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Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. INFECTION GENETICS AND EVOLUTION 2017; 63:295-306. [PMID: 28951202 DOI: 10.1016/j.meegid.2017.09.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Catarina Branco
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, Washington, DC, United States; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal.
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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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Development of a reverse genetic system for infectious salmon anemia virus: rescue of recombinant fluorescent virus by using salmon internal transcribed spacer region 1 as a novel promoter. Appl Environ Microbiol 2016; 81:1210-24. [PMID: 25480750 DOI: 10.1128/aem.03153-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Infectious salmon anemia (ISA) is a serious disease of marine-farmed Atlantic salmon (Salmo salar) caused by ISA virus (ISAV), belonging to the genus Isavirus, family Orthomyxoviridae. There is an urgent need to understand the virulence factors and pathogenic mechanisms of ISAV and to develop new vaccine approaches. Using a recombinant molecular biology approach, we report the development of a plasmid-based reverse genetic system for ISAV, which includes the use of a novel fish promoter, the Atlantic salmon internal transcribed spacer region 1 (ITS-1). Salmon cells cotransfected with pSS-URG-based vectors expressing the eight viral RNA segments and four cytomegalovirus (CMV)-based vectors that express the four proteins of the ISAV ribonucleoprotein complex allowed the generation of infectious recombinant ISAV (rISAV). We generated three recombinant viruses, wild-type rISAV(901_09) and rISAVr(S6-NotI-HPR) containing a NotI restriction site and rISAV(S6/EGFP-HPR) harboring the open reading frame of enhanced green fluorescent protein (EGFP), both within the highly polymorphic region (HPR) of segment 6. All rescued viruses showed replication activity and cytopathic effect in Atlantic salmon kidney-infected cells. The fluorescent recombinant viruses also showed a characteristic cytopathic effect in salmon cells, and the viruses replicated to a titer of 6.5105 PFU/ml,similar to that of the wild-type virus. This novel reverse genetics system offers a powerful tool to study the molecular biology of ISAV and to develop a new generation of ISAV vaccines to prevent and mitigate ISAV infection, which has had a profound effect on the salmon industry.
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Kibenge F, Kibenge M. Orthomyxoviruses of Fish. AQUACULTURE VIROLOGY 2016. [PMCID: PMC7173593 DOI: 10.1016/b978-0-12-801573-5.00019-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The family Orthomyxoviridae is well known for containing influenza viruses with a segmented RNA genome that is prone to gene reassortment in mixed infections (known as antigenic shift) resulting in new virus subtypes that cause pandemics, and cumulative mutations (known as antigenic drift), resulting in new virus strains that cause epidemics. This family also contains infectious salmon anemia virus (ISAV) and tilapia lake virus (TiLV), which are a unique orthomyxoviruses that infect fish and is unable to replicate above room temperature (24°C). This chapter describes the comparative virology of members in the family Orthomyxoviridae in general, helping to understand the emergent teleost orthomyxoviruses, ISAV and TiLV. The most current information on virus–host interactions of the fish orthomyxoviruses, particularly ISAV, as they relate to variations in virus structure, virulence, persistence, host range and immunological aspects is presented in detail.
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Bellec L, Cabon J, Bergmann S, de Boisséson C, Engelsma M, Haenen O, Morin T, Olesen NJ, Schuetze H, Toffan A, Way K, Bigarré L. Evolutionary dynamics and genetic diversity from three genes of Anguillid rhabdovirus. J Gen Virol 2014; 95:2390-2401. [PMID: 25081977 DOI: 10.1099/vir.0.069443-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Wild freshwater eel populations have dramatically declined in recent past decades in Europe and America, partially through the impact of several factors including the wide spread of infectious diseases. The anguillid rhabdoviruses eel virus European X (EVEX) and eel virus American (EVA) potentially play a role in this decline, even if their real contribution is still unclear. In this study, we investigate the evolutionary dynamics and genetic diversity of anguiillid rhabdoviruses by analysing sequences from the glycoprotein, nucleoprotein and phosphoprotein (P) genes of 57 viral strains collected from seven countries over 40 years using maximum-likelihood and Bayesian approaches. Phylogenetic trees from the three genes are congruent and allow two monophyletic groups, European and American, to be clearly distinguished. Results of nucleotide substitution rates per site per year indicate that the P gene is expected to evolve most rapidly. The nucleotide diversity observed is low (2-3 %) for the three genes, with a significantly higher variability within the P gene, which encodes multiple proteins from a single genomic RNA sequence, particularly a small C protein. This putative C protein is a potential molecular marker suitable for characterization of distinct genotypes within anguillid rhabdoviruses. This study provides, to our knowledge, the first molecular characterization of EVA, brings new insights to the evolutionary dynamics of two genotypes of Anguillid rhabdovirus, and is a baseline for further investigations on the tracking of its spread.
