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Infectious salmon anaemia virus (ISAV) isolated from the ISA disease outbreaks in Chile diverged from ISAV isolates from Norway around 1996 and was disseminated around 2005, based on surface glycoprotein gene sequences.

Kibenge FS, Godoy MG, Wang Y, Kibenge MJ, Gherardelli V, Mansilla S, Lisperger A, Jarpa M, Larroquete G, AvendaƱo F, Lara M, Gallardo A - Virol. J. (2009)

Bottom Line: This paper describes the genetic characterization of a large number of ISAV strains associated with extensive outbreaks in Chile starting in June 2007, and their phylogenetic relationships with selected European and North American isolates that are representative of the genetic diversity of ISAV.This is considered a manifestation of ISAV quasispecies HE protein sequence diversity.This is the first comprehensive report tracing ISAV from Europe to South America.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pathology and Microbiology, OIE Reference Laboratory for ISA, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada. kibenge@upei.ca

ABSTRACT

Background: Infectious salmon anaemia (ISA) virus (ISAV) is a pathogen of marine-farmed Atlantic salmon (Salmo salar); a disease first diagnosed in Norway in 1984. For over 25 years ISAV has caused major disease outbreaks in the Northern hemisphere, and remains an emerging fish pathogen because of the asymptomatic infections in marine wild fish and the potential for emergence of new epidemic strains. ISAV belongs to the family Orthomyxoviridae, together with influenza viruses but is sufficiently different to be assigned to its own genus, Isavirus. The Isavirus genome consists of eight single-stranded RNA species, and the virions have two surface glycoproteins; fusion (F) protein encoded on segment 5 and haemagglutinin-esterase (HE) protein encoded on segment 6. However, comparison between different ISAV isolates is complicated because there is presently no universally accepted nomenclature system for designation of genetic relatedness between ISAV isolates. The first outbreak of ISA in marine-farmed Atlantic salmon in the Southern hemisphere occurred in Chile starting in June 2007. In order to describe the molecular characteristics of the virus so as to understand its origins, how ISAV isolates are maintained and spread, and their virulence characteristics, we conducted a study where the viral sequences were directly amplified, cloned and sequenced from tissue samples collected from several ISA-affected fish on the different fish farms with confirmed or suspected ISA outbreaks in Chile. This paper describes the genetic characterization of a large number of ISAV strains associated with extensive outbreaks in Chile starting in June 2007, and their phylogenetic relationships with selected European and North American isolates that are representative of the genetic diversity of ISAV.

Results: RT-PCR for ISAV F and HE glycoprotein genes was performed directly on tissue samples collected from ISA-affected fish on different farms among 14 fish companies in Chile during the ISA outbreaks that started in June 2007. The genes of the F and HE glycoproteins were cloned and sequenced for 51 and 78 new isolates, respectively. An extensive comparative analysis of ISAV F and HE sequence data, including reference isolates sampled from Norway, Faroe Islands, Scotland, USA, and Canada was performed. Based on phylogenetic analysis of concatenated ISAV F and HE genes of 103 individual isolates, the isolates from the ISA outbreaks in Chile grouped in their own cluster of 7 distinct strains within Genotype I (European genotype) of ISAV, with the closest relatedness to Norwegian ISAVs isolated in 1997. The phylogenetic software program, BACKTRACK, estimated the Chile isolates diverged from Norway isolates about 1996 and, therefore, had been present in Chile for some time before the recent outbreaks. Analysis of the deduced F protein sequence showed 43 of 51 Chile isolates with an 11-amino acid insert between 265N and 266Q, with 100% sequence identity with Genotype I ISAV RNA segment 2. Twenty four different HE-HPRs, including HPR0, were detected, with HPR7b making up 79.7%. This is considered a manifestation of ISAV quasispecies HE protein sequence diversity.

Conclusion: Taken together, these findings suggest that the ISA outbreaks were caused by virus that was already present in Chile that mutated to new strains. This is the first comprehensive report tracing ISAV from Europe to South America.

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Related in: MedlinePlus

Phylogenetic trees showing the relationships between the different ISAV isolates; Combined RNA segments 5 and 6 showing the relationships between ISAV Genotype I isolates. For easy identification of the phylogenetic trees, some branches have been marked with letters or numