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Kembou-Ringert JE, Hotio FN, Steinhagen D, Thompson KD, Surachetpong W, Rakus K, Daly JM, Goonawardane N, Adamek M. Knowns and unknowns of TiLV-associated neuronal disease. Virulence 2024; 15:2329568. [PMID: 38555518 PMCID: PMC10984141 DOI: 10.1080/21505594.2024.2329568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Tilapia Lake Virus (TiLV) is associated with pathological changes in the brain of infected fish, but the mechanisms driving the virus's neuropathogenesis remain poorly characterized. TiLV establishes a persistent infection in the brain of infected fish even when the virus is no longer detectable in the peripheral organs, rendering therapeutic interventions and disease management challenging. Moreover, the persistence of the virus in the brain may pose a risk for viral reinfection and spread and contribute to ongoing tissue damage and neuroinflammatory processes. In this review, we explore TiLV-associated neurological disease. We discuss the possible mechanism(s) used by TiLV to enter the central nervous system (CNS) and examine TiLV-induced neuroinflammation and brain immune responses. Lastly, we discuss future research questions and knowledge gaps to be addressed to significantly advance this field.
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Affiliation(s)
- Japhette E. Kembou-Ringert
- Department of infection, immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Fortune N. Hotio
- Department of Animal Biology, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Dieter Steinhagen
- Fish Disease Research Unit, Institute for parasitology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Kim D. Thompson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK
| | - Win Surachetpong
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Krzysztof Rakus
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Janet M. Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Niluka Goonawardane
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Mikolaj Adamek
- Fish Disease Research Unit, Institute for parasitology, University of Veterinary Medicine Hannover, Hannover, Germany
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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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Parry RH, Slonchak A, Campbell LJ, Newton ND, Debat HJ, Gifford RJ, Khromykh AA. A novel tamanavirus ( Flaviviridae) of the European common frog ( Rana temporaria) from the UK. J Gen Virol 2023; 104:001927. [PMID: 38059479 PMCID: PMC10770923 DOI: 10.1099/jgv.0.001927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023] Open
Abstract
Flavivirids are small, enveloped, positive-sense RNA viruses from the family Flaviviridae with genomes of ~9-13 kb. Metatranscriptomic analyses of metazoan organisms have revealed a diversity of flavivirus-like or flavivirid viral sequences in fish and marine invertebrate groups. However, no flavivirus-like virus has been identified in amphibians. To remedy this, we investigated the virome of the European common frog (Rana temporaria) in the UK, utilizing high-throughput sequencing at six catch locations. De novo assembly revealed a coding-complete virus contig of a novel flavivirid ~11.2 kb in length. The virus encodes a single ORF of 3456 aa and 5' and 3' untranslated regions (UTRs) of 227 and 666 nt, respectively. We named this virus Rana tamanavirus (RaTV), as BLASTp analysis of the polyprotein showed the closest relationships to Tamana bat virus (TABV) and Cyclopterus lumpus virus from Pteronotus parnellii and Cyclopterus lumpus, respectively. Phylogenetic analysis of the RaTV polyprotein compared to Flavivirus and Flavivirus-like members indicated that RaTV was sufficiently divergent and basal to the vertebrate Tamanavirus clade. In addition to the Mitcham strain, partial but divergent RaTV, sharing 95.64-97.39 % pairwise nucleotide identity, were also obtained from the Poole and Deal samples, indicating that RaTV is widespread in UK frog samples. Bioinformatic analyses of predicted secondary structures in the 3'UTR of RaTV showed the presence of an exoribonuclease-resistant RNA (xrRNA) structure standard in flaviviruses and TABV. To examine this biochemically, we conducted an in vitro Xrn1 digestion assay showing that RaTV probably forms a functional Xrn1-resistant xrRNA.
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Affiliation(s)
- Rhys H. Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Andrii Slonchak
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Lewis J. Campbell
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Institute of Zoology, Zoological Society of London, London, UK
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - Natalee D. Newton
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Humberto J. Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola (UFYMA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5020ICA, Argentina
| | | | - Alexander A. Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
- AIDRC Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
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Grimwood RM, Fortune-Kelly G, Holmes EC, Ingram T, Geoghegan JL. Host specificity shapes fish viromes across lakes on an isolated remote island. Virology 2023; 587:109884. [PMID: 37757732 DOI: 10.1016/j.virol.2023.109884] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Fish viromes often provide insights into the origin and evolution of viruses affecting tetrapods, including those associated with imporant human diseases. However, despite fish being the most diverse vertebrate group, their viruses are still understudied. We investigated the viromes of fish on Chatham Island (Rēkohu), a geographically isolated island housing 9% of New Zealand's threatened endemic fish species. Using metatranscriptomics, we analyzed samples from seven host species across 16 waterbodies. We identified 19 fish viruses, including 16 potentially novel species, expanding families such as the Coronaviridae, Hantaviridae, Poxviridae, and the recently proposed Tosoviridae. Surprisingly, virome composition was not influenced by the ecological factors measured and smelt (Retropinna retropinna) viromes were consistent across lakes despite differences in host life history, seawater influence, and community richness. Overall, fish viromes across Rēkohu were highly diverse and revealed a long history of co-divergence between host and virus despite their unique and geographically isolated ecosystem.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | | | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Travis Ingram
- Department of Zoology, University of Otago, Dunedin, 9016, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand; Institute of Environmental Science and Research, Wellington, 5018, New Zealand.
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Rao SS, Lunde HS, Dolan DWP, Fond AK, Petersen K, Haugland GT. Transcriptome-wide analyses of early immune responses in lumpfish leukocytes upon stimulation with poly(I:C). Front Immunol 2023; 14:1198211. [PMID: 37388730 PMCID: PMC10300353 DOI: 10.3389/fimmu.2023.1198211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/26/2023] [Indexed: 07/01/2023] Open
Abstract
Background Both bacterial and viral diseases are a major threat to farmed fish. As the antiviral immune mechanisms in lumpfish (Cyclopterus lumpus L.) are poorly understood, lumpfish leukocytes were stimulated with poly(I:C), a synthetic analog of double stranded RNA, which mimic viral infections, and RNA sequencing was performed. Methods To address this gap, we stimulated lumpfish leukocytes with poly(I:C) for 6 and 24 hours and did RNA sequencing with three parallels per timepoint. Genome guided mapping was performed to define differentially expressed genes (DEGs). Results Immune genes were identified, and transcriptome-wide analyses of early immune responses showed that 376 and 2372 transcripts were significantly differentially expressed 6 and 24 hours post exposure (hpe) to poly(I:C), respectively. The most enriched GO terms when time had been accounted for, were immune system processes (GO:0002376) and immune response (GO:0006955). Analysis of DEGs showed that among the most highly upregulated genes were TLRs and genes belonging to the RIG-I signaling pathway, including LGP2, STING and MX, as well as IRF3 and IL12A. RIG-I was not identified, but in silico analyses showed that genes encoding proteins involved in pathogen recognition, cell signaling, and cytokines of the TLR and RIG-I signaling pathway are mostly conserved in lumpfish when compared to mammals and other teleost species. Conclusions Our analyses unravel the innate immune pathways playing a major role in antiviral defense in lumpfish. The information gathered can be used in comparative studies and lay the groundwork for future functional analyses of immune and pathogenicity mechanisms. Such knowledge is also necessary for the development of immunoprophylactic measures for lumpfish, which is extensively cultivated for use as cleaner fish in the aquaculture for removal of sea lice from Atlantic salmon (Salmo salar L.).
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Affiliation(s)
- Shreesha S. Rao
- Department of Biological Sciences, Bergen High-Technology Centre, University of Bergen, Bergen, Norway
| | - Harald S. Lunde
- Department of Biological Sciences, Bergen High-Technology Centre, University of Bergen, Bergen, Norway
| | - David W. P. Dolan
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Amanda K. Fond
- Department of Biological Sciences, Bergen High-Technology Centre, University of Bergen, Bergen, Norway
| | - Kjell Petersen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Gyri T. Haugland
- Department of Biological Sciences, Bergen High-Technology Centre, University of Bergen, Bergen, Norway
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6
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Mifsud JCO, Costa VA, Petrone ME, Marzinelli EM, Holmes EC, Harvey E. Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians. Virus Evol 2022; 9:veac124. [PMID: 36694816 PMCID: PMC9854234 DOI: 10.1093/ve/veac124] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 12/27/2022] Open
Abstract
The flavivirids (family Flaviviridae) are a group of positive-sense RNA viruses that include well-documented agents of human disease. Despite their importance and ubiquity, the timescale of flavivirid evolution is uncertain. An ancient origin, spanning millions of years, is supported by their presence in both vertebrates and invertebrates and by the identification of a flavivirus-derived endogenous viral element in the peach blossom jellyfish genome (Craspedacusta sowerbii, phylum Cnidaria), implying that the flaviviruses arose early in the evolution of the Metazoa. To date, however, no exogenous flavivirid sequences have been identified in these hosts. To help resolve the antiquity of the Flaviviridae, we mined publicly available transcriptome data across the Metazoa. From this, we expanded the diversity within the family through the identification of 32 novel viral sequences and extended the host range of the pestiviruses to include amphibians, reptiles, and ray-finned fish. Through co-phylogenetic analysis we found cross-species transmission to be the predominate macroevolutionary event across the non-vectored flavivirid genera (median, 68 per cent), including a cross-species transmission event between bats and rodents, although long-term virus-host co-divergence was still a regular occurrence (median, 23 per cent). Notably, we discovered flavivirus-like sequences in basal metazoan species, including the first associated with Cnidaria. This sequence formed a basal lineage to the genus Flavivirus and was closer to arthropod and crustacean flaviviruses than those in the tamanavirus group, which includes a variety of invertebrate and vertebrate viruses. Combined, these data attest to an ancient origin of the flaviviruses, likely close to the emergence of the metazoans 750-800 million years ago.
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Affiliation(s)
- Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Vincenzo A Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Mary E Petrone
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney NSW 2006, Australia
- Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW 2088, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551 Singapore
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia
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7
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Abstract
Flaviviruses are positive-sense single-stranded RNA viruses, including some well-known human pathogens such as Zika, dengue, and yellow fever viruses, which are primarily associated with mosquito and tick vectors. The vast majority of flavivirus research has focused on terrestrial environments; however, recent findings indicate that a range of flaviviruses are also present in aquatic environments, both marine and freshwater. These flaviviruses are found in various hosts, including fish, crustaceans, molluscs, and echinoderms. Although the effects of aquatic flaviviruses on the hosts they infect are not all known, some have been detected in farmed species and may have detrimental effects on the aquaculture industry. Exploration of the evolutionary history through the discovery of the Wenzhou shark flavivirus in both a shark and crab host is of particular interest since the potential dual-host nature of this virus may indicate that the invertebrate-vertebrate relationship seen in other flaviviruses may have a more profound evolutionary root than previously expected. Potential endogenous viral elements and the range of novel aquatic flaviviruses discovered thus shed light on virus origins and evolutionary history and may indicate that, like terrestrial life, the origins of flaviviruses may lie in aquatic environments.
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Affiliation(s)
- Megan J. Lensink
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Yiqiao Li
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Sebastian Lequime
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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8
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Bamford CGG, de Souza WM, Parry R, Gifford RJ. Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae). Virus Evol 2022; 8:veac085. [PMID: 36533146 PMCID: PMC9752770 DOI: 10.1093/ve/veac085] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/06/2022] [Accepted: 09/05/2022] [Indexed: 01/24/2023] Open
Abstract
Flavivirids (family Flaviviridae) are a group of positive-strand ribonucleic acid (RNA) viruses that pose serious risks to human and animal health on a global scale. Here, we use flavivirid-derived deoxyribonucleic acid (DNA) sequences, identified in animal genomes, to reconstruct the long-term evolutionary history of family Flaviviridae. We demonstrate that flavivirids are >100 million years old and show that this timing can be combined with dates inferred from co-phyletic analysis to produce a cohesive overview of their evolution, distribution, and diversity wherein the main flavivirid subgroups originate in early animals and broadly co-diverge with major animal phyla. In addition, we reveal evidence that the 'classical flaviviruses' of vertebrates, most of which are transmitted via blood-feeding arthropod vectors, originally evolved in haematophagous arachnids and later acquired the capacity to be transmitted by insects. Our findings imply that the biological properties of flavivirids have been acquired gradually over the course of animal evolution. Thus, broad-scale comparative analysis will likely reveal fundamental insights into their biology. We therefore published our results via an open, extensible, database (Flavivirid-GLUE), which we constructed to facilitate the wider utilisation of genomic data and evolution-related domain knowledge in flavivirid research.
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Campbell LJ, Castillo NA, Dunn CD, Perez A, Schmitter-Soto JJ, Mejri SC, Boucek RE, Corujo RS, Adams AJ, Rehage JS, Goldberg TL. Viruses of Atlantic Bonefish ( Albula vulpes) in Florida and the Caribbean show geographic patterns consistent with population declines. ENVIRONMENTAL BIOLOGY OF FISHES 2022; 106:303-317. [PMID: 35965638 PMCID: PMC9362051 DOI: 10.1007/s10641-022-01306-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Atlantic Bonefish (Albula vulpes) are economically important due to their popularity with recreational anglers. In the State of Florida, USA, bonefish population numbers declined by approximately 60% between the 1990s and 2015. Habitat loss, water quality impairment, chemical inputs, and other anthropogenic factors have been implicated as causes, but the role of pathogens has been largely overlooked, especially with respect to viruses. We used a metagenomic approach to identify and quantify viruses in the blood of 103 A. vulpes sampled throughout their Western Atlantic range, including populations in Florida that have experienced population declines and populations in Belize, Mexico, Puerto Rico, and The Bahamas that have remained apparently stable. We identified four viruses, all of which are members of families known to infect marine fishes (Flaviviridae, Iflaviridae, Narnaviridae, and Nodaviridae), but all of which were previously undescribed. Bonefish from Florida and Mexico had higher viral richness (numbers of distinct viruses per individual fish) than fish sampled from other areas, and bonefish from the Upper Florida Keys had the highest prevalence of viral infection (proportion of positive fish) than fish sampled from any other location. Bonefish from Florida also had markedly higher viral loads than fish sampled from any other area, both for a novel narnavirus and for all viruses combined. Bonefish viruses may be indicators of environmentally driven physiological and immunological compromise, causes of ill health, or both. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10641-022-01306-9.
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Affiliation(s)
- Lewis J. Campbell
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
| | - Nicholas A. Castillo
- Department of Earth and Environment, Florida International University, Miami, FL USA
| | - Christopher D. Dunn
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
| | | | - Juan J. Schmitter-Soto
- Departamento de Sistemática y Ecología Acuática, El Colegio de la Frontera Sur, Q.R, Campeche, Mexico
| | - Sahar C. Mejri
- Department of Aquaculture and Stock Enhancement, Florida Atlantic University, Fort Pierce, FL USA
| | | | | | - Aaron J. Adams
- Bonefish & Tarpon Trust, Miami, FL USA
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL USA
| | - Jennifer S. Rehage
- Department of Earth and Environment, Florida International University, Miami, FL USA
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
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Mjølnerød EB, Srivastava A, Moore LJ, Plarre H, Nylund A. Identification of housekeeping genes of Candidatus Branchiomonas cysticola associated with epitheliocystis in Atlantic salmon (Salmo salar L.). Arch Microbiol 2022; 204:365. [PMID: 35661924 PMCID: PMC9167185 DOI: 10.1007/s00203-022-02966-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022]
Abstract
Candidatus Branchiomonas cysticola is an intracellular, gram-negative Betaproteobacteria causing epitheliocystis in Atlantic Salmon (Salmo salar L.). The bacterium has not been genetically characterized at the intraspecific level despite its high prevalence among salmon suffering from gill disease in Norwegian aquaculture. DNA from gill samples of Atlantic salmon PCR positive for Cand. B. cysticola and displaying pathological signs of gill disease, was, therefore, extracted and subject to next-generation sequencing (mNGS). Partial sequences of four housekeeping (HK) genes (aceE, lepA, rplB, rpoC) were ultimately identified from the sequenced material. Assays for real-time RT-PCR and fluorescence in-situ hybridization, targeting the newly acquired genes, were simultaneously applied with existing assays targeting the previously characterized 16S rRNA gene. Agreement in both expression and specificity between these putative HK genes and the 16S gene was observed in all instances, indicating that the partial sequences of these HK genes originate from Cand. B. cysticola. The knowledge generated from the present study constitutes a major prerequisite for the future design of novel genotyping schemes for this bacterium.