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Affiliation(s)
- Laure Bellec
- European University of Brittany, France.,French Agency for Food, Environmental and Occupational Health & Safety, Ploufragan-Plouzané Laboratory, Unit Viral Disease of Fish, Plouzané, France
| | - Joelle Cabon
- European University of Brittany, France.,French Agency for Food, Environmental and Occupational Health & Safety, Ploufragan-Plouzané Laboratory, Unit Viral Disease of Fish, Plouzané, France
| | | | - Claire de Boisséson
- French Agency for Food, Environmental and Occupational Health & Safety, Ploufragan-Plouzané Laboratory, Unit Biosecurity and Viral Genetics, Ploufragan, France
| | - Marc Engelsma
- Central Veterinary Institute of Wageningen, Lelystad, The Netherlands
| | - Olga Haenen
- Central Veterinary Institute of Wageningen, Lelystad, The Netherlands
| | - Thierry Morin
- European University of Brittany, France.,French Agency for Food, Environmental and Occupational Health & Safety, Ploufragan-Plouzané Laboratory, Unit Viral Disease of Fish, Plouzané, France
| | - Niels Jørgen Olesen
- National Veterinary Institute, Technical University of Denmark, Åarhus, Denmark
| | | | - Anna Toffan
- Research & Innovation Department, Division of Biomedical Science, Legnaro, Italy
| | - Keith Way
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Laurent Bigarré
- European University of Brittany, France.,French Agency for Food, Environmental and Occupational Health & Safety, Ploufragan-Plouzané Laboratory, Unit Viral Disease of Fish, Plouzané, France
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Tello M, Vergara F, Spencer E. Genomic adaptation of the ISA virus to Salmo salar codon usage. Virol J 2013; 10:223. [PMID: 23829271 PMCID: PMC3706250 DOI: 10.1186/1743-422x-10-223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 07/01/2013] [Indexed: 01/09/2023] Open
Abstract
Background The ISA virus (ISAV) is an Orthomyxovirus whose genome encodes for at least 10 proteins. Low protein identity and lack of genetic tools have hampered the study of the molecular mechanism behind its virulence. It has been shown that viral codon usage controls several processes such as translational efficiency, folding, tuning of protein expression, antigenicity and virulence. Despite this, the possible role that adaptation to host codon usage plays in virulence and viral evolution has not been studied in ISAV. Methods Intergenomic adaptation between viral and host genomes was calculated using the codon adaptation index score with EMBOSS software and the Kazusa database. Classification of host genes according to GeneOnthology was performed using Blast2go. A non parametric test was applied to determine the presence of significant correlations among CAI, mortality and time. Results Using the codon adaptation index (CAI) score, we found that the encoding genes for nucleoprotein, matrix protein M1 and antagonist of Interferon I signaling (NS1) are the ISAV genes that are more adapted to host codon usage, in agreement with their requirement for production of viral particles and inactivation of antiviral responses. Comparison to host genes showed that ISAV shares CAI values with less than 0.45% of Salmo salar genes. GeneOntology classification of host genes showed that ISAV genes share CAI values with genes from less than 3% of the host biological process, far from the 14% shown by Influenza A viruses and closer to the 5% shown by Influenza B and C. As well, we identified a positive correlation (p<0.05) between CAI values of a virus and the duration of the outbreak disease in given salmon farms, as well as a weak relationship between codon adaptation values of PB1 and the mortality rates of a set of ISA viruses. Conclusions Our analysis shows that ISAV is the least adapted viral Salmo salar pathogen and Orthomyxovirus family member less adapted to host codon usage, avoiding the general behavior of host genes. This is probably due to its recent emergence among farmed Salmon populations.
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Affiliation(s)
- Mario Tello
- Centro de Biotecnología Acuícola, Laboratorio de Virología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O'Higgins 3363, Santiago, Chile.
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Lyngstad TM, Kristoffersen AB, Hjortaas MJ, Devold M, Aspehaug V, Larssen RB, Jansen PA. Low virulent infectious salmon anaemia virus (ISAV-HPR0) is prevalent and geographically structured in Norwegian salmon farming. DISEASES OF AQUATIC ORGANISMS 2012; 101:197-206. [PMID: 23324416 DOI: 10.3354/dao02520] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Infectious salmon anaemia (ISA) is a severe disease in farmed Atlantic salmon Salmo salar that has caused epidemic outbreaks in most salmon-producing countries worldwide. The disease is caused by virulent ISA virus (ISAV). Low virulent variants of the virus, characterised by a full-length sequence in the highly polymorphic region of segment 6 in the virus genome, have been reported with increasing frequencies. These variants of the virus, termed HPR0, have been proposed to be ancestors of virulent ISAV. We examined this idea through studies of the phylogeographic and environmental distribution of ISAV-HPR0, as well as phylogeographic associations between virulent ISAV and ISAV-HPR0. Samples from 232 fish groups were screened for ISAV. Real-time RT-PCR was used for detection of ISAV, and the ISAV haemagglutinin esterase (HE) gene was characterised for positive samples. A Mantel test was used to test phylogeographic associations between pairs of ISAV-HPR0 HE gene sequences. A rank test was used to test associations between HE gene sequences from virulent ISAV and ISAV-HPR0. ISAV-HPR0 was detected in fish groups both in freshwater and marine environments, and in juveniles, on-grown marine salmon and broodstock salmon. Genetic and geographic distances between pairs of ISAV-HPR0 HE gene sequences were positively correlated, suggesting that the population of ISAV-HPR0 is geographically structured. Finally, we found a spatial association between fish groups with virulent ISAV (n = 21) and fish groups with ISAV-HPR0 (n = 27), supporting the hypothesis that ISAV-HPR0 may undergo a transition to virulent ISAV.
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Affiliation(s)
- Trude M Lyngstad
- Norwegian Veterinary Institute, PO Box 750 Sentrum, 0106 Oslo, Norway.
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Kibenge FS, Godoy MG, Fast M, Workenhe S, Kibenge MJ. Countermeasures against viral diseases of farmed fish. Antiviral Res 2012; 95:257-81. [DOI: 10.1016/j.antiviral.2012.06.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 06/01/2012] [Accepted: 06/09/2012] [Indexed: 12/24/2022]
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