L, Feldhaus A, Fey D, Emde S, Schütze H, Adamek M, Hellmann J. Virus infections of the European Eel in North Rhine Westphalian rivers. JOURNAL OF FISH DISEASES 2022; 45:69-76. [PMID: 34585388 DOI: 10.1111/jfd.13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Viral infections have been suggested to play a role in the decline of the panmictic population of the European eel (Anguilla anguilla). However, despite the importance of knowledge about pathogenic eel viruses, little is known about their spread in the wild European eel population and only a few eel pathogenic viruses have been described so far. In this study, we aimed to investigate the health status of the A. anguilla stock in North Rhine Westphalia (NRW) State of Germany. For this purpose, we examined tissue samples of 16 elvers, 100 yellow eels and 6 silver eels, sampled from the rivers Rhine, Lippe and Ems. Virus detection was performed via a combination of cell culture and PCR. Next to the detection of frequently encountered pathogenic eel viruses (anguillid herpesvirus 1 and eel virus European X (EVEX)), we isolated the eel picornavirus 1 (EPV-1) from tissue of yellow eels and elvers and demonstrate the distribution of EPV-1 in wild eel population in NRW.
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Affiliation(s)
- Linna Danne
- Environment and Consumer Protection, Fisheries Ecology and Aquaculture, North Rhine Westphalian State Agency for Nature, Kirchhundem-Albaum, Germany
| | - Lisa Horn
- Environment and Consumer Protection, Fisheries Ecology and Aquaculture, North Rhine Westphalian State Agency for Nature, Kirchhundem-Albaum, Germany
| | - Anita Feldhaus
- Environment and Consumer Protection, Fisheries Ecology and Aquaculture, North Rhine Westphalian State Agency for Nature, Kirchhundem-Albaum, Germany
| | - Daniel Fey
- Environment and Consumer Protection, Fisheries Ecology and Aquaculture, North Rhine Westphalian State Agency for Nature, Kirchhundem-Albaum, Germany
| | - Sebastian Emde
- Environment and Consumer Protection, Fisheries Ecology and Aquaculture, North Rhine Westphalian State Agency for Nature, Kirchhundem-Albaum, Germany
| | - Heike Schütze
- Friedrich-Loeffler-Institute, Institute of Infectology, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Mikolaj Adamek
- Fish Disease Research Unit, Centre for Infection Medicine, University of Veterinary Medicine, Hannover, Germany
| | - John Hellmann
- Environment and Consumer Protection, Fisheries Ecology and Aquaculture, North Rhine Westphalian State Agency for Nature, Kirchhundem-Albaum, Germany
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6
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Hargitai R, Pankovics P, Boros Á, Mátics R, Altan E, Delwart E, Reuter G. Novel picornavirus (family Picornaviridae) from freshwater fishes (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) in Hungary. Arch Virol 2021; 166:2627-2632. [PMID: 34255185 PMCID: PMC8322000 DOI: 10.1007/s00705-021-05167-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/21/2021] [Indexed: 12/01/2022]
Abstract
In this study, a novel picornavirus (perchPV/M9/2015/HUN, GenBank accession no. MW590713) was detected in eight (12.9%) out of 62 faecal samples collected from three (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) out of 13 freshwater fish species tested and genetically characterized using viral metagenomics and RT-PCR methods. The complete genome of perchPV/M9/2015/HUN is 7,741 nt long, excluding the poly(A) tail, and has the genome organization 5'UTRIRES-?/P1(VP0-VP3-VP1)/P2(2A1NPG↓P-2A2H-box/NC-2B-2C)/P3(3A-3BVPg-3CPro-3DPol)/3'UTR-poly(A). The P1, 2C, and 3CD proteins had 41.4%, 38.1%, and 47.3% amino acid sequence identity to the corresponding proteins of Wenling lepidotrigla picornavirus (MG600079), eel picornavirus (NC_022332), and Wenling pleuronectiformes picornavirus (MG600098), respectively, as the closest relatives in the genus Potamipivirus. PerchPV/M9/2015/HUN represents a potential novel fish-origin species in an unassigned genus in the family Picornaviridae.
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Affiliation(s)
- Renáta Hargitai
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., 7624, Pecs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., 7624, Pecs, Hungary
| | - Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., 7624, Pecs, Hungary
| | | | - Eda Altan
- Vitalant Research Institute, San Francisco, CA, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., 7624, Pecs, Hungary.
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7
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Scherbatskoy EC, Subramaniam K, Al-Hussinee L, Imnoi K, Thompson PM, Popov VL, Ng TFF, Kelley KL, Alvarado R, Wolf JC, Pouder DB, Yanong RPE, Waltzek TB. Characterization of a novel picornavirus isolated from moribund aquacultured clownfish. J Gen Virol 2021; 101:735-745. [PMID: 32421489 DOI: 10.1099/jgv.0.001421] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Over the last decade, a number of USA aquaculture facilities have experienced periodic mortality events of unknown aetiology in their clownfish (Amphiprion ocellaris). Clinical signs of affected individuals included lethargy, altered body coloration, reduced body condition, tachypnea, and abnormal positioning in the water column. Samples from outbreaks were processed for routine parasitological, bacteriological, and virological diagnostic testing, but no consistent parasitic or bacterial infections were observed. Histopathological evaluation revealed individual cell necrosis and mononuclear cell inflammation in the branchial cavity, pharynx, oesophagus and/or stomach of four examined clownfish, and large basophilic inclusions within the pharyngeal mucosal epithelium of one fish. Homogenates from pooled external and internal tissues from these outbreaks were inoculated onto striped snakehead (SSN-1) cells for virus isolation and cytopathic effects were observed, resulting in monolayer lysis in the initial inoculation and upon repassage. Transmission electron microscopy of infected SSN-1 cells revealed small round particles (mean diameter=20.0-21.7 nm) within the cytoplasm, consistent with the ultrastructure of a picornavirus. Full-genome sequencing of the purified virus revealed a novel picornavirus most closely related to the bluegill picornavirus and other members of the genus Limnipivirus. Additionally, pairwise protein alignments between the clownfish picornavirus (CFPV) and other known members of the genus Limnipivirus yielded results in accordance with the current International Committee on Taxonomy of Viruses criteria for members of the same genus. Thus, CFPV represents a proposed new limnipivirus species. Future experimental challenge studies are needed to determine the role of CFPV in disease.