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Affiliation(s)
- Even Bysveen Mjølnerød
- Department of Biological Sciences, Fish Disease Research Group, University of Bergen, PO Box 7803, 5020, Bergen, Norway.
| | - Aashish Srivastava
- Department of Clinical Science, University of Bergen, PO Box 7804, 5020, Bergen, Norway
| | - Lindsey J Moore
- Department of Biological Sciences, Fish Disease Research Group, University of Bergen, PO Box 7803, 5020, Bergen, Norway
| | - Heidrun Plarre
- Department of Biological Sciences, Fish Disease Research Group, University of Bergen, PO Box 7803, 5020, Bergen, Norway
| | - Are Nylund
- Department of Biological Sciences, Fish Disease Research Group, University of Bergen, PO Box 7803, 5020, Bergen, Norway
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11
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Establishment and Characterization of a Novel Gill Cell Line, LG-1, from Atlantic Lumpfish ( Cyclopterus lumpus L.). Cells 2021; 10:cells10092442. [PMID: 34572091 PMCID: PMC8467979 DOI: 10.3390/cells10092442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/19/2021] [Accepted: 09/04/2021] [Indexed: 11/17/2022] Open
Abstract
The use of lumpfish (Cyclopterus lumpus) as a cleaner fish to fight sea lice infestation in farmed Atlantic salmon has become increasingly common. Still, tools to increase our knowledge about lumpfish biology are lacking. Here, we successfully established and characterized the first Lumpfish Gill cell line (LG-1). LG-1 are adherent, homogenous and have a flat, stretched-out and almost transparent appearance. Transmission electron microscopy revealed cellular protrusions and desmosome-like structures that, together with their ability to generate a transcellular epithelial/endothelial resistance, suggest an epithelial or endothelial cell type. Furthermore, the cells exert Cytochrome P450 1A activity. LG-1 supported the propagation of several viruses that may lead to severe infectious diseases with high mortalities in fish farming, including viral hemorrhagic septicemia virus (VHSV) and infectious hematopoietic necrosis virus (IHNV). Altogether, our data indicate that the LG-1 cell line originates from an epithelial or endothelial cell type and will be a valuable in vitro research tool to study gill cell function as well as host-pathogen interactions in lumpfish.
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12
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Zammit A, Helwerda L, Olsthoorn RCL, Verbeek FJ, Gultyaev AP. A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions. Bioinformatics 2021; 37:956-962. [PMID: 32866223 PMCID: PMC8128465 DOI: 10.1093/bioinformatics/btaa759] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
Motivation The Flavivirus genus includes several important pathogens, such as Zika, dengue and yellow fever virus. Flavivirus RNA genomes contain a number of functionally important structures in their 3′ untranslated regions (3′UTRs). Due to the diversity of sequences and topologies of these structures, their identification is often difficult. In contrast, predictions of such structures are important for understanding of flavivirus replication cycles and development of antiviral strategies. Results We have developed an algorithm for structured pattern search in RNA sequences, including secondary structures, pseudoknots and triple base interactions. Using the data on known conserved flavivirus 3′UTR structures, we constructed structural descriptors which covered the diversity of patterns in these motifs. The descriptors and the search algorithm were used for the construction of a database of flavivirus 3′UTR structures. Validating this approach, we identified a number of domains matching a general pattern of exoribonuclease Xrn1-resistant RNAs in the growing group of insect-specific flaviviruses. Availability and implementation The Leiden Flavivirus RNA Structure Database is available at https://rna.liacs.nl. The search algorithm is available at https://github.com/LeidenRNA/SRHS. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alan Zammit
- Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - Leon Helwerda
- Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - René C L Olsthoorn
- Group Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
| | - Fons J Verbeek
- Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - Alexander P Gultyaev
- Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands.,Department of Viroscience, Erasmus Medical Center, Rotterdam, 3000 CA, The Netherlands
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13
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Kobayashi D, Watanabe M, Faizah AN, Amoa-Bosompem M, Higa Y, Tsuda Y, Sawabe K, Isawa H. Discovery of a Novel Flavivirus (Flaviviridae) From the Horse Fly, Tabanus rufidens (Diptera: Tabanidae): The Possible Coevolutionary Relationships Between the Classical Insect-Specific Flaviviruses and Host Dipteran Insects. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:880-890. [PMID: 33710314 DOI: 10.1093/jme/tjaa193] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Indexed: 06/12/2023]
Abstract
Tabanid flies (Tabanidae: Diptera) are common hematophagous insects known to transmit some pathogens mechanically or biologically to animals; they are widely distributed throughout the world. However, no tabanid-borne viruses, except mechanically transmitted viruses, have been reported to date. In this study, we conducted RNA virome analysis of several human-biting tabanid species in Japan, to discover and characterize viruses associated with tabanids. A novel flavivirus was encountered during the study in the Japanese horse fly, Tabanus rufidens (Bigot, 1887). The virus was detected only in T. rufidens, but not in other tabanid species, and as such was designated Tabanus rufidens flavivirus (TrFV). TrFV could not be isolated using a mammalian cell line and showed a closer phylogenetic relationship to the classical insect-specific flaviviruses (cISFs) rather than the vertebrate-infecting flaviviruses (VIFs), suggesting that it is a novel member of the cISFs. The first discovery of a cISF from Brachycera provides new insight into the evolutionary history and dynamics of flaviviruses.
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Affiliation(s)
- Daisuke Kobayashi
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
- Department of Research Promotion, Japan Agency for Medical Research and Development, Otemachi, Chiyoda-ku, Tokyo, Japan
| | - Mamoru Watanabe
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Astri Nur Faizah
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Michael Amoa-Bosompem
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Yukiko Higa
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Yoshio Tsuda
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Kyoko Sawabe
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Haruhiko Isawa
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
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14
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Harima H, Orba Y, Torii S, Qiu Y, Kajihara M, Eto Y, Matsuta N, Hang'ombe BM, Eshita Y, Uemura K, Matsuno K, Sasaki M, Yoshii K, Nakao R, Hall WW, Takada A, Abe T, Wolfinger MT, Simuunza M, Sawa H. An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3'-untranslated region. Sci Rep 2021; 11:4883. [PMID: 33649491 PMCID: PMC7921595 DOI: 10.1038/s41598-021-84365-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa. Herein, we report that a novel flavivirus, Mpulungu flavivirus (MPFV), was discovered in a Rhipicephalus muhsamae tick in Zambia. MPFV was found to be genetically related to Ngoye virus detected in ticks in Senegal, and these viruses formed a unique lineage in the genus Flavivirus. Analyses of dinucleotide contents of flaviviruses indicated that MPFV was similar to those of other TBFVs with a typical vertebrate genome signature, suggesting that MPFV may infect vertebrate hosts. Bioinformatic analyses of the secondary structures in the 3′-untranslated regions (UTRs) revealed that MPFV exhibited unique exoribonuclease-resistant RNA (xrRNA) structures. Utilizing biochemical approaches, we clarified that two xrRNA structures of MPFV in the 3′-UTR could prevent exoribonuclease activity. In summary, our findings provide new information regarding the geographical distribution of TBFV and xrRNA structures in the 3′-UTR of flaviviruses.
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Affiliation(s)
- Hayato Harima
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shiho Torii
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yongjin Qiu
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshiki Eto
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoya Matsuta
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Bernard M Hang'ombe
- Department of Para-Clinical Studies, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia
| | - Yuki Eshita
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Uemura
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Keita Matsuno
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Yoshii
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - William W Hall
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, Ireland.,Centre for Research in Infectious Diseases, School of Medicine, University College Dublin, Dublin, Ireland.,Global Virus Network, Baltimore, MD, USA
| | - Ayato Takada
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Takashi Abe
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Martin Simuunza
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia. .,Global Virus Network, Baltimore, MD, USA. .,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.
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15
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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: 22] [Impact Index Per Article: 7.3] [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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16
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Hewson I, Johnson MR, Tibbetts IR. An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome. Viruses 2020; 12:v12091057. [PMID: 32972018 PMCID: PMC7551563 DOI: 10.3390/v12091057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022] Open
Abstract
Sea cucumbers (Holothuroidea; Echinodermata) are ecologically significant constituents of benthic marine habitats. We surveilled RNA viruses inhabiting eight species (representing four families) of holothurian collected from four geographically distinct locations by viral metagenomics, including a single specimen of Apostichopus californicus affected by a hitherto undocumented wasting disease. The RNA virome comprised genome fragments of both single-stranded positive sense and double stranded RNA viruses, including those assigned to the Picornavirales, Ghabrivirales, and Amarillovirales. We discovered an unconventional flavivirus genome fragment which was most similar to a shark virus. Ghabivirales-like genome fragments were most similar to fungal totiviruses in both genome architecture and homology and had likely infected mycobiome constituents. Picornavirales, which are commonly retrieved in host-associated viral metagenomes, were similar to invertebrate transcriptome-derived picorna-like viruses. The greatest number of viral genome fragments was recovered from the wasting A. californicus library compared to the asymptomatic A. californicus library. However, reads from the asymptomatic library recruited to nearly all recovered wasting genome fragments, suggesting that they were present but not well represented in the grossly normal specimen. These results expand the known host range of flaviviruses and suggest that fungi and their viruses may play a role in holothurian ecology.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA;
- Correspondence: ; Tel.: +1-607-255-0151
| | | | - Ian R. Tibbetts
- School of Biological Sciences, University of Queensland, St Lucia, Brisbane, QLD 4072, Australia;
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17
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Hedil M, Nakasu EYT, Nagata T, Wen J, Jan E, Michereff-Filho M, Inoue-Nagata AK. New features on the genomic organization of a novel dicistrovirus identified from the sweet potato whitefly Bemisia tabaci. Virus Res 2020; 288:198112. [PMID: 32777388 DOI: 10.1016/j.virusres.2020.198112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 11/26/2022]
Abstract
The whitefly Bemisia tabaci is an agricultural pest causing large economic losses worldwide. We analysed the genomic sequence of a new viral member of the family Dicistroviridae identified by high-throughput sequencing of total RNA extracted from whiteflies. The virus, tentatively named Bemisia-associated dicistrovirus 2 (BaDV-2), has a genome of 8012 nucleotides with a polyadenylated 3' end. In contrast to typical dicistroviruses, BaDV-2 has a genome containing three open reading frames (ORFs) encoding predicted proteins of 1078 (ORF1a), 481 (ORF1b) and 834 (ORF2) amino acids, which correspond to replicase A (containing helicase and cysteine protease domains), replicase B (a domain of an RNA-dependent RNA polymerase - RdRP) and capsid proteins, respectively. The 3' end of ORF1a contains a potential frameshift signal, suggesting that ORF1a and ORF1b may be expressed as a single polyprotein (replicaseFS), corresponding to other dicistroviruses. The BaDV-2 genomic sequence shares the highest nucleotide identity (61.1 %) with Bemisia-associated dicistrovirus 1 (BaDV-1), another dicistrovirus identified from whiteflies. The full BaDV-2 replicaseFS polyprotein clustered with aparaviruses, whereas the capsid polyprotein clustered with cripaviruses in phylogenetic analyses, as with BaDV-1. The intergenic region (IGR) between ORF1b and ORF2 is predicted to adopt a secondary structure with atypical features that resembles the dicistrovirus IGR IRES structure. Our analyses indicate that BaDV-2 is a novel dicistrovirus and that BaDV-2 together with BaDV-1 may not be appropriately grouped in any of the three currently accepted dicistrovirus genera.
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Affiliation(s)
| | | | - Tatsuya Nagata
- Department of Cell Biology, University of Brasilia, Brasília, Brazil
| | - Jing Wen
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
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18
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First Isolation of a Novel Aquatic Flavivirus from Chinook Salmon (Oncorhynchus tshawytscha) and Its In Vivo Replication in a Piscine Animal Model. J Virol 2020; 94:JVI.00337-20. [PMID: 32434883 DOI: 10.1128/jvi.00337-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/12/2020] [Indexed: 01/17/2023] Open
Abstract
The first isolation of a flavivirus from fish was made from moribund Chinook salmon (Oncorhynchus tshawytscha) from the Eel River, California, USA. Following the observation of cytopathic effect in a striped-snakehead fish cell line, 35-nm virions with flaviviral morphology were visualized using electron microcopy. Next-generation sequencing and rapid amplification of cDNA ends obtained the complete genome. Reverse transcriptase quantitative PCR (RT-qPCR) confirmed the presence of viral RNA in formalin-fixed tissues from the wild salmon. For the first time, in vivo replication of an aquatic flavivirus was demonstrated following intracoelomic injection in a Chinook salmon model of infection. RT-qPCR demonstrated viral replication in salmon brains up to 15 days postinjection. Infectious virus was then reisolated in culture, fulfilling Rivers' postulates. Only limited replication occurred in the kidneys of Chinook salmon or in tissues of rainbow trout (Oncorhynchus mykiss). The proposed salmon flavivirus (SFV) has a 10.3-kb genome that encodes a rare dual open reading frame, a feature uncharacteristic of classical flaviviruses. Phylogenetic analysis places SFV in a basal position among a new subgroup of recently recognized aquatic and bat flaviviruses distinct from the established mosquito-borne, tick-borne, insect-only, and unknown-vector flavivirus groups. While the pathogenic potential of the virus remains to be fully elucidated, its basal phylogeny and the in vivo infection model will allow SFV to serve as a prototype for aquatic flaviviruses. Ongoing field and laboratory studies will facilitate better understanding of the potential impacts of SFV infection on ecologically and economically important salmonid species.IMPORTANCE Chinook salmon are a keystone fish species of great ecological and commercial significance in their native northern Pacific range and in regions to which they have been introduced. Threats to salmon populations include habitat degradation, climate change, and infectious agents, including viruses. While the first isolation of a flavivirus from wild migrating salmon may indicate an emerging disease threat, characterization of the genome provides insights into the ecology and long evolutionary history of this important group of viruses affecting humans and other animals and into an expanding group of recently discovered aquatic flaviviruses.
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19
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Liver colour scoring index, carotenoids and lipid content assessment as a proxy for lumpfish (Cyclopterus lumpus L.) health and welfare condition. Sci Rep 2020; 10:8927. [PMID: 32488000 PMCID: PMC7265535 DOI: 10.1038/s41598-020-65535-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 05/06/2020] [Indexed: 11/16/2022] Open
Abstract
Ensuring lumpfish health and welfare in salmon farms is vital to reduce the high mortality rates reported and to guarantee a high delousing efficiency. Recent observations of farmed lumpfish livers have shown colours ranging from pale (colours 1 and 2), through bright orange (colours 3 and 4), to dark reddish-brown (colours 5 and 6), some of which may be related to welfare condition. To characterize the status of lumpfish deployed in four Faroese salmon farms, several welfare indicators were assessed: a weight-length relationship, scoring of external physical damage, and after dissection, stomach content and liver colour scoring. Liver samples were weighed, stored and analysed for lipid content, lipid classes, total pigments, fatty acid profile and histopathology to explain the differences between the mentioned liver colours. Bright orange livers, liver colours 3 and 4, were related to increased levels of carotenoid pigments rather than levels of lipids and appear to reflect good fish welfare. However, dark reddish-brown colours, liver colours 5 and 6, were associated with very low levels of triacyl glycerides in the liver, indicating use of lipid reserves and poor welfare condition. Histopathology confirmed that the dark reddish-brown livers, liver colours 5 and 6, formed a distinct group. Thus, liver colour was shown to be a good welfare indicator and should be monitored in farms.
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20
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Baidaliuk A, Lequime S, Moltini-Conclois I, Dabo S, Dickson LB, Prot M, Duong V, Dussart P, Boyer S, Shi C, Matthijnssens J, Guglielmini J, Gloria-Soria A, Simon-Lorière E, Lambrechts L. Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations. Virus Evol 2020; 6:veaa018. [PMID: 32368352 PMCID: PMC7189118 DOI: 10.1093/ve/veaa018] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Flaviviruses encompass not only medically relevant arthropod-borne viruses (arboviruses) but also insect-specific flaviviruses (ISFs) that are presumably maintained primarily through vertical transmission in the insect host. Interestingly, ISFs are commonly found infecting important arbovirus vectors such as the mosquito Aedes aegypti. Cell-fusing agent virus (CFAV) was the first described ISF of mosquitoes more than four decades ago. Despite evidence for widespread CFAV infections in A.aegypti populations and for CFAV potential to interfere with arbovirus transmission, little is known about CFAV evolutionary history. Here, we generated six novel CFAV genome sequences by sequencing three new virus isolates and subjecting three mosquito samples to untargeted viral metagenomics. We used these new genome sequences together with published ones to perform a global phylogenetic analysis of CFAV genetic diversity. Although there was some degree of geographical clustering among CFAV sequences, there were also notable discrepancies between geography and phylogeny. In particular, CFAV sequences from Cambodia and Thailand diverged significantly, despite confirmation that A.aegypti populations from both locations are genetically close. The apparent phylogenetic discrepancy between CFAV and its A.aegypti host in Southeast Asia indicates that other factors than host population structure shape CFAV genetic diversity.
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Affiliation(s)
- Artem Baidaliuk
- Insect-Virus Interactions Unit, Department of Virology, Institut Pasteur, UMR2000, CNRS, 28 rue du Docteur Roux, 75015 Paris, France.,Sorbonne Université, Collège Doctoral, Paris F-75005, France
| | - Sébastian Lequime
- Insect-Virus Interactions Unit, Department of Virology, Institut Pasteur, UMR2000, CNRS, 28 rue du Docteur Roux, 75015 Paris, France.,KU Leuven Department of Microbiology and Immunology, Rega Institute, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Isabelle Moltini-Conclois
- Insect-Virus Interactions Unit, Department of Virology, Institut Pasteur, UMR2000, CNRS, 28 rue du Docteur Roux, 75015 Paris, France
| | - Stéphanie Dabo
- Insect-Virus Interactions Unit, Department of Virology, Institut Pasteur, UMR2000, CNRS, 28 rue du Docteur Roux, 75015 Paris, France
| | - Laura B Dickson
- Insect-Virus Interactions Unit, Department of Virology, Institut Pasteur, UMR2000, CNRS, 28 rue du Docteur Roux, 75015 Paris, France
| | - Matthieu Prot
- Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Boulevard, 12201, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Boulevard, 12201, Phnom Penh, Cambodia
| | - Sébastien Boyer
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Boulevard, 12201, Phnom Penh, Cambodia
| | - Chenyan Shi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Herestraat 49, 3000 Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Herestraat 49, 3000 Leuven, Belgium
| | - Julien Guglielmini
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, 28 rue du Docteur Roux, 75015 Paris, France
| | - Andrea Gloria-Soria
- Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, 123 Huntington Street, 06511 New Haven, CT, USA.,Ecology and Evolutionary Biology Department, Yale University, 165 Prospect Street, 06520-8106 New Haven, CT, USA
| | - Etienne Simon-Lorière
- Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Department of Virology, Institut Pasteur, UMR2000, CNRS, 28 rue du Docteur Roux, 75015 Paris, France
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21
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Toffan A, De Salvador M, Scholz F, Pretto T, Buratin A, Rodger HD, Toson M, Cuenca A, Vendramin N. Lumpfish (Cyclopterus lumpus, Linnaeus) is susceptible to viral nervous necrosis: Result of an experimental infection with different genotypes of Betanodavirus. JOURNAL OF FISH DISEASES 2019; 42:1667-1676. [PMID: 31612537 DOI: 10.1111/jfd.13088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
In recent years, the use of cleaner fish for biological control of sea lice has increased considerably. Along with this, a number of infectious diseases have emerged. The aim of this study was to investigate the susceptibility of lumpfish (Cyclopterus lumpus) to Betanodavirus since it was detected in asymptomatic wild wrasses in Norway and Sweden. Three betanodaviruses were used to challenge lumpfish: one RGNNV genotype and two BFNNV genotypes. Fish were injected and monitored for 4 weeks. Brain samples from clinically affected specimens, from weekly randomly selected fish and survivors were subjected to molecular testing, viral isolation, histopathology and immunohistochemistry. Reduced survival was observed but was attributed to tail-biting behaviour, since no nervous signs were observed throughout the study. Betanodavirus RNA was detected in all samples, additionally suggesting an active replication of the virus in the brain. Viral isolation confirmed molecular biology results and revealed a high viral titre in BFNNV-infected groups associated with typical lesions in brains and eyes of survivor fish. We concluded that lumpfish are susceptible to Betanodavirus, as proven by the high viral titre and brain lesions detected, but further studies are necessary to understand if Betanodavirus can cause clinical disease in this species.
