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Solarte-Murillo L, Reyes H, Ojeda L, Cárcamo JG, Pontigo JP, Loncoman CA. Analyses and Insights into Genetic Reassortment and Natural Selection as Key Drivers of Piscine orthoreovirus Evolution. Viruses 2024; 16:556. [PMID: 38675898 PMCID: PMC11053957 DOI: 10.3390/v16040556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 04/28/2024] Open
Abstract
Piscine orthoreovirus (PRV) is a pathogen that causes heart and skeletal muscle inflammation in Salmo salar and has also been linked to circulatory disorders in other farmed salmonids, such as Oncorhynchus kisutch and Oncorhynchus mykiss. The virus has a segmented, double-stranded RNA genome, which makes it possible to undergo genetic reassortment and increase its genomic diversity through point mutations. In this study, genetic reassortment in PRV was assessed using the full genome sequences available in public databases. This study used full genome sequences that were concatenated and genome-wide reassortment events, and phylogenetic analyses were performed using the recombination/reassortment detection program version 5 (RDP5 V 5.5) software. Additionally, each segment was aligned codon by codon, and overall mean distance and selection was tested using the Molecular Evolutionary Genetics Analysis X software, version 10.2 (MEGA X version 10.2). The results showed that there were 17 significant reassortment events in 12 reassortant sequences, involving genome exchange between low and highly virulent genotypes. PRV sequences from different salmonid host species did not appear to limit the reassortment. This study found that PRV frequently undergoes reassortment events to increase the diversity of its segmented genome, leading to antigenic variation and increased virulence. This study also noted that to date, no reassortment events have been described between PRV-1 and PRV-3 genotypes. However, the number of complete genomic sequences within each genotype is uneven. This is important because PRV-3 induces cross-protection against PRV-1, making it a potential vaccine candidate.
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Affiliation(s)
- Laura Solarte-Murillo
- Laboratorio de Virología Molecular, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile;
| | - Humberto Reyes
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile;
| | - Loreto Ojeda
- Laboratorio de Bioquímica Farmacológica, Virología y Biotecnología, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Interdisciplinary Center for Aquaculture Research, INCAR, Concepción 4030000, Chile
| | - Juan G. Cárcamo
- Laboratorio de Bioquímica Farmacológica, Virología y Biotecnología, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Interdisciplinary Center for Aquaculture Research, INCAR, Concepción 4030000, Chile
| | - Juan Pablo Pontigo
- Laboratorio Institucional, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Universidad San Sebastián, Puerto Montt 5400000, Chile;
| | - Carlos A. Loncoman
- Laboratorio de Virología Molecular, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile;
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2
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He WT, Lu M, Xing G, Shao Y, Zhang M, Yang Y, Li X, Zhang L, Li G, Cao Z, Su S, Veit M, He H. Emergence and adaptive evolution of influenza D virus. Microb Pathog 2021; 160:105193. [PMID: 34536503 DOI: 10.1016/j.micpath.2021.105193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 10/20/2022]
Abstract
As a novel member of the Orthomyxoviridae, influenza D virus (IDV) was firstly isolated from swine. However, cattle were found to serve as its primary reservoir. The study of IDV emergence can shed light into the dynamics of zoonotic infections and interspecies transmission. Although there is an increasing number of strains and sequenced IDV strains, their origin, epidemiology and evolutionary dynamics remain unclear. In this study, we reconstruct the diversity and evolutionary dynamics of IDVs. Molecular detection of swine tissue samples shows that six IDV positive samples were identified in the Eastern China. Phylogenetic analyses suggest three major IDV lineages designated as D/Japan, D/OK and D/660 as well as intermediate lineages. IDVs show strong association with geographical location indicating a high level of local transmission, which suggests IDVs tend to establish a local lineage of in situ evolution. In addition, the D/OK lineage widely circulates in swine in Eastern China, and all of the Chinese virus isolates form a distinct sub-clade (D/China sub-lineage). Furthermore, we identified important amino acids in the HEF gene under positive selection that might affect its receptor binding cavity relevant for its broader cell tropism. The combined results highlight that more attention should be paid to the potential threat of IDV to livestock and farming in China.
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Affiliation(s)
- Wan-Ting He
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Meng Lu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Gang Xing
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, China
| | - Yuekun Shao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Meng Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yichen Yang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xinxin Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Letian Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Gairu Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zongxi Cao
- Hainan Academician Workstation, Institute of Animal Husbandry and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Shuo Su
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China; San-ya Research Institute of Nanjing Agricultural University, Hainan, Sanya, China.
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Robert-von-Ostertag-Straße 7-13, 14163, Berlin, Germany
| | - Haijian He
- Agricultural College, Jinhua Poletecnic, Jinhua, 321007, China.
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Mohr PG, Crane MSJ, Hoad J, Williams LM, Cummins D, Neave MJ, Shiell B, Beddome G, Michalski WP, Peck GR, Samsing F, Wynne JW, Crameri SG, Hyatt AD, Moody NJG. Pilchard orthomyxovirus (POMV). I. Characterisation of an emerging virus isolated from pilchards Sardinops sagax and Atlantic salmon Salmo salar. DISEASES OF AQUATIC ORGANISMS 2020; 139:35-50. [PMID: 32351235 DOI: 10.3354/dao03470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
An orthomyxo-like virus was first isolated in 1998 as an incidental discovery from pilchards Sardinops sagax collected from waters off the South Australian coast. In the following 2 decades, orthomyxo-like viruses have been isolated from healthy pilchards in South Australia and Tasmania. In 2006, an orthomyxo-like virus was also isolated from farmed Atlantic salmon Salmo salar in Tasmania during routine surveillance and, again, from 2012 onwards from diseased Atlantic salmon. Using transmission electron microscopy, these viruses were identified as belonging to the family Orthomyxoviridae. To further characterise the viruses, the genomes of 11 viral isolates were sequenced. The open reading frames (ORFs) that encode 10 putative proteins from 8 viral genome segments were assembled from Illumina MiSeq next generation sequencing (NGS) data. The complete genome of a 2014 isolate was also assembled from NGS, RNA-sequencing (RNA-seq) data, that included conserved motifs that shared commonalities with infectious salmon anaemia virus, rainbow trout orthomyxovirus and Influenzavirus A. The presence of 8 viral proteins translated from genome segments was confirmed by mass spectrometric analysis including 2 novel proteins with no known orthologs. Sequence analysis of the ORFs, non-coding regions and proteins indicated that the viruses had minimal diversity and hence were named pilchard orthomyxovirus (POMV), based on the fish host species of its first isolation. The low homology of POMV proteins with previously characterised orthomyxoviruses suggests that POMV is the first virus to be characterised from a new genus within the Orthomyxoviridae. To facilitate more rapid detection and subsequent diagnostic confirmation of POMV infections, TaqMan and conventional nested PCRs were designed.
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Affiliation(s)
- Peter G Mohr
- CSIRO Australian Animal Health Laboratory, 5 Portarlington Rd, East Geelong, Victoria 3220, Australia
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4
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Rimstad E, Markussen T. Infectious salmon anaemia virus-molecular biology and pathogenesis of the infection. J Appl Microbiol 2020; 129:85-97. [PMID: 31885186 DOI: 10.1111/jam.14567] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 11/29/2022]
Abstract
Aquaculture has a long history in many parts of the world, but it is still young at an industrial scale. Marine fish farming in open nets of a single fish species at high densities compared to their wild compatriots opens a plethora of possible infections. Infectious salmon anaemia (ISA) is an example of disease that surfaced after large-scale farming of Atlantic salmon (Salmo salar) appeared. Here, a review of the molecular biology of the ISA virus (ISAV) with emphasis on its pathogenicity is presented. The avirulent HPR0 variant of ISAV has resisted propagation in cell cultures, which has restricted the ability to perform in vivo experiments with this variant. The transition from avirulent HPR0 to virulent HPRΔ has not been methodically studied under controlled experimental conditions, and the triggers of the transition from avirulent to virulent forms have not been mapped. Genetic segment reassortment, recombination and mutations are important mechanisms in ISAV evolution, and for the development of virulence. In the 25 years since the ISAV was identified, large amounts of sequence data have been collected for epidemiologic and transmission studies, however, the lack of good experimental models for HPR0 make the risk evaluation of the presence of this avirulent, ubiquitous variant uncertain. This review summarizes the current knowledge related to molecular biology and pathogenicity of this important aquatic orthomyxovirus.
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Affiliation(s)
- E Rimstad
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - T Markussen
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
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Madhun AS, Mæhle S, Wennevik V, Karlsbakk E. Prevalence and genotypes of infectious salmon anaemia virus (ISAV) in returning wild Atlantic salmon (Salmo salar L.) in northern Norway. JOURNAL OF FISH DISEASES 2019; 42:1217-1221. [PMID: 31192460 PMCID: PMC6851747 DOI: 10.1111/jfd.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/12/2019] [Accepted: 04/14/2019] [Indexed: 06/09/2023]
Affiliation(s)
| | - Stig Mæhle
- Institute of Marine ResearchBergenNorway
| | | | - Egil Karlsbakk
- Institute of Marine ResearchBergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
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6
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Nylund A, Brattespe J, Plarre H, Kambestad M, Karlsen M. Wild and farmed salmon (Salmo salar) as reservoirs for infectious salmon anaemia virus, and the importance of horizontal- and vertical transmission. PLoS One 2019; 14:e0215478. [PMID: 30990853 PMCID: PMC6467415 DOI: 10.1371/journal.pone.0215478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/02/2019] [Indexed: 11/19/2022] Open
Abstract
The infectious salmon anaemia virus (ISAV) is an important pathogen on farmed salmon in Europe. The virus occurs as low- and high virulent variants where the former seem to be a continuous source of new high virulent ISAV. The latter are controlled in Norway by stamping out infected populations while the former are spreading uncontrolled among farmed salmon. Evidence of vertical transmission has been presented, but there is still an ongoing discussion of the importance of circulation of ISAV via salmon brood fish. The only known wild reservoirs are in trout (Salmo trutta) and salmon (Salmo salar). This study provides the first ISAV sequences from wild salmonids in Norway and evaluates the importance of this reservoir with respect to outbreaks of ISA among farmed salmon. Phylogenetic analyses of the surface protein hemagglutinin-esterase gene from nearly all available ISAV from Norway, Faeroe Islands, Scotland, Chile and wild salmonids in Norway show that they group into four major clades. Including virulent variants in the analysis show that they belong in the same four clades supporting the hypothesis that there is a high frequency of transition from low to high virulent variants in farmed populations of salmon. There is little support for a hypothesis suggesting that the wild salmonids feed the virus into farmed populations. This study give support to earlier studies that have documented local horizontal transmission of high virulent ISAV, but the importance of transition from low- to high virulent variants has been underestimated. Evidence of vertical transmission and long distance spreading of ISAV via movement of embryos and smolt is presented. We recommend that the industry focus on removing the low virulent ISAV from the brood fish and that ISAV-free brood fish salmon are kept in closed containment systems (CCS).
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Affiliation(s)
- Are Nylund
- University of Bergen, Fish Diseases Research Group, Bergen, Norway
- * E-mail:
| | - Jarle Brattespe
- University of Bergen, Fish Diseases Research Group, Bergen, Norway
| | - Heidrun Plarre
- University of Bergen, Fish Diseases Research Group, Bergen, Norway
| | - Martha Kambestad
- University of Bergen, Fish Diseases Research Group, Bergen, Norway
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Cárdenas C, Ojeda N, Labra Á, Marshall SH. Molecular features associated with the adaptive evolution of Infectious Salmon Anemia Virus (ISAV) in Chile. INFECTION GENETICS AND EVOLUTION 2018; 68:203-211. [PMID: 30592977 DOI: 10.1016/j.meegid.2018.12.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/12/2018] [Accepted: 12/24/2018] [Indexed: 02/05/2023]
Abstract
Infectious salmon anemia virus (ISAV) is an Orthomyxovirus challenging salmon production, with a particular impact in Chile. During 2007-2010 a devastating and of unexpected consequences epizootic event almost destroyed a blooming industry in the country. The event was caused by an aggressive variant with a distinctive deletion in Segment 6, one of the eight genomic segments of the virus. After the outburst, although the infective viral variant seemed to have disappeared, a non-infective variant, not previously reported, was discovered and is characterized by a complete, non-deleted coding segment 6, which has prevailed in the fish population until now. This variant, known as HPR0, appears to be the ancestor strain of ISAV from which novel infective variants are generated. Additional variations in segment 5 have also been associated with the virulence observed in the field, an analysis of the differences in these two protein coding segments has been performed. It appears to us that a combinatorial effect exists between the features displayed by segments 5 and 6 which modulate the intensity of viral outbursts. As a result, a theoretical integrative model is presented which explains the different degree of virulence observed in the field based only on molecular data, this could help estimating the intensity of damage a given variant might exert over a productive farm.
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Affiliation(s)
- Constanza Cárdenas
- Núcleo de Biotecnología Curauma Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
| | - Nicolás Ojeda
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
| | - Álvaro Labra
- Laboratorio de referencia ISAV - OIE- Sernapesca, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
| | - Sergio H Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile; Núcleo de Biotecnología Curauma Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile; Laboratorio de referencia ISAV - OIE- Sernapesca, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
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8
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Gallagher MD, Matejusova I, Nguyen L, Ruane NM, Falk K, Macqueen DJ. Nanopore sequencing for rapid diagnostics of salmonid RNA viruses. Sci Rep 2018; 8:16307. [PMID: 30397226 PMCID: PMC6218516 DOI: 10.1038/s41598-018-34464-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/19/2018] [Indexed: 12/16/2022] Open
Abstract
Analysis of pathogen genome variation is essential for informing disease management and control measures in farmed animals. For farmed fish, the standard approach is to use PCR and Sanger sequencing to study partial regions of pathogen genomes, with second and third-generation sequencing tools yet to be widely applied. Here we demonstrate rapid and accurate sequencing of two disease-causing viruses affecting global salmonid aquaculture, salmonid alphavirus (SAV) and infectious salmon anaemia virus (ISAV), using third-generation nanopore sequencing on the MinION platform (Oxford Nanopore Technologies). Our approach complements PCR from infected material with MinION sequencing to recover genomic information that matches near perfectly to Sanger-verified references. We use this method to present the first SAV subtype-6 genome, which branches as the sister to all other SAV lineages in a genome-wide phylogenetic reconstruction. MinION sequencing offers an effective strategy for fast, genome-wide analysis of fish viruses, with major potential applications for diagnostics and robust investigations into the origins and spread of disease outbreaks.
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Affiliation(s)
- Michael D Gallagher
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, United Kingdom
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
| | - Iveta Matejusova
- Marine Scotland Science, Marine Laboratory, Aberdeen, AB11 9DB, United Kingdom
| | - Lien Nguyen
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, United Kingdom
| | - Neil M Ruane
- Fish Health Unit, Marine Institute, Rinville Oranmore, Co, Galway, Ireland
| | - Knut Falk
- Norwegian Veterinary Institute, Ullevålsveien 68, 0454, Oslo, Norway
| | - Daniel J Macqueen
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, United Kingdom.
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, United Kingdom.
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9
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Gagné N, LeBlanc F. Overview of infectious salmon anaemia virus (ISAV) in Atlantic Canada and first report of an ISAV North American-HPR0 subtype. JOURNAL OF FISH DISEASES 2018; 41:421-430. [PMID: 28782809 DOI: 10.1111/jfd.12670] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 06/07/2023]
Abstract
The infectious salmon anaemia virus (ISAV) is an important viral disease of farmed Atlantic salmon that has caused considerable financial losses for salmon farmers around the world, including Atlantic Canada. It is listed as a notifiable disease by the World Organization for Animal Health, and to this day, culling of infected cages or farms remains the current practice in many countries to mitigate the spread of the virus. In Atlantic Canada, ISAV was first detected in 1996 and continues to be detected. While some outbreaks seemed to have arisen from isolated infections of unknown source, others were local clusters resulting from horizontal spread of infection. This study provides a description of the detected ISAV isolates in Atlantic Canada between 2012 and 2016, and explores the phylogenetic relatedness between these ISAV isolates. A key finding is the detection for the first time of a North American-HPR0 ISAV subtype, which was predicted to exist for many years. Through phylogenetic analysis, a scenario emerges with at least three separate incursions of ISAV in Atlantic Canada. An initial ISAV introduction follows a genotypic separation between North America and Europe which resulted in the NA and EU genotypes known today; this separation predates the salmon aquaculture industry. The second incursion of ISAV from Europe to North America led to a sublineage in Atlantic Canada consisting of EU-HPR∆ isolates detected in Nova Scotia and New Brunswick, and the predominant form of ISAV-HPR0 (EU). Finally, we observed what could be the third and most recent incursion of ISAV in Newfoundland, in the form of an isolate highly similar to ISAV EU-HPR0 isolates found in the Faroe Islands and the one isolate from Norway.
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Affiliation(s)
- N Gagné
- Fisheries and Oceans Canada, Gulf Fisheries Center, Moncton, NB, Canada
| | - F LeBlanc
- Fisheries and Oceans Canada, Gulf Fisheries Center, Moncton, NB, Canada
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10
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Cárdenas C, Ojeda N, Labra A, Marshall SH. An updated proposal for classification of infectious salmon anemia virus strains. Arch Virol 2017; 162:2861-2867. [DOI: 10.1007/s00705-017-3440-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/31/2017] [Indexed: 10/19/2022]
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11
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Molecular characterization of a novel orthomyxovirus from rainbow and steelhead trout (Oncorhynchus mykiss). Virus Res 2017; 230:38-49. [PMID: 28088362 PMCID: PMC7111338 DOI: 10.1016/j.virusres.2017.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/06/2017] [Accepted: 01/08/2017] [Indexed: 11/23/2022]
Abstract
A novel virus, rainbow trout orthomyxovirus (RbtOV), was isolated in 1997 and again in 2000 from commercially-reared rainbow trout (Oncorhynchus mykiss) in Idaho, USA. The virus grew optimally in the CHSE-214 cell line at 15°C producing a diffuse cytopathic effect; however, juvenile rainbow trout exposed to cell culture-grown virus showed no mortality or gross pathology. Electron microscopy of preparations from infected cell cultures revealed the presence of typical orthomyxovirus particles. The complete genome of RbtOV is comprised of eight linear segments of single-stranded, negative-sense RNA having highly conserved 5' and 3'-terminal nucleotide sequences. Another virus isolated in 2014 from steelhead trout (also O. mykiss) in Wisconsin, USA, and designated SttOV was found to have eight genome segments with high amino acid sequence identities (89-99%) to the corresponding genes of RbtOV, suggesting these new viruses are isolates of the same virus species and may be more widespread than currently realized. The new isolates had the same genome segment order and the closest pairwise amino acid sequence identities of 16-42% with Infectious salmon anemia virus (ISAV), the type species and currently only member of the genus Isavirus in the family Orthomyxoviridae. However, pairwise comparisons of the predicted amino acid sequences of the 10 RbtOV and SttOV proteins with orthologs from representatives of the established orthomyxoviral genera and a phylogenetic analysis using the PB1 protein showed that while RbtOV and SttOV clustered most closely with ISAV, they diverged sufficiently to merit consideration as representatives of a novel genus. A set of PCR primers was designed using conserved regions of the PB1 gene to produce amplicons that may be sequenced for identification of similar fish orthomyxoviruses in the future.
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12
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Miller KM, Günther OP, Li S, Kaukinen KH, Ming TJ. Molecular indices of viral disease development in wild migrating salmon †. CONSERVATION PHYSIOLOGY 2017; 5:cox036. [PMID: 28702195 PMCID: PMC5499884 DOI: 10.1093/conphys/cox036] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/08/2017] [Accepted: 05/25/2017] [Indexed: 05/07/2023]
Abstract
Infectious diseases can impact the physiological performance of individuals, including their mobility, visual acuity, behavior and tolerance and ability to effectively respond to additional stressors. These physiological effects can influence competitiveness, social hierarchy, habitat usage, migratory behavior and risk to predation, and in some circumstances, viability of populations. While there are multiple means of detecting infectious agents (microscopy, culture, molecular assays), the detection of infectious diseases in wild populations in circumstances where mortality is not observable can be difficult. Moreover, if infection-related physiological compromise leaves individuals vulnerable to predation, it may be rare to observe wildlife in a late stage of disease. Diagnostic technologies designed to diagnose cause of death are not always sensitive enough to detect early stages of disease development in live-sampled organisms. Sensitive technologies that can differentiate agent carrier states from active disease states are required to demonstrate impacts of infectious diseases in wild populations. We present the discovery and validation of salmon host transcriptional biomarkers capable of distinguishing fish in an active viral disease state [viral disease development (VDD)] from those carrying a latent viral infection, and viral versus bacterial disease states. Biomarker discovery was conducted through meta-analysis of published and in-house microarray data, and validation performed on independent datasets including disease challenge studies and farmed salmon diagnosed with various viral, bacterial and parasitic diseases. We demonstrate that the VDD biomarker panel is predictive of disease development across RNA-viral species, salmon species and salmon tissues, and can recognize a viral disease state in wild-migrating salmon. Moreover, we show that there is considerable overlap in the biomarkers resolved in our study in salmon with those based on similar human viral influenza research, suggesting a highly conserved suite of host genes associated with viral disease that may be applicable across a broad range of vertebrate taxa.
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Affiliation(s)
- Kristina M. Miller
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia, Canada V9T 6N7
- Corresponding author: Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia, Canada V9T 6N7.
| | - Oliver P. Günther
- Günther Analytics, 402-5775 Hampton Place, Vancouver, British Columbia, Canada V6T 2G6
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia, Canada V9T 6N7
| | - Karia H. Kaukinen
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia, Canada V9T 6N7
| | - Tobi J. Ming
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia, Canada V9T 6N7
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13
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Lago M, Bandín I, Olveira JG, Dopazo CP. In vitro reassortment between Infectious Pancreatic Necrosis Virus (IPNV) strains: The mechanisms involved and its effect on virulence. Virology 2016; 501:1-11. [PMID: 27838422 DOI: 10.1016/j.virol.2016.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 10/23/2016] [Accepted: 11/03/2016] [Indexed: 12/31/2022]
Abstract
Reassortment is one of the main mechanisms of evolution in dsRNA viruses with segmented genomes. It contributes to generate genetic diversity and plays an important role in the emergence and spread of new strains with altered virulence. Natural reassorment has been demonstrated among infectious pancreatic necrosis-like viruses (genus Aquabirnavirus, Birnaviridae). In the present study, coinfections between different viral strains, and genome sequencing by the Sanger and Illumina methods were applied to analyze the frequency of reassortment of this virus in vitro, the possible mechanisms involved, and its effect on virulence. Results have demonstrated that reassortment is a cell-dependent and non-random process, probably through differential expression of the different mRNA classes in the ribosomes of a specific cell, and by specific associations between the components to construct the ribonucleoprotein (RNP) complexes and/or RNP cross-inhibition. However, the precise mechanisms involved, known in other viruses, still remain to be demonstrated in birnaviruses.
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Affiliation(s)
- María Lago
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura-Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain.
| | - Isabel Bandín
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura-Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain.
| | - José G Olveira
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura-Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain.
| | - Carlos P Dopazo
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura-Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain.
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Kibenge MJ, Iwamoto T, Wang Y, Morton A, Routledge R, Kibenge FS. Discovery of variant infectious salmon anaemia virus (ISAV) of European genotype in British Columbia, Canada. Virol J 2016; 13:3. [PMID: 26732772 PMCID: PMC4702313 DOI: 10.1186/s12985-015-0459-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/28/2015] [Indexed: 12/12/2022] Open
Abstract
Background Infectious salmon anaemia (ISA) virus (ISAV) belongs to the genus Isavirus, family Orthomyxoviridae. ISAV occurs in two basic genotypes, North American and European. The European genotype is more widespread and shows greater genetic variation and greater virulence variation than the North American genotype. To date, all of the ISAV isolates from the clinical disease, ISA, have had deletions in the highly polymorphic region (HPR) on ISAV segment 6 (ISAV-HPRΔ) relative to ISAV-HPR0, named numerically from ISAV-HPR1 to over ISAV-HPR30. ISA outbreaks have only been reported in farmed Atlantic salmon, although ISAV has been detected by RT-PCR in wild fish. It is recognized that asymptomatically ISAV-infected fish exist. There is no universally accepted ISAV RT-qPCR TaqMan® assay. Most diagnostic laboratories use the primer-probe set targeting a 104 bp-fragment on ISAV segment 8. Some laboratories and researchers have found a primer-probe set targeting ISAV segment 7 to be more sensitive. Other researchers have published different ISAV segment 8 primer-probe sets that are highly sensitive. Methods In this study, we tested 1,106 fish tissue samples collected from (i) market-bought farmed salmonids and (ii) wild salmon from throughout British Columbia (BC), Canada, for ISAV using real time RT-qPCR targeting segment 8 and/or conventional RT-PCR with segment 8 primers and segment 6 HPR primers, and by virus isolation attempts using Salmon head kidney (SHK-1 and ASK-2) cell line monolayers. The sequences from the conventional PCR products were compared by multiple alignment and phylogenetic analyses. Results Seventy-nine samples were “non-negative” with at least one of these tests in one or more replicates. The ISAV segment 6 HPR sequences from the PCR products matched ISAV variants, HPR5 on 29 samples, one sample had both HPR5 and HPR7b and one matched HPR0. All sequences were of European genotype. In addition, alignment of sequences of the conventional PCR product segment 8 showed they had a single nucleotide mutation in the region of the probe sequence and a 9-nucleotide overlap with the reverse primer sequence of the real time RT-qPCR assay. None of the classical ISAV segment 8 sequences in the GenBank have this mutation in the probe-binding site of the assay, suggesting the presence of a novel ISAV variant in BC. A phylogenetic tree of these sequences showed that some ISAV sequences diverted early from the classical European genotype sequences, while others have evolved separately. All virus isolation attempts on the samples were negative, and thus the samples were considered “negative” in terms of the threshold trigger set for Canadian federal regulatory action; i.e., successful virus isolation in cell culture. Conclusions This is the first published report of the detection of ISAV sequences in fish from British Columbia, Canada. The sequences detected, both of ISAV-HPRΔ and ISAV-HPR0 are of European genotype. These sequences are different from the classical ISAV segment 8 sequences, and this difference suggests the presence of a new ISAV variant of European genotype in BC. Our results further suggest that ISAV-HPRΔ strains can be present without clinical disease in farmed fish and without being detected by virus isolation using fish cell lines. Electronic supplementary material The online version of this article (doi:10.1186/s12985-015-0459-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Molly Jt Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada.
| | - Tokinori Iwamoto
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada. .,Current address: Diagnostic Services Unit, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada.
| | - Yingwei Wang
- Department of Computer Science, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada.
| | - Alexandra Morton
- Raincoast Research Society, Box 399, 390 1st Street, Sointula, BC, V0N 3E0, Canada.
| | - Richard Routledge
- Department of Statistics and Actuarial Science, Simon Fraser University, 8888 University Drive, Burnaby, B.C., V5A 1S6, Canada.
| | - Frederick Sb Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada.
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15
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Godoy MG, Suarez R, Lazo ES, Llegues KO, Kibenge MJT, Wang Y, Kibenge FSB. Genetic analysis and comparative virulence of infectious salmon anemia virus (ISAV) types HPR7a and HPR7b from recent field outbreaks in Chile. Virol J 2014; 11:204. [PMID: 25472899 PMCID: PMC4272776 DOI: 10.1186/s12985-014-0204-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/15/2014] [Indexed: 12/02/2022] Open
Abstract
Background Infectious salmon anemia (ISA) is a serious disease of marine farmed Atlantic salmon, Salmo salar L. caused by ISA virus (ISAV). ISAV genomic segments 5 and 6 encode surface glycoproteins hemagglutinin-esterase (HE) and F protein important for the pathogenicity of ISAV. In this study, we describe the genetic characteristics and relationship between ISAV-HPR7a and ISAV-HPR7b strains that caused the ISA outbreaks in Chile in 2013 and 2014, respectively, and the evolution of the ISAV clades since 2009 based on segment 5 and 6 sequences. Methods The study material included samples from six ISA cases in Chile. RNA was extracted from salmon tissues and ISAV isolated from cell culture; segments 5 and 6 were amplified by RT-PCR and compared by alignment with ISAV sequences from the GenBank database. Results ISAV-HPR7a and ISAV-HPR7b belong to the European Genotype I strains only found in Europe and Chile, and in both cases, show high similarity in segments 5 and 6 with identity between 95–96%. Our data confirm the hypothesis that the original virus was introduced to Chile in 1996. Compared to the 2007 ISAV-HPR7b isolate, the 2014 ISAV-HPR7b does not have an insertion in segment 5 and was associated with low mortality, which suggests that ISAV virulence was attenuated by the absence of the insertion in segment 5. In contrast, the highly virulent ISAV-HPR14 from April 2013 outbreak did not have the insertion in segment 5 either. Conclusion Variability in the ISAV virulence markers supports the quasispecies theory that multiple evolution forces are likely to shape ISAV genetic diversity. Our findings provide evidence of continuing evolution of ISAV in the Chilean aquaculture industry. Electronic supplementary material The online version of this article (doi:10.1186/s12985-014-0204-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcos G Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile. .,Facultad de Medicina Veterinaria, Universidad San Sebastian, Lago Panguipulli 1390, Puerto Montt, Chile. .,ETECMA, Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile.
| | - Rudy Suarez
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile.
| | - Eduardo S Lazo
- ETECMA, Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile.
| | - Katerina O Llegues
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile.
| | - Molly J T Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, P.E.I., C1A 4P3, Canada.
| | - Yingwei Wang
- Department of Computer Science and Information Technology, University of Prince Edward Island, 550 University Avenue, Charlottetown, P.E.I., C1A 4P3, Canada.
| | - Frederick S B Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, P.E.I., C1A 4P3, Canada.
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Miller KM, Teffer A, Tucker S, Li S, Schulze AD, Trudel M, Juanes F, Tabata A, Kaukinen KH, Ginther NG, Ming TJ, Cooke SJ, Hipfner JM, Patterson DA, Hinch SG. Infectious disease, shifting climates, and opportunistic predators: cumulative factors potentially impacting wild salmon declines. Evol Appl 2014; 7:812-55. [PMID: 25469162 PMCID: PMC4227861 DOI: 10.1111/eva.12164] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 03/06/2014] [Indexed: 12/23/2022] Open
Abstract
Emerging diseases are impacting animals under high-density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity in wild populations, as once the host dies, there are limited opportunities to infect new individuals. Instead, moderately virulent microparasites persisting for long periods across multiple environments are of greatest concern. Evolved resistance to endemic microparasites may reduce susceptibilities, but as barriers to microparasite distributions are weakened, and environments become more stressful, unexposed populations may be impacted and pathogenicity enhanced. We provide an overview of the evolutionary and ecological impacts of infectious diseases in wild salmon and suggest ways in which modern technologies can elucidate the microparasites of greatest potential import. We present four case studies that resolve microparasite impacts on adult salmon migration success, impact of river warming on microparasite replication, and infection status on susceptibility to predation. Future health of wild salmon must be considered in a holistic context that includes the cumulative or synergistic impacts of multiple stressors. These approaches will identify populations at greatest risk, critically needed to manage and potentially ameliorate the shifts in current or future trajectories of wild populations.
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Affiliation(s)
- Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
- Forest and Conservation Sciences, University of British ColumbiaVancouver, BC, Canada
| | - Amy Teffer
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Strahan Tucker
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Marc Trudel
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Francis Juanes
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Norma G Ginther
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton UniverisyOttawa, ON, Canada
| | - J Mark Hipfner
- Environment Canada, Wildlife Research DivisionDelta, BC, Canada
| | - David A Patterson
- Fisheries and Oceans Canada, School of Resource and Environmental Management, Simon Fraser University, Science BranchBurnaby, BC, Canada
| | - Scott G Hinch
- Forest and Conservation Sciences, University of British ColumbiaVancouver, BC, Canada
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Vike S, Oelckers K, Duesund H, Erga SR, Gonzalez J, Hamre B, Frette O, Nylund A. Infectious salmon anemia (ISA) virus: infectivity in seawater under different physical conditions. JOURNAL OF AQUATIC ANIMAL HEALTH 2014; 26:33-42. [PMID: 24689956 DOI: 10.1080/08997659.2013.864720] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Infectious salmon anemia (ISA) virus (genus Isavirus, family Orthomyxoviridae), present in all major salmon producing countries, is the causative agent for a serious and commercially important disease affecting Atlantic Salmon Salmo salar. Nearly all ISA outbreaks occur in the marine production phase and knowledge about survival time for ISA virions in seawater is crucial for an adequate strategy to combat the disease. To acquire knowledge about this important factor, a study of ISA virus exposed to four different physical conditions was carried out. The virions' survival was tested in sterile seawater, sterile seawater with normal ultraviolet light radiation (UVR), natural seawater, and natural seawater with UVR. During the 72-h experiment both presence of ISA virus RNA and the infectivity of ISA virions were monitored. The result of this study showed that the infectivity of ISA virions is lost within 3 h of exposure to natural seawater or sterile seawater with UVR. However, it was possible to detect ISA virus RNA throughout the experimental period. This indicates that the effect of both UVR and biological activity of natural seawater limits the survival time of ISA virions under normal conditions. The survival time of ISA virions in sterile seawater was less than 24 h. Based on the available literature and the present study it is not very likely that passive horizontal transmission in seawater over long distances can occur. This is due to the following factors: (1) the effect of UVR and biological activity on ISA virions infectivity found in the present study, (2) the speed and dilution effect in seawater currents in salmon farming areas, (3) the temperature during the major outbreak periods, and (4) the need for an infective dose of ISA virions to reach naive Atlantic Salmon.
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Affiliation(s)
- Siri Vike
- a Cermaq , Dronning Eufemias gate 16 , Oslo , N-0102 , Norway
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18
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Godoy MG, Kibenge MJT, Suarez R, Lazo E, Heisinger A, Aguinaga J, Bravo D, Mendoza J, Llegues KO, Avendaño-Herrera R, Vera C, Mardones F, Kibenge FSB. Infectious salmon anaemia virus (ISAV) in Chilean Atlantic salmon (Salmo salar) aquaculture: emergence of low pathogenic ISAV-HPR0 and re-emergence of virulent ISAV-HPR∆: HPR3 and HPR14. Virol J 2013; 10:344. [PMID: 24268071 PMCID: PMC4222741 DOI: 10.1186/1743-422x-10-344] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 11/18/2013] [Indexed: 11/10/2022] Open
Abstract
ABSTACT Infectious salmon anaemia (ISA) is a serious disease of marine-farmed Atlantic salmon (Salmo salar) caused by ISA virus (ISAV), which belongs to the genus Isavirus, family Orthomyxoviridae. ISA is caused by virulent ISAV strains with deletions in a highly polymorphic region (HPR) of the hemagglutinin-esterase (HE) protein (designated virulent ISAV-HPR∆). This study shows the historic dynamics of ISAV-HPR∆ and ISAV-HPR0 in Chile, the genetic relationship among ISAV-HPR0 reported worldwide and between ISAV-HPR0 and ISAV-HPR∆ in Chile, and reports the 2013 ISA outbreak in Chile. The first ISA outbreak in Chile occurred from mid-June 2007 to 2010 and involved the virulent ISAV-HPR7b, which was then replaced by a low pathogenic ISAV-HPR0 variant. We analyzed this variant in 66 laboratory-confirmed ISAV-HPR0 cases in Chile in comparison to virulent ISAV-HPR∆ that caused two new ISA outbreaks in April 2013. Multiple alignment and phylogenetic analysis of HE sequences from all ISAV-HPR0 viruses allowed us to identify three genomic clusters, which correlated with three residue patterns of ISAV-HPR0 (360PST362, 360PAN362 and 360PAT362) in HPR. The virus responsible for the 2013 ISAV-HPR∆ cases in Chile belonged to ISAV-HPR3 and ISAV-HPR14, and in phylogenetic analyses, both clustered with the ISAV-HPR0 found in Chile. The ISAV-HPR14 had the ISAV-HPR0 residue pattern 360PAT362, which is the only type of ISAV-HPR0 variant found in Chile. This suggested to us that the 2013 ISAV-HPR∆ re-emerged from ISAV-HPR0 that is enzootic in Chilean salmon aquaculture and were not new introductions of virulent ISAV-HPR∆ to Chile. The clinical presentations and diagnostic evidence of the 2013 ISA cases indicated a mixed infection of ISAV with the ectoparasite Caligus rogercresseyi and the bacterium Piscirickettsia salmonis, which underscores the need for active ISAV surveillance in areas where ISAV-HPR0 is enzootic, to ensure early detection and control of new ISA outbreaks, as it is considered a risk factor. This is the first report of ISA linked directly to the presence of ISAV-HPR0, and provides strong evidence supporting the contention that ISAV-HPR0 shows a strong relationship to virulent ISAV-HPR∆ viruses and the possibility that it could mutate to virulent ISAV-HPR∆.
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Affiliation(s)
- Marcos G Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Diego de Almagro Norte 1013, No. 8, Puerto Montt, Chile
- Facultad de Ciencias, Universidad San Sebastián, Lago Panguipulli 1390, Puerto Montt, Chile
- ETECMA, Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile
| | - Molly JT Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, P.E.I., C1A 4P3, Canada
| | - Rudy Suarez
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Diego de Almagro Norte 1013, No. 8, Puerto Montt, Chile
- ETECMA, Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile
| | - Eduardo Lazo
- ETECMA, Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile
| | | | - Javier Aguinaga
- ETECMA, Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile
| | - Diego Bravo
- ETECMA, Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile
| | - Julio Mendoza
- Mainstream Chile S.A, Av. Diego Portales 2000, piso 10 y 11, Puerto Montt, Chile
| | - Katerina O Llegues
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Diego de Almagro Norte 1013, No. 8, Puerto Montt, Chile
- ETECMA, Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile
| | - Rubén Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Cristian Vera
- ETECMA, Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile
| | - Fernando Mardones
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California 95616, USA
| | - Frederick SB Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, P.E.I., C1A 4P3, Canada
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Svingerud T, Holand JK, Robertsen B. Infectious salmon anemia virus (ISAV) replication is transiently inhibited by Atlantic salmon type I interferon in cell culture. Virus Res 2013; 177:163-70. [DOI: 10.1016/j.virusres.2013.08.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/09/2013] [Accepted: 08/10/2013] [Indexed: 12/17/2022]
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Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements. ISME JOURNAL 2013; 8:746-56. [PMID: 24173459 PMCID: PMC3960531 DOI: 10.1038/ismej.2013.186] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/04/2013] [Accepted: 09/09/2013] [Indexed: 12/25/2022]
Abstract
Renibacterium salmoninarum is the causative agent of bacterial kidney disease, a major pathogen of salmonid fish species worldwide. Very low levels of intra-species genetic diversity have hampered efforts to understand the transmission dynamics and recent evolutionary history of this Gram-positive bacterium. We exploited recent advances in the next-generation sequencing technology to generate genome-wide single-nucleotide polymorphism (SNP) data from 68 diverse R. salmoninarum isolates representing broad geographical and temporal ranges and different host species. Phylogenetic analysis robustly delineated two lineages (lineage 1 and lineage 2); futhermore, dating analysis estimated that the time to the most recent ancestor of all the isolates is 1239 years ago (95% credible interval (CI) 444–2720 years ago). Our data reveal the intercontinental spread of lineage 1 over the last century, concurrent with anthropogenic movement of live fish, feed and ova for aquaculture purposes and stocking of recreational fisheries, whilst lineage 2 appears to have been endemic in wild Eastern Atlantic salmonid stocks before commercial activity. The high resolution of the SNP-based analyses allowed us to separate closely related isolates linked to neighboring fish farms, indicating that they formed part of single outbreaks. We were able to demonstrate that the main lineage 1 subgroup of R. salmoninarum isolated from Norway and the UK likely represent an introduction to these areas ∼40 years ago. This study demonstrates the promise of this technology for analysis of micro and medium scale evolutionary relationships in veterinary and environmental microorganisms, as well as human pathogens.
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Kibenge MJT, Iwamoto T, Wang Y, Morton A, Godoy MG, Kibenge FSB. Whole-genome analysis of piscine reovirus (PRV) shows PRV represents a new genus in family Reoviridae and its genome segment S1 sequences group it into two separate sub-genotypes. Virol J 2013; 10:230. [PMID: 23844948 PMCID: PMC3711887 DOI: 10.1186/1743-422x-10-230] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/05/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Piscine reovirus (PRV) is a newly discovered fish reovirus of anadromous and marine fish ubiquitous among fish in Norwegian salmon farms, and likely the causative agent of heart and skeletal muscle inflammation (HSMI). HSMI is an increasingly economically significant disease in Atlantic salmon (Salmo salar) farms. The nucleotide sequence data available for PRV are limited, and there is no genetic information on this virus outside of Norway and none from wild fish. METHODS RT-PCR amplification and sequencing were used to obtain the complete viral genome of PRV (10 segments) from western Canada and Chile. The genetic diversity among the PRV strains and their relationship to Norwegian PRV isolates were determined by phylogenetic analyses and sequence identity comparisons. RESULTS PRV is distantly related to members of the genera Orthoreovirus and Aquareovirus and an unambiguous new genus within the family Reoviridae. The Canadian and Norwegian PRV strains are most divergent in the segment S1 and S4 encoded proteins. Phylogenetic analysis of PRV S1 sequences, for which the largest number of complete sequences from different "isolates" is available, grouped Norwegian PRV strains into a single genotype, Genotype I, with sub-genotypes, Ia and Ib. The Canadian PRV strains matched sub-genotype Ia and Chilean PRV strains matched sub-genotype Ib. CONCLUSIONS PRV should be considered as a member of a new genus within the family Reoviridae with two major Norwegian sub-genotypes. The Canadian PRV diverged from Norwegian sub-genotype Ia around 2007 ± 1, whereas the Chilean PRV diverged from Norwegian sub-genotype Ib around 2008 ± 1.
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Affiliation(s)
- Molly JT Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI C1A 4P3, Canada
| | - Tokinori Iwamoto
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI C1A 4P3, Canada
| | - Yingwei Wang
- Department of Computer Science and Information Technology, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI C1A 4P3, Canada
| | - Alexandra Morton
- Raincoast Research Society, Box 399, 390 1st Street, Sointula, BC V0N 3E0, Canada
| | - Marcos G Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Diego de Almagro Norte 1013, No. 10, Puerto Montt, Chile
- Universidad San Sebastián. Facultad de Ciencias, Lago Panguipulli 1390, Puerto Montt, Chile
- ETECMA, Diego de Almagro Norte 1013 No. 10, Sector Cardonal, Puerto Montt, X Región, Chile
| | - Frederick SB Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI C1A 4P3, Canada
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