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Affiliation(s)
- Elizabeth C Scherbatskoy
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Lowia Al-Hussinee
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Kamonchai Imnoi
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Patrick M Thompson
- Present address: Whitney Laboratory for Marine Bioscience, St Augustine, FL, USA
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Terry Fei Fan Ng
- College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Karen L Kelley
- Electron Microscopy Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Rodolfo Alvarado
- Electron Microscopy Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Jeffrey C Wolf
- Experimental Pathology Laboratories, Inc., Sterling, VA, USA
| | - Deborah B Pouder
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, IFAS, University of Florida, Ruskin, FL, USA
| | - Roy P E Yanong
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, IFAS, University of Florida, Ruskin, FL, USA
| | - Thomas B Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
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Neufurth M, Wang X, Wang S, Schröder HC, Müller WEG. Caged Dexamethasone/Quercetin Nanoparticles, Formed of the Morphogenetic Active Inorganic Polyphosphate, are Strong Inducers of MUC5AC. Mar Drugs 2021; 19:64. [PMID: 33513822 PMCID: PMC7910845 DOI: 10.3390/md19020064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/17/2021] [Accepted: 01/24/2021] [Indexed: 02/07/2023] Open
Abstract
Inorganic polyphosphate (polyP) is a widely distributed polymer found from bacteria to animals, including marine species. This polymer exhibits morphogenetic as well as antiviral activity and releases metabolic energy after enzymatic hydrolysis also in human cells. In the pathogenesis of the coronavirus disease 2019 (COVID-19), the platelets are at the frontline of this syndrome. Platelets release a set of molecules, among them polyP. In addition, the production of airway mucus, the first line of body defense, is impaired in those patients. Therefore, in this study, amorphous nanoparticles of the magnesium salt of polyP (Mg-polyP-NP), matching the size of the coronavirus SARS-CoV-2, were prepared and loaded with the secondary plant metabolite quercetin or with dexamethasone to study their effects on the respiratory epithelium using human alveolar basal epithelial A549 cells as a model. The results revealed that both compounds embedded into the polyP nanoparticles significantly increased the steady-state-expression of the MUC5AC gene. This mucin species is the major mucus glycoprotein present in the secreted gel-forming mucus. The level of gene expression caused by quercetin or with dexamethasone, if caged into polyP NP, is significantly higher compared to the individual drugs alone. Both quercetin and dexamethasone did not impair the growth-supporting effect of polyP on A549 cells even at concentrations of quercetin which are cytotoxic for the cells. A possible mechanism of the effects of the two drugs together with polyP on mucin expression is proposed based on the scavenging of free oxygen species and the generation of ADP/ATP from the polyP, which is needed for the organization of the protective mucin-based mucus layer.
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Affiliation(s)
| | - Xiaohong Wang
- ERC Advanced Investigator Grant Research Group, Institute for Physiological Chemistry, University Medical Center, Johannes Gutenberg University, Duesbergweg 6, 55128 Mainz, Germany; (M.N.); (S.W.); (H.C.S.)
| | | | | | - Werner E. G. Müller
- ERC Advanced Investigator Grant Research Group, Institute for Physiological Chemistry, University Medical Center, Johannes Gutenberg University, Duesbergweg 6, 55128 Mainz, Germany; (M.N.); (S.W.); (H.C.S.)
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9
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Costa VA, Mifsud JCO, Gilligan D, Williamson JE, Holmes EC, Geoghegan JL. Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia. Virus Evol 2021; 7:veab034. [PMID: 34017611 PMCID: PMC8121191 DOI: 10.1093/ve/veab034] [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: 12/18/2022] Open
Abstract
Biological invasions are among the biggest threats to freshwater biodiversity. This is increasingly relevant in the Murray-Darling Basin, Australia, particularly since the introduction of the common carp (Cyprinus carpio). This invasive species now occupies up to ninety per cent of fish biomass, with hugely detrimental impacts on native fauna and flora. To address the ongoing impacts of carp, cyprinid herpesvirus 3 (CyHV-3) has been proposed as a potentially effective biological control agent. Crucially, however, it is unknown whether CyHV-3 and other cyprinid herpesviruses already exist in the Murray-Darling. Further, little is known about those viruses that naturally occur in wild freshwater fauna, and the frequency with which these viruses jump species boundaries. To document the evolution and diversity of freshwater fish viromes and better understand the ecological context to the proposed introduction of CyHV-3, we performed a meta-transcriptomic viral survey of invasive and native fish across the Murray-Darling Basin, covering over 2,200 km of the river system. Across a total of thirty-six RNA libraries representing ten species, we failed to detect CyHV-3 nor any closely related viruses. Rather, meta-transcriptomic analysis identified eighteen vertebrate-associated viruses that could be assigned to the Arenaviridae, Astroviridae, Bornaviridae, Caliciviridae, Coronaviridae, Chuviridae, Flaviviridae, Hantaviridae, Hepeviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae and Rhabdoviridae families, and a further twenty-seven that were deemed to be associated with non-vertebrate hosts. Notably, we revealed a marked lack of viruses that are shared among invasive and native fish sampled here, suggesting that there is little virus transmission from common carp to native fish species, despite co-existing for over fifty years. Overall, this study provides the first data on the viruses naturally circulating in a major river system and supports the notion that fish harbour a large diversity of viruses with often deep evolutionary histories.
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Affiliation(s)
- Vincenzo A Costa
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jonathon C O Mifsud
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Dean Gilligan
- NSW Department of Primary Industries, Batemans Bay Fisheries Office, Batemans Bay 2536, Australia
| | - Jane E Williamson
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Institute of Environmental Science and Research, Wellington, Porirua 5022, New Zealand
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10
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Draft Genome Sequence of a Novel Picornavirus Isolated from Japanese Eel ( Anguilla japonica). Microbiol Resour Announc 2020; 9:9/42/e00878-20. [PMID: 33060267 PMCID: PMC7561686 DOI: 10.1128/mra.00878-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We report the draft genome sequence of a novel member of the order Picornavirales that was obtained from the gills of farmed Japanese eel (Anguilla japonica). A putative polyprotein encoded by the genome was similar to that of other picornaviruses and shared 31% amino acid identity with eel picornavirus 1. We report the draft genome sequence of a novel member of the order Picornavirales that was obtained from the gills of farmed Japanese eel (Anguilla japonica). A putative polyprotein encoded by the genome was similar to that of other picornaviruses and shared 31% amino acid identity with that of eel picornavirus 1.
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11
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Zheng Z, Yang J, Ge J, Chi H, Chen B, Fang Q, Gong H. Development and characterization of a continuous cell line (EL) from the liver of European eel Anguilla anguilla. Cell Biol Int 2019; 44:808-820. [PMID: 31814207 PMCID: PMC7028054 DOI: 10.1002/cbin.11276] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/06/2019] [Indexed: 01/31/2023]
Abstract
In the present study, a new hepatic tissue‐origin cell line from European eel Anguilla anguilla has been developed and characterized. This cell line designated EL has been maintained in Leibovitz L‐15 supplemented with 10% fetal bovine serum over 72 months, and subcultured more than 90 times. The EL cell line consisted predominantly of fibroblast‐like cells, which could survive over 100 days in vitro, and could grow at 15–32°C. The optimum temperature for growth was 27°C. The chromosome analysis revealed a modal diploid karyotype of 2n = 38. The origin of this cell line was confirmed by the 18S recombinant (r)RNA sequencing. The susceptibility test indicated significant cytopathic effects in the EL cells with regard to the Rana grylio virus and the Herpesvirus anguillae. The viral replication was confirmed by transmission electron microscopy and polymerase chain reaction analysis. Following poly (I:C) exposure, the expression levels of the immune‐related molecules interferon regulatory factor‐7 (irf7) and transforming growth factor‐β (TGF‐β) were downregulated in EL cells, whereas the expression levels of the rf3 and the cytochrome P450 (CYP450) were upregulated. All four genes were significantly upregulated following inflammation by lipopolysaccharide (LPS). These data suggested the application of EL cell line for viral identification, as well as for immunodiagnosis and pharmacological targeting.