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Affiliation(s)
- Anna Toffan
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Padua, Italy
| | | | - Felix Scholz
- FishVet Group Ireland, Oranmore, Galway, Ireland
| | - Tobia Pretto
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Padua, Italy
| | - Alessandra Buratin
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Padua, Italy
| | | | - Marica Toson
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Padua, Italy
| | - Argelia Cuenca
- National Institute of Aquatic Resources, EURL for fish and crustacean diseases, Technical University of Denmark, Lyngby, Denmark
| | - Niccolò Vendramin
- National Institute of Aquatic Resources, EURL for fish and crustacean diseases, Technical University of Denmark, Lyngby, Denmark
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Parry R, Asgari S. Discovery of Novel Crustacean and Cephalopod Flaviviruses: Insights into the Evolution and Circulation of Flaviviruses between Marine Invertebrate and Vertebrate Hosts. J Virol 2019; 93:e00432-19. [PMID: 31068424 PMCID: PMC6600200 DOI: 10.1128/jvi.00432-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
Most described flaviviruses (family Flaviviridae) are disease-causing pathogens of vertebrates maintained in zoonotic cycles between mosquitoes or ticks and vertebrate hosts. Poor sampling of flaviviruses outside vector-borne flaviviruses such as Zika virus and dengue virus has presented a narrow understanding of flavivirus diversity and evolution. In this study, we discovered three crustacean flaviviruses (Gammarus chevreuxi flavivirus, Gammarus pulex flavivirus, and Crangon crangon flavivirus) and two cephalopod flaviviruses (Southern Pygmy squid flavivirus and Firefly squid flavivirus). Bayesian and maximum likelihood phylogenetic methods demonstrate that crustacean flaviviruses form a well-supported clade and share a more closely related ancestor with terrestrial vector-borne flaviviruses than with classical insect-specific flaviviruses. In addition, we identify variants of Wenzhou shark flavivirus in multiple gazami crab (Portunus trituberculatus) populations, with active replication supported by evidence of an active RNA interference response. This suggests that Wenzhou shark flavivirus moves horizontally between sharks and gazami crabs in ocean ecosystems. Analyses of the mono- and dinucleotide composition of marine flaviviruses compared to that of flaviviruses with known host status suggest that some marine flaviviruses share a nucleotide bias similar to that of vector-borne flaviviruses. Furthermore, we identify crustacean flavivirus endogenous viral elements that are closely related to elements of terrestrial vector-borne flaviviruses. Taken together, these data provide evidence of flaviviruses circulating between marine vertebrates and invertebrates, expand our understanding of flavivirus host range, and offer potential insights into the evolution and emergence of terrestrial vector-borne flaviviruses.IMPORTANCE Some flaviviruses are known to cause disease in vertebrates and are typically transmitted by blood-feeding arthropods such as ticks and mosquitoes. While an ever-increasing number of insect-specific flaviviruses have been described, we have a narrow understanding of flavivirus incidence and evolution. To expand this understanding, we discovered a number of novel flaviviruses that infect a range of crustaceans and cephalopod hosts. Phylogenetic analyses of these novel marine flaviviruses suggest that crustacean flaviviruses share a close ancestor to all terrestrial vector-borne flaviviruses, and squid flaviviruses are the most divergent of all known flaviviruses to date. Additionally, our results indicate horizontal transmission of a marine flavivirus between crabs and sharks. Taken together, these data suggest that flaviviruses move horizontally between invertebrates and vertebrates in ocean ecosystems. This study demonstrates that flavivirus invertebrate-vertebrate host associations have arisen in flaviviruses at least twice and may potentially provide insights into the emergence or origin of terrestrial vector-borne flaviviruses.
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Affiliation(s)
- Rhys Parry
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
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Einarsdottir T, Sigurdardottir H, Bjornsdottir TS, Einarsdottir E. Moritella viscosa in lumpfish (Cyclopterus lumpus) and Atlantic salmon (Salmo salar). JOURNAL OF FISH DISEASES 2018; 41:1751-1758. [PMID: 30132897 DOI: 10.1111/jfd.12884] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
Winter ulcer disease, caused by Moritella viscosa, is a significant problem in cold water salmonid farming, although the bacterium can infect and cause disease in a number of other fish species, such as lumpfish (Cyclopterus lumpus). Lumpfish are used as cleaner fish, to eat sea lice from Atlantic salmon (Salmo salar) in sea pens. It remains to be established whether M. viscosa can be transmitted between the fish species. In this study, we examined whether a salmon isolate of M. viscosa could infect and cause disease in lumpfish. We further examined whether a lumpfish isolate of M. viscosa could infect and cause disease in salmon. Finally, we examined whether vaccination of salmon with a salmon isolate of M. viscosa conferred protection against a lumpfish isolate. The data indicate that while lumpfish appeared to be resistant to a salmon isolate of M. viscosa, the salmon could be infected with a lumpfish isolate of M. viscosa. Vaccination protected the salmon against the salmon isolate of M. viscosa but did not confer sufficient protection to prevent infection with the lumpfish isolate.
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Affiliation(s)
- Thorbjorg Einarsdottir
- Institute for Experimental Pathology, University of Iceland, Reykjavik, Iceland
- BioMedical Center, University of Iceland, Reykjavik, Iceland
| | | | | | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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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: 41] [Impact Index Per Article: 6.8] [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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