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Affiliation(s)
- Zaiyu Zheng
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Wusi Road 247, Fuzhou, Fujian, 350003, China
| | - Jinxian Yang
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Wusi Road 247, Fuzhou, Fujian, 350003, China
| | - Junqing Ge
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Wusi Road 247, Fuzhou, Fujian, 350003, China
| | - Hongshu Chi
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Wusi Road 247, Fuzhou, Fujian, 350003, China
| | - Bin Chen
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Wusi Road 247, Fuzhou, Fujian, 350003, China.,Ningde Fufa Fisheries Company Ltd., Ningde, Fujian, China
| | - Qinmei Fang
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Wusi Road 247, Fuzhou, Fujian, 350003, China
| | - Hui Gong
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Wusi Road 247, Fuzhou, Fujian, 350003, China
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12
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Genome Characterization, Prevalence, and Transmission Mode of a Novel Picornavirus Associated with the Threespine Stickleback Fish (Gasterosteus aculeatus). J Virol 2019; 93:JVI.02277-18. [PMID: 30760574 DOI: 10.1128/jvi.02277-18] [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: 12/19/2018] [Accepted: 02/05/2019] [Indexed: 01/31/2023] Open
Abstract
The complete genome sequence of an RNA virus was assembled from RNA sequencing of virus particles purified from threespine stickleback intestine tissue samples. This new virus is most closely related to the Eel picornavirus and can be assigned to the genus Potamipivirus in the family Picornaviridae Its unique genetic properties are enough to establish a new species, dubbed the Threespine Stickleback picornavirus (TSPV). Due to their broad geographic distribution throughout the Northern Hemisphere and parallel adaptation to freshwater, threespine sticklebacks have become a model in evolutionary ecology. Further analysis using diagnostic PCRs revealed that TSPV is highly prevalent in both anadromous and freshwater populations of threespine sticklebacks, infects almost all fish tissues, and is transmitted vertically to offspring obtained from in vitro fertilization in laboratory settings. Finally, TSPV was found in Sequence Reads Archives of transcriptome of Gasterosteus aculeatus, further demonstrating its wide distribution and unsought prevalence in samples. It is thus necessary to test the impact of TSPV on the biology of threespine sticklebacks, as this widespread virus could interfere with the behavioral, physiological, or immunological studies that employ this fish as a model system.IMPORTANCE The threespine stickleback species complex is an important model system in ecological and evolutionary studies because of the large number of isolated divergent populations that are experimentally tractable. For similar reasons, its coevolution with the cestode parasite Schistocephalus solidus, its interaction with gut microbes, and the evolution of its immune system are of growing interest. Herein we describe the discovery of an RNA virus that infects both freshwater and anadromous populations of sticklebacks. We show that the virus is transmitted vertically in laboratory settings and found it in Sequence Reads Archives, suggesting that experiments using sticklebacks were conducted in the presence of the virus. This discovery can serve as a reminder that the presence of viruses in wild-caught animals is possible, even when animals appear healthy. Regarding threespine sticklebacks, the impact of Threespine Stickleback picornavirus (TSPV) on the fish biology should be investigated further to ensure that it does not interfere with experimental results.
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13
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Altan E, Kubiski SV, Boros Á, Reuter G, Sadeghi M, Deng X, Creighton EK, Crim MJ, Delwart E. A Highly Divergent Picornavirus Infecting the Gut Epithelia of Zebrafish ( Danio rerio) in Research Institutions Worldwide. Zebrafish 2019; 16:291-299. [PMID: 30939077 DOI: 10.1089/zeb.2018.1710] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Zebrafish have been extensively used as a model system for research in vertebrate development and pathogen-host interactions. We describe the complete genome of a novel picornavirus identified during a viral metagenomics analysis of zebrafish gut tissue. The closest relatives of this virus showed identity of <20% in their P1 capsids and <36% in their RdRp qualifying zebrafish picornavirus-1 (ZfPV-1) as member of a novel genus with a proposed name of Cyprivirus. Reverse transcription (RT)-PCR testing of zebrafish from North America, Europe, and Asia showed ZfPV-1 to be globally distributed, being detected in 23 of 41 (56%) institutions tested. In situ hybridization of whole zebrafish showed viral RNA was restricted to a subset of enterocytes and cells in the subjacent lamina propria of the intestine and the intestinal mucosa. This naturally occurring and apparently asymptomatic infection (in wild-type zebrafish lineage AB) provides a natural infection system to study picornavirus-host interactions in an advanced vertebrate model organism. Whether ZfPV-1 infection affects any immunological, developmental, or other biological processes in wild-type or mutant zebrafish lineages remains to be determined.
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Affiliation(s)
- Eda Altan
- 1 Vitalant Research Institute, San Francisco, California.,2 Department of Laboratory Medicine, University of California, San Francisco, California
| | - Steven V Kubiski
- 3 Institute for Conservation Research, San Diego Zoo Global, San Diego, California
| | - Ákos Boros
- 4 Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.,5 Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Gábor Reuter
- 5 Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Mohammadreza Sadeghi
- 1 Vitalant Research Institute, San Francisco, California.,6 Department of Virology, University of Helsinki, Helsinki, Finland
| | - Xutao Deng
- 1 Vitalant Research Institute, San Francisco, California.,2 Department of Laboratory Medicine, University of California, San Francisco, California
| | | | | | - Eric Delwart
- 1 Vitalant Research Institute, San Francisco, California.,2 Department of Laboratory Medicine, University of California, San Francisco, California
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14
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Chen B, Zheng Z, Yang J, Chi H, Huang H, Gong H. Development and characterization of a new cell line derived from European eel Anguilla anguilla kidney. Biol Open 2019; 8:bio.037507. [PMID: 30429125 PMCID: PMC6361207 DOI: 10.1242/bio.037507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A new cell line derived from the kidney of European eel, Anguilla anguilla, has been established and characterized. This cell line, designated as EK (eel kidney), has been maintained in Leibovitz's L-15 supplemented with 10% fetal bovine serum for over 24 months, and subcultured more than 60 times. This cell line consists predominantly of fibroblast-like cells, and can grow at 15–37°C under an optimum temperature of 26°C. The origin of this cell line was confirmed by polymerase chain reaction (PCR) amplification and 18s recombinant (r)RNA sequencing. The chromosome analysis of EK cells at passage 58 revealed an ananeuploid karyotype. The EK cells were successfully transfected with the Pegfp-N1 plasmid, suggesting its potential in genetic studies. The susceptibility test showed a significant cytopathic effect (CPE) in EK cells for Rana grylio virus, and the viral replication was evidenced with quantitative real-time PCR (qRT-PCR) assay. After poly (I:C) stimulation, the expression of the immune-related molecules including interferon regulatory factor-3 (irf3), interferon regulatory factor-7 (irf7) and cytochrome P450 (CYP450) were significantly upregulated in EK cells, while the expression of transforming growth factor (TGF-β) was downregulated. These results suggested the potential of EK cell line as a model in gene engineering, virus identification and environmental toxicology. Summary: The first visceral cell line of an endangered species, Anguilla anguilla has been established; this aneuploid cell line is fibroblast-like, and suitable for gene expression and virus isolation.
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Affiliation(s)
- Bin Chen
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, High-tech building 1506, Wusi Road 247, Fuzhou 350003, Fujian, China
| | - Zaiyu Zheng
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, High-tech building 1506, Wusi Road 247, Fuzhou 350003, Fujian, China
| | - Jinxian Yang
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, High-tech building 1506, Wusi Road 247, Fuzhou 350003, Fujian, China
| | - Hongshu Chi
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, High-tech building 1506, Wusi Road 247, Fuzhou 350003, Fujian, China
| | - He Huang
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, High-tech building 1506, Wusi Road 247, Fuzhou 350003, Fujian, China
| | - Hui Gong
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, High-tech building 1506, Wusi Road 247, Fuzhou 350003, Fujian, China
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15
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Geoghegan JL, Di Giallonardo F, Cousins K, Shi M, Williamson JE, Holmes EC. Hidden diversity and evolution of viruses in market fish. Virus Evol 2018; 4:vey031. [PMID: 30397510 PMCID: PMC6208713 DOI: 10.1093/ve/vey031] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aquaculture is the fastest growing industry worldwide. Aquatic diseases have had enormous economic and environmental impacts in the recent past and the emergence of new aquatic pathogens, particularly viruses, poses a continuous threat. Nevertheless, little is known about the diversity, abundance and evolution of fish viruses. We used a meta-transcriptomic approach to help determine the virome of seemingly healthy fish sold at a market in Sydney, Australia. Specifically, by identifying and quantifying virus transcripts we aimed to determine (i) the abundance of viruses in market fish, (ii) test a key component of epidemiological theory that large and dense host populations harbour a greater number of viruses compared to their more solitary counterparts and (iii) reveal the relative roles of virus–host co-divergence and cross-species transmission in the evolution of fish viruses. The species studied comprised both shoaling fish—eastern sea garfish (Hyporhamphus australis) and Australasian snapper (Chrysophrys auratus)—and more solitary fish—eastern red scorpionfish (Scorpaena jacksoniensis) and largetooth flounder (Pseudorhombus arsius). Our analysis identified twelve potentially novel viruses, eight of which were likely vertebrate-associated across four viral families and that exhibited frequent cross-species transmission. Notably, the most solitary of the fish species studied, the largetooth flounder, harboured the least number of viruses while eastern sea garfish, a densely shoaling fish, had the highest number of viruses. These results support the emerging view that fish harbour a large and largely uncharacterised virome.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Francesca Di Giallonardo
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.,The Kirby Institute, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Kate Cousins
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Jane E Williamson
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
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16
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Zaulet M, Petrovan V, Birladeanu AM, Stoian AMM, Kevorkian SEM, Nichita C, Eloit M, Buburuzan L. Identification and prevalence of swine pasivirus 1 in eastern Romanian pig farms. J Vet Diagn Invest 2017; 29:305-311. [PMID: 28363267 DOI: 10.1177/1040638717696044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Swine pasivirus 1 (SPaV-1) was first detected in the feces of healthy pigs in France as a new species in family Picornaviridae. We investigated the presence, distribution, and genetic variability of this virus in 7 geographic areas with intensive pig breeding farms in eastern Romania. A total of 564 porcine specimens, including 82 fecal specimens and 482 pools of organs, were collected from healthy pigs in different stages of production from pathogen-free swine farming units. The virus was found in 6 of 7 areas investigated. Of the 564 samples analyzed, 218 were positive for SPaV-1, with the highest prevalence of the virus in organ homogenates (39% positive) followed by feces (37% positive). The highest susceptibility to infection was found in nurseries (50% positive in both the first and second months of feeding). Sequencing analysis of VP0 revealed 3 different Romanian sequences. The phylogenetic investigations suggest that the Romanian sequences cluster with other Pasivirus strains selected from the GenBank database, forming a separate clade from other Picornaviridae genera and defining the described Pasivirus.
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Affiliation(s)
- Mihaela Zaulet
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest 5th District, Romania (Zaulet, Birladeanu, Buburuzan).,Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Petrovan, Stoian).,Faculty of Medicine, Pharmacy and Dental Medicine, "Vasile Goldis" Western University of Arad, Arad, Romania (Kevorkian).,Nano-SAE research center, Faculty of Physics, University of Bucharest, Bucharest-Magurele, Romania (Nichita).,Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, Paris, France (Eloit).,PathoQuest, Bâtiment François Jacob, Paris, France (Eloit).,Ecole Nationale Vétérinaire d'Alfort, Maisons Alfort, France (Eloit).,National Institute for Chemical-Pharmaceutical Research and Development, Bucharest, Romania (Nichita)
| | - Vlad Petrovan
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest 5th District, Romania (Zaulet, Birladeanu, Buburuzan).,Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Petrovan, Stoian).,Faculty of Medicine, Pharmacy and Dental Medicine, "Vasile Goldis" Western University of Arad, Arad, Romania (Kevorkian).,Nano-SAE research center, Faculty of Physics, University of Bucharest, Bucharest-Magurele, Romania (Nichita).,Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, Paris, France (Eloit).,PathoQuest, Bâtiment François Jacob, Paris, France (Eloit).,Ecole Nationale Vétérinaire d'Alfort, Maisons Alfort, France (Eloit).,National Institute for Chemical-Pharmaceutical Research and Development, Bucharest, Romania (Nichita)
| | - Andrada M Birladeanu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest 5th District, Romania (Zaulet, Birladeanu, Buburuzan).,Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Petrovan, Stoian).,Faculty of Medicine, Pharmacy and Dental Medicine, "Vasile Goldis" Western University of Arad, Arad, Romania (Kevorkian).,Nano-SAE research center, Faculty of Physics, University of Bucharest, Bucharest-Magurele, Romania (Nichita).,Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, Paris, France (Eloit).,PathoQuest, Bâtiment François Jacob, Paris, France (Eloit).,Ecole Nationale Vétérinaire d'Alfort, Maisons Alfort, France (Eloit).,National Institute for Chemical-Pharmaceutical Research and Development, Bucharest, Romania (Nichita)
| | - Ana Maria M Stoian
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest 5th District, Romania (Zaulet, Birladeanu, Buburuzan).,Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Petrovan, Stoian).,Faculty of Medicine, Pharmacy and Dental Medicine, "Vasile Goldis" Western University of Arad, Arad, Romania (Kevorkian).,Nano-SAE research center, Faculty of Physics, University of Bucharest, Bucharest-Magurele, Romania (Nichita).,Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, Paris, France (Eloit).,PathoQuest, Bâtiment François Jacob, Paris, France (Eloit).,Ecole Nationale Vétérinaire d'Alfort, Maisons Alfort, France (Eloit).,National Institute for Chemical-Pharmaceutical Research and Development, Bucharest, Romania (Nichita)
| | - Steliana E M Kevorkian
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest 5th District, Romania (Zaulet, Birladeanu, Buburuzan).,Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Petrovan, Stoian).,Faculty of Medicine, Pharmacy and Dental Medicine, "Vasile Goldis" Western University of Arad, Arad, Romania (Kevorkian).,Nano-SAE research center, Faculty of Physics, University of Bucharest, Bucharest-Magurele, Romania (Nichita).,Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, Paris, France (Eloit).,PathoQuest, Bâtiment François Jacob, Paris, France (Eloit).,Ecole Nationale Vétérinaire d'Alfort, Maisons Alfort, France (Eloit).,National Institute for Chemical-Pharmaceutical Research and Development, Bucharest, Romania (Nichita)
| | - Cornelia Nichita
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest 5th District, Romania (Zaulet, Birladeanu, Buburuzan).,Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Petrovan, Stoian).,Faculty of Medicine, Pharmacy and Dental Medicine, "Vasile Goldis" Western University of Arad, Arad, Romania (Kevorkian).,Nano-SAE research center, Faculty of Physics, University of Bucharest, Bucharest-Magurele, Romania (Nichita).,Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, Paris, France (Eloit).,PathoQuest, Bâtiment François Jacob, Paris, France (Eloit).,Ecole Nationale Vétérinaire d'Alfort, Maisons Alfort, France (Eloit).,National Institute for Chemical-Pharmaceutical Research and Development, Bucharest, Romania (Nichita)
| | - Marc Eloit
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest 5th District, Romania (Zaulet, Birladeanu, Buburuzan).,Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Petrovan, Stoian).,Faculty of Medicine, Pharmacy and Dental Medicine, "Vasile Goldis" Western University of Arad, Arad, Romania (Kevorkian).,Nano-SAE research center, Faculty of Physics, University of Bucharest, Bucharest-Magurele, Romania (Nichita).,Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, Paris, France (Eloit).,PathoQuest, Bâtiment François Jacob, Paris, France (Eloit).,Ecole Nationale Vétérinaire d'Alfort, Maisons Alfort, France (Eloit).,National Institute for Chemical-Pharmaceutical Research and Development, Bucharest, Romania (Nichita)
| | - Laura Buburuzan
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest 5th District, Romania (Zaulet, Birladeanu, Buburuzan).,Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Petrovan, Stoian).,Faculty of Medicine, Pharmacy and Dental Medicine, "Vasile Goldis" Western University of Arad, Arad, Romania (Kevorkian).,Nano-SAE research center, Faculty of Physics, University of Bucharest, Bucharest-Magurele, Romania (Nichita).,Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, Paris, France (Eloit).,PathoQuest, Bâtiment François Jacob, Paris, France (Eloit).,Ecole Nationale Vétérinaire d'Alfort, Maisons Alfort, France (Eloit).,National Institute for Chemical-Pharmaceutical Research and Development, Bucharest, Romania (Nichita)
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17
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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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18
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Pankovics P, Boros Á, Tóth Z, Phan TG, Delwart E, Reuter G. Genetic characterization of a second novel picornavirus from an amphibian host, smooth newt (Lissotriton vulgaris). Arch Virol 2016; 162:1043-1050. [PMID: 28005212 DOI: 10.1007/s00705-016-3198-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/02/2016] [Indexed: 11/30/2022]
Abstract
In this study, a novel picornavirus was identified in faecal samples from smooth newts (Lissotriton vulgaris). The complete genome of picornavirus strain newt/II-5-Pilis/2014/HUN (KX463670) is 7755 nt long with type-IV IRES and has 39.6% aa sequence identity in the protein P1 to the corresponding protein of bat picornavirus (KJ641686, unassigned) and 42.7% and 53.5% aa sequence identity in the 2C and 3CD protein, respectively, to oscivirus (GU182410, genus Oscivirus). Interestingly, the L-protein of newt/II-5-Pilis/2014/HUN has conserved aa motifs that are similar to those found in phosphatase-1 catalytic (PP1C) subunit binding region (pfam10488) proteins. This second amphibian-origin picornavirus could represent a novel species and could be a founding member of a potential novel picornavirus genus.
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Affiliation(s)
- Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pecs, Hungary
- Department of Medical Microbiology and Immunology, University of Pécs, Szigeti út 12., Pecs, 7624, Hungary
| | - Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pecs, Hungary
- Department of Medical Microbiology and Immunology, University of Pécs, Szigeti út 12., Pecs, 7624, Hungary
| | - Zoltán Tóth
- Lendület Evolutionary Ecology Research Group, Plant Protection Institute, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pecs, Hungary.
- Department of Medical Microbiology and Immunology, University of Pécs, Szigeti út 12., Pecs, 7624, Hungary.
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19
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Marschang RE, Ihász K, Kugler R, Lengyel G, Fehér E, Marton S, Bányai K, Aqrawi T, Farkas SL. Development of a consensus reverse transcription PCR assay for the specific detection of tortoise picornaviruses. J Vet Diagn Invest 2016; 28:309-14. [DOI: 10.1177/1040638716628584] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Picornaviruses (PVs) of different terrestrial tortoise species, previously designated as Virus “X,” have been frequently detected from various tissues by virus isolation in Terrapene heart cell culture as the preferred laboratory method for diagnosis. Here, we describe the development of 2 diagnostic reverse transcription (RT)-PCR–based assays for the identification and characterization of tortoise PVs belonging to the tentative genus Topivirus. To test the novel diagnostic systems, PVs were isolated from swab and tissue samples collected in Germany, Italy, and Hungary between 2000 and 2013. All 25 tested isolates gave positive results with both novel consensus primer sets. Sequencing of the amplified products confirmed that all studied viruses were members of the new proposed genus Topivirus. Phylogenetic analyses clearly distinguished 2 lineages within the genus. Based on sequence analysis, no association was observed between the geographic distribution and genetic relatedness. Furthermore, no strict host specificity was indicated. The PCR-based diagnosis may provide a time-saving and sensitive method to detect tortoise PVs, and evaluation of PV presence in these animals may help control virus spread.
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Affiliation(s)
- Rachel E. Marschang
- LABOKLIN GmbH & Co. KG, Laboratory for Clinical Diagnostics, Bad Kissingen, Germany (Marschang)
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary (Ihász, Kugler, Fehér, Marton, Bányai, Farkas)
- Medical Centre of Hungarian Defense Forces, Force Health Laboratory Institute, Budapest, Hungary (Lengyel)
- FG für Umweltund Tierhygiene, University of Hohenheim, Stuttgart, Germany (Aqrawi)
| | - Katalin Ihász
- LABOKLIN GmbH & Co. KG, Laboratory for Clinical Diagnostics, Bad Kissingen, Germany (Marschang)
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary (Ihász, Kugler, Fehér, Marton, Bányai, Farkas)
- Medical Centre of Hungarian Defense Forces, Force Health Laboratory Institute, Budapest, Hungary (Lengyel)
- FG für Umweltund Tierhygiene, University of Hohenheim, Stuttgart, Germany (Aqrawi)
| | - Renáta Kugler
- LABOKLIN GmbH & Co. KG, Laboratory for Clinical Diagnostics, Bad Kissingen, Germany (Marschang)
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary (Ihász, Kugler, Fehér, Marton, Bányai, Farkas)
- Medical Centre of Hungarian Defense Forces, Force Health Laboratory Institute, Budapest, Hungary (Lengyel)
- FG für Umweltund Tierhygiene, University of Hohenheim, Stuttgart, Germany (Aqrawi)
| | - György Lengyel
- LABOKLIN GmbH & Co. KG, Laboratory for Clinical Diagnostics, Bad Kissingen, Germany (Marschang)
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary (Ihász, Kugler, Fehér, Marton, Bányai, Farkas)
- Medical Centre of Hungarian Defense Forces, Force Health Laboratory Institute, Budapest, Hungary (Lengyel)
- FG für Umweltund Tierhygiene, University of Hohenheim, Stuttgart, Germany (Aqrawi)
| | - Enikő Fehér
- LABOKLIN GmbH & Co. KG, Laboratory for Clinical Diagnostics, Bad Kissingen, Germany (Marschang)
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary (Ihász, Kugler, Fehér, Marton, Bányai, Farkas)
- Medical Centre of Hungarian Defense Forces, Force Health Laboratory Institute, Budapest, Hungary (Lengyel)
- FG für Umweltund Tierhygiene, University of Hohenheim, Stuttgart, Germany (Aqrawi)
| | - Szilvia Marton
- LABOKLIN GmbH & Co. KG, Laboratory for Clinical Diagnostics, Bad Kissingen, Germany (Marschang)
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary (Ihász, Kugler, Fehér, Marton, Bányai, Farkas)
- Medical Centre of Hungarian Defense Forces, Force Health Laboratory Institute, Budapest, Hungary (Lengyel)
- FG für Umweltund Tierhygiene, University of Hohenheim, Stuttgart, Germany (Aqrawi)
| | - Krisztián Bányai
- LABOKLIN GmbH & Co. KG, Laboratory for Clinical Diagnostics, Bad Kissingen, Germany (Marschang)
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary (Ihász, Kugler, Fehér, Marton, Bányai, Farkas)
- Medical Centre of Hungarian Defense Forces, Force Health Laboratory Institute, Budapest, Hungary (Lengyel)
- FG für Umweltund Tierhygiene, University of Hohenheim, Stuttgart, Germany (Aqrawi)
| | - Tara Aqrawi
- LABOKLIN GmbH & Co. KG, Laboratory for Clinical Diagnostics, Bad Kissingen, Germany (Marschang)
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary (Ihász, Kugler, Fehér, Marton, Bányai, Farkas)
- Medical Centre of Hungarian Defense Forces, Force Health Laboratory Institute, Budapest, Hungary (Lengyel)
- FG für Umweltund Tierhygiene, University of Hohenheim, Stuttgart, Germany (Aqrawi)
| | - Szilvia L. Farkas
- LABOKLIN GmbH & Co. KG, Laboratory for Clinical Diagnostics, Bad Kissingen, Germany (Marschang)
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary (Ihász, Kugler, Fehér, Marton, Bányai, Farkas)
- Medical Centre of Hungarian Defense Forces, Force Health Laboratory Institute, Budapest, Hungary (Lengyel)
- FG für Umweltund Tierhygiene, University of Hohenheim, Stuttgart, Germany (Aqrawi)
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20
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Pankovics P, Boros Á, Bíró H, Horváth KB, Phan TG, Delwart E, Reuter G. Novel picornavirus in domestic rabbits (Oryctolagus cuniculus var. domestica). INFECTION GENETICS AND EVOLUTION 2015; 37:117-22. [PMID: 26588888 PMCID: PMC7172602 DOI: 10.1016/j.meegid.2015.11.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/20/2015] [Accepted: 11/14/2015] [Indexed: 12/12/2022]
Abstract
Picornaviruses (family Picornaviridae) are small, non-enveloped viruses with positive sense, single-stranded RNA genomes. The numbers of the novel picornavirus species and genera are continuously increasing. Picornaviruses infect numerous vertebrate species from fish to mammals, but have not been identified in a member of the Lagomorpha order (pikas, hares and rabbits). In this study, a novel picornavirus was identified in 16 (28.6%) out of 56 faecal samples collected from clinically healthy rabbits (Oryctolagus cuniculus var. domestica) in two (one commercial and one family farms) of four rabbit farms in Hungary. The 8364 nucleotide (2486 amino acid) long complete genome sequence of strain Rabbit01/2013/HUN (KT325852) has typical picornavirus genome organization with type-V IRES at the 5'UTR, encodes a leader (L) and a single 2A(H-box/NC) proteins, contains a hepatitis-A-virus-like cis-acting replication element (CRE) in the 2A, but it does not contain the sequence forming a "barbell-like" secondary structure in the 3'UTR. Rabbit01/2013/HUN has 52.9%, 52% and 57.2% amino acid identity to corresponding proteins of species Aichivirus A (genus Kobuvirus): to murine Kobuvirus (JF755427) in P1, to canine Kobuvirus (JN387133) in P2 and to feline Kobuvirus (KF831027) in P3, respectively. The sequence and phylogenetic analysis indicated that Rabbit01/2013/HUN represents a novel picornavirus species possibly in genus Kobuvirus. This is the first report of detection of picornavirus in rabbit. Further study is needed to clarify whether this novel picornavirus plays a part in any diseases in domestic or wild rabbits.
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Affiliation(s)
- Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | | | - Katalin Barbara Horváth
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, USA; University of California, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.
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21
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Mor SK, Phelps NBD, Barbknecht M, Hoffman MA, Goyal SM. A multiplex RT-PCR assay for the detection of fish picornaviruses. J Virol Methods 2015; 221:131-4. [PMID: 25962537 DOI: 10.1016/j.jviromet.2015.04.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 12/23/2022]
Abstract
With the emergence of high profile fish diseases in the Great Lakes region, surveillance and regulatory inspections of fish populations have increased. This has resulted in a better understanding of known pathogens and isolation of many new pathogens of fish. In this study, a multiplex RT-PCR assay was developed for the detection of three newly discovered fish picornaviruses: bluegill picornavirus-1 (BGPV-1), fathead minnow picornavirus (FHMPV), and eel picornavirus-1 (EPV-1). This assay was found to be very sensitive with a detection limit of 81.9pg/μl of extracted RNA from a pool of FHMPV and BGPV-1 and was able to detect 501 and 224 gene copies/μl of BGPV-1 and FHMPV, respectively. The assay was highly reproducible and did not cross react with other closely related pathogens. We believe that this new assay provides a rapid and cost effective tool for confirming cell culture isolates and conducting prevalence studies of these newly detected fish picornaviruses.
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Affiliation(s)
- Sunil K Mor
- Minnesota Veterinary Diagnostic Laboratory, Department of Veterinary Population Medicine, University of Minnesota, 1333 Gortner Avenue Street, Paul, MN 55108, USA.
| | - Nicholas B D Phelps
- Minnesota Veterinary Diagnostic Laboratory, Department of Veterinary Population Medicine, University of Minnesota, 1333 Gortner Avenue Street, Paul, MN 55108, USA
| | - Marisa Barbknecht
- Department of Microbiology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, USA
| | - Michael A Hoffman
- Department of Microbiology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, USA
| | - Sagar M Goyal
- Minnesota Veterinary Diagnostic Laboratory, Department of Veterinary Population Medicine, University of Minnesota, 1333 Gortner Avenue Street, Paul, MN 55108, USA
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22
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Rabovirus: a proposed new picornavirus genus that is phylogenetically basal to enteroviruses and sapeloviruses. Arch Virol 2015; 160:2569-75. [PMID: 26168710 DOI: 10.1007/s00705-015-2523-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/02/2015] [Indexed: 01/28/2023]
Abstract
We have sequenced the genome of a novel picornavirus, rabovirus A (rat-borne virus, RaBoV-A, NC_026314), which was present in the feces of a Norway rat (Rattus norvegicus) from Berlin, Germany. This virus is related to members of the genera Enterovirus and Sapelovirus. RaboV-A contains a type II IRES that is unlike the type I IRES elements of enteroviruses and the type IV elements of sapeloviruses. Its genome is marked by an L protein and a chymotrypsin-like 2A protease. Our analysis of genome organization, pairwise identities, motif, phylogenic and UTR (GIMPU) indicates that RaBoV-A potentially represents a new picornavirus genus, for which we propose the name "Rabovirus". Spread by their rodent hosts and detected in New York and Berlin rats, these viruses may have a wide geographic distribution.
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23
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Reuter G, Boros Á, Tóth Z, Gia Phan T, Delwart E, Pankovics P. A highly divergent picornavirus in an amphibian, the smooth newt (Lissotriton vulgaris). J Gen Virol 2015; 96:2607-2613. [PMID: 26018961 DOI: 10.1099/vir.0.000198] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genetically highly divergent picornavirus (Newt/2013/HUN, KP770140) was detected using viral metagenomics in faecal samples of free-living smooth newts (Lissotriton vulgaris). Newt picornavirus was identified by reverse transcription-polymerase chain reaction (RT-PCR) in six (25 %) of the 24 samples originating from individuals caught in two out of the six investigated natural ponds in Hungary. The first picornavirus in amphibians expands the host range of members of the Picornaviridae, and opens a new research field in picornavirus evolution in lower vertebrates. Newt picornavirus represents a novel species in a novel genus within the family Picornaviridae, provisionally named genus Ampivirus (amphibian picornavirus).
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Affiliation(s)
- Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.,University of California, San Francisco, CA, USA.,Blood Systems Research Institute, San Francisco, CA, USA
| | - Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Zoltán Tóth
- Lendület Evolutionary Ecology Research Group, Plant Protection Institute, Hungarian Academy of Science, Budapest, Hungary
| | - Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, USA.,University of California, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA.,University of California, San Francisco, CA, USA
| | - Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
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24
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Xu WJ, Qin ZD, Shi H, Jiang N, Zhou Y, Liu XL, Xie JJ, Wang GS, Wang WM, Asim M, Zeng LB, Lin L. Mass mortality associated with a viral-induced anaemia in cage-reared large yellow croaker, Larimichthys crocea (Richardson). JOURNAL OF FISH DISEASES 2015; 38:499-502. [PMID: 24910090 DOI: 10.1111/jfd.12270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/05/2014] [Accepted: 05/07/2014] [Indexed: 06/03/2023]
Affiliation(s)
- W J Xu
- Marine Fisheries Research Institute of Zhejiang Province, Zhoushan, Zhejiang, China
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25
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Ng TFF, Wellehan JFX, Coleman JK, Kondov NO, Deng X, Waltzek TB, Reuter G, Knowles NJ, Delwart E. A tortoise-infecting picornavirus expands the host range of the family Picornaviridae. Arch Virol 2015; 160:1319-23. [PMID: 25721297 DOI: 10.1007/s00705-015-2366-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/09/2015] [Indexed: 12/26/2022]
Abstract
While picornaviruses can cause diseases in many mammals, little is known of their host range for replication in non-mammalian vertebrates. Here, a picornavirus in liver and kidney tissues from diseased Sulawesi tortoises (Indotestudo forsteni) was genetically characterized. Tortoise rafivirus A (ToRaV-A, KJ415177) represents a potential new genus in the family Picornaviridae, for which we propose the name "Rafivirus". Our finding confirms the susceptibility of reptiles to picornaviruses.
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26
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Boros Á, Pankovics P, Reuter G. Avian picornaviruses: molecular evolution, genome diversity and unusual genome features of a rapidly expanding group of viruses in birds. INFECTION GENETICS AND EVOLUTION 2014; 28:151-66. [PMID: 25278047 DOI: 10.1016/j.meegid.2014.09.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/15/2014] [Accepted: 09/21/2014] [Indexed: 12/29/2022]
Abstract
Picornaviridae is one of the most diverse families of viruses infecting vertebrate species. In contrast to the relative small number of mammal species compared to other vertebrates, the abundance of mammal-infecting picornaviruses was significantly overrepresented among the presently known picornaviruses. Therefore most of the current knowledge about the genome diversity/organization patterns and common genome features were based on the analysis of mammal-infecting picornaviruses. Beside the well known reservoir role of birds in case of several emerging viral pathogens, little is known about the diversity of picornaviruses circulating among birds, although in the last decade the number of known avian picornavirus species with complete genome was increased from one to at least 15. However, little is known about the geographic distribution, host spectrum or pathogenic potential of the recently described picornaviruses of birds. Despite the low number of known avian picornaviruses, the phylogenetic and genome organization diversity of these viruses were remarkable. Beside the common L-4-3-4 and 4-3-4 genome layouts unusual genome patterns (3-4-4; 3-5-4, 3-6-4; 3-8-4) with variable, multicistronic 2A genome regions were found among avian picornaviruses. The phylogenetic and genomic analysis revealed the presence of several conserved structures at the untranslated regions among phylogenetically distant avian and non-avian picornaviruses as well as at least five different avian picornavirus phylogenetic clusters located in every main picornavirus lineage with characteristic genome layouts which suggests the complex evolution history of these viruses. Based on the remarkable genetic diversity of the few known avian picornaviruses, the emergence of further divergent picornaviruses causing challenges in the current taxonomy and also in the understanding of the evolution and genome organization of picornaviruses will be strongly expected. In this review we would like to summarize the current knowledge about the taxonomy, pathogenic potential, phylogenetic/genomic diversity and evolutional relationship of avian picornaviruses.
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Affiliation(s)
- Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.
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27
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Liao Q, Zheng L, Yuan Y, Shi J, Zhang D. Genomic characterization of a novel picornavirus in Pekin ducks. Vet Microbiol 2014; 172:78-91. [DOI: 10.1016/j.vetmic.2014.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 04/28/2014] [Accepted: 05/03/2014] [Indexed: 12/26/2022]
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28
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Wang X, Liu N, Wang F, Ning K, Li Y, Zhang D. Genetic characterization of a novel duck-origin picornavirus with six 2A proteins. J Gen Virol 2014; 95:1289-1296. [PMID: 24659102 DOI: 10.1099/vir.0.063313-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A novel virus was detected from diseased ducks and completely determined. The virus was shown to have a picornavirus-like genome layout. Interestingly, the genome contained a total of up to six 2As, including four 2As (2A1-2A4) each having an NPGP motif, an AIG1-like 2A5, and a parechovirus-like 2A6. The 5'UTR was predicted to possess a hepacivirus/pestivirus-like internal ribosome entry site (IRES). However, the subdomain IIIe consisted of a 3 nt stem and five unpaired bases, distinct from those found in all other HP-like IRESs. The virus was most closely related to duck hepatitis A virus, with amino acid identities of 37.7 %, 39 % and 43.7 % in the P1, P2 and P3 regions, respectively. Based on these investigations, together with phylogenetic analyses, the virus could be considered as the founding member of a novel picornavirus genus that we tentatively named 'Aalivirus', with 'Aalivirus A' as the type species.
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Affiliation(s)
- Xiaoyan Wang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 2 Yuanmingyuan West Road, Haidian, Beijing 100193, PR China
| | - Ning Liu
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 2 Yuanmingyuan West Road, Haidian, Beijing 100193, PR China
| | - Fumin Wang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 2 Yuanmingyuan West Road, Haidian, Beijing 100193, PR China
| | - Kang Ning
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 2 Yuanmingyuan West Road, Haidian, Beijing 100193, PR China
| | - Yanbo Li
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 2 Yuanmingyuan West Road, Haidian, Beijing 100193, PR China
| | - Dabing Zhang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 2 Yuanmingyuan West Road, Haidian, Beijing 100193, PR China
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29
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Lange J, Groth M, Fichtner D, Granzow H, Keller B, Walther M, Platzer M, Sauerbrei A, Zell R. Virus isolate from carp: genetic characterization reveals a novel picornavirus with two aphthovirus 2A-like sequences. J Gen Virol 2014; 95:80-90. [PMID: 24337965 DOI: 10.1099/vir.0.058172-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Picornaviruses have been isolated from a variety of hosts, mainly mammals and birds. Here, we describe the sequence analysis of carp picornavirus 1 (CPV-1) F37/06 that was isolated from an organ pool (heart, brain, liver) of a common carp (Cyprinus carpio). This carp perished after an accidental discharge of liquid manure into a fish pond and presented without obvious clinical symptoms. Experimental intraperitoneal infection of young carp with CPV-1 revealed no clinical signs, but the virus was re-isolated from various organs. Sequence analysis of almost the complete genome (7632 nt excluding the poly-A tract) revealed a novel picornavirus clade. In phylogenetic trees, the polymerase sequence clusters with parechoviruses, duck hepatitis A virus, eel picornavirus and aquamavirus A. The ORF includes 6807 nt and encodes a polyprotein of 2269 amino acids. CPV-1 has a genome layout like that of picornaviruses except for the presence of two aphthovirus 2A-like NPGP sequence motifs: VPg+5'UTR[1AB-1C-1D-2A1(npgp)/2A2(npgp)-2B-2C(ATPase)/3A-3B(VPg)-3C(pro)-3D(pol)]3'UTR-poly-A. 2A1(npgp) and 2A2(npgp) are separated by 133 amino acids. The proteins 2A2(npgp), 2B, 3A and 3B(VPg) have no significant similarity to the corresponding proteins of other picornaviruses. Amino acid identities of the orthologous proteins P1, 2C, 3C(pro) and 3D(pol) range from 16.4 to 40.8 % in the eel picornavirus/CPV-1 comparison. 3D(pol) shows the closest similarity to eel picornavirus, with an amino acid identity of 40.8 %, followed by human parechovirus (36.5 %), duck hepatitis A virus (32.7 %) and swine pasivirus (29.3 %). Both the unique genome organization and low sequence similarity support the assignment of CPV-1 to a novel picornavirus species within a novel genus.
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Affiliation(s)
- Jeannette Lange
- Department of Virology and Antiviral Therapy, Jena University Hospital, Friedrich Schiller University, Hans Knoell Str. 2, 07745 Jena, Germany
| | - Marco Groth
- Genome Analysis, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Dieter Fichtner
- Institute of Infectiology, Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Harald Granzow
- Institute of Infectiology, Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Barbara Keller
- Lower Saxony State Office for Consumer Protection and Food Safety, Eintrachtweg 17, 30173 Hannover, Germany
| | - Mario Walther
- Institute of Medical Statistics, Computer Sciences and Documentation, Jena University Hospital, Friedrich Schiller University Jena, 07740 Jena, Germany
| | - Matthias Platzer
- Genome Analysis, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Andreas Sauerbrei
- Department of Virology and Antiviral Therapy, Jena University Hospital, Friedrich Schiller University, Hans Knoell Str. 2, 07745 Jena, Germany
| | - Roland Zell
- Department of Virology and Antiviral Therapy, Jena University Hospital, Friedrich Schiller University, Hans Knoell Str. 2, 07745 Jena, Germany
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30
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Phelps NBD, Mor SK, Armien AG, Batts W, Goodwin AE, Hopper L, McCann R, Ng TFF, Puzach C, Waltzek TB, Delwart E, Winton J, Goyal SM. Isolation and molecular characterization of a novel picornavirus from baitfish in the USA. PLoS One 2014; 9:e87593. [PMID: 24586283 PMCID: PMC3931614 DOI: 10.1371/journal.pone.0087593] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 12/23/2013] [Indexed: 12/15/2022] Open
Abstract
During both regulatory and routine surveillance sampling of baitfish from the states of Illinois, Minnesota, Montana, and Wisconsin, USA, isolates (n = 20) of a previously unknown picornavirus were obtained from kidney/spleen or entire viscera of fathead minnows (Pimephales promelas) and brassy minnows (Hybognathus hankinsoni). Following the appearance of a diffuse cytopathic effect, examination of cell culture supernatant by negative contrast electron microscopy revealed the presence of small, round virus particles (∼ 30-32 nm), with picornavirus-like morphology. Amplification and sequence analysis of viral RNA identified the agent as a novel member of the Picornaviridae family, tentatively named fathead minnow picornavirus (FHMPV). The full FHMPV genome consisted of 7834 nucleotides. Phylogenetic analysis based on 491 amino acid residues of the 3D gene showed 98.6% to 100% identity among the 20 isolates of FHMPV compared in this study while only 49.5% identity with its nearest neighbor, the bluegill picornavirus (BGPV) isolated from bluegill (Lepomis macrochirus). Based on complete polyprotein analysis, the FHMPV shared 58% (P1), 33% (P2) and 43% (P3) amino acid identities with BGPV and shared less than 40% amino acid identity with all other picornaviruses. Hence, we propose the creation of a new genus (Piscevirus) within the Picornaviridae family. The impact of FHMPV on the health of fish populations is unknown at present.
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Affiliation(s)
- Nicholas B. D. Phelps
- Minnesota Veterinary Diagnostic Laboratory, St. Paul, Minnesota, United States of America
- University of Minnesota, Department of Veterinary Population Medicine, St. Paul, Minnesota, United States of America
| | - Sunil K. Mor
- Minnesota Veterinary Diagnostic Laboratory, St. Paul, Minnesota, United States of America
| | - Anibal G. Armien
- Minnesota Veterinary Diagnostic Laboratory, St. Paul, Minnesota, United States of America
- University of Minnesota, Department of Veterinary Population Medicine, St. Paul, Minnesota, United States of America
| | - William Batts
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, Washington, United States of America
| | - Andrew E. Goodwin
- U.S. Fish and Wildlife Service, Portland, Oregon, United States of America
| | - Lacey Hopper
- U.S. Fish and Wildlife Service, Bozeman Fish Health Center, Bozeman, Montana, United States of America
| | - Rebekah McCann
- U.S. Fish and Wildlife Service, La Crosse Fish Health Center, Onalaska, Wisconsin, United States of America
| | - Terry Fei Fan Ng
- Blood Systems Research Institute, San Francisco, California, United States of America
- University of California, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Corey Puzach
- U.S. Fish and Wildlife Service, La Crosse Fish Health Center, Onalaska, Wisconsin, United States of America
| | - Thomas B. Waltzek
- University of Florida, College of Veterinary Medicine, Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
- University of California, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - James Winton
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, Washington, United States of America
| | - Sagar M. Goyal
- Minnesota Veterinary Diagnostic Laboratory, St. Paul, Minnesota, United States of America
- University of Minnesota, Department of Veterinary Population Medicine, St. Paul, Minnesota, United States of America
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Barbknecht M, Sepsenwol S, Leis E, Tuttle-Lau M, Gaikowski M, Knowles NJ, Lasee B, Hoffman MA. Characterization of a new picornavirus isolated from the freshwater fish Lepomis macrochirus. J Gen Virol 2013; 95:601-613. [PMID: 24337169 DOI: 10.1099/vir.0.061960-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The freshwater fish Lepomis macrochirus (bluegill) is common to North American waters, and important both ecologically and as a sport fish. In 2001 an unknown virus was isolated from bluegills following a bluegill fish kill. This virus was identified as a picornavirus [termed bluegill picornavirus (BGPV)] and a diagnostic reverse transcriptase PCR was developed. A survey of bluegills in Wisconsin waters showed the presence of BGPV in 5 of 17 waters sampled, suggesting the virus is widespread in bluegill populations. Experimental infections of bluegills confirmed that BGPV can cause morbidity and mortality in bluegills. Molecular characterization of BGPV revealed several distinct genome characteristics, the most unusual of which is the presence of a short poly(C) tract in the 3' UTR. Additionally, the genome encodes a polyprotein lacking a leader peptide and a VP0 maturation cleavage site, and is predicted to encode two distinct 2A proteins. Sequence comparison showed that the virus is most closely related to a phylogenetic cluster of picornaviruses that includes the genera Aquamavirus, Avihepatovirus and Parechovirus. However, it is distinct enough, for example sharing only about 38% sequence identity to the parechoviruses in the 3D region, that it may represent a new genus in the family Picornaviridae.
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Affiliation(s)
- Marisa Barbknecht
- Department of Microbiology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI, 54601, USA
| | - Sol Sepsenwol
- Department of Biology, University of Wisconsin-Stevens Point, 2100 Main Street, Stevens Point, WI, 54481, USA
| | - Eric Leis
- US Fish and Wildlife Service, La Crosse Fish Health Center, 555 Lester Avenue, Onalaska, WI, 54650, USA
| | - Maren Tuttle-Lau
- US Geological Survey-Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Road, La Crosse, WI, 54603, USA.,US Fish and Wildlife Service, La Crosse Fish Health Center, 555 Lester Avenue, Onalaska, WI, 54650, USA
| | - Mark Gaikowski
- US Geological Survey-Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Road, La Crosse, WI, 54603, USA
| | - Nick J Knowles
- Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Becky Lasee
- US Fish and Wildlife Service, La Crosse Fish Health Center, 555 Lester Avenue, Onalaska, WI, 54650, USA
| | - Michael A Hoffman
- Department of Microbiology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI, 54601, USA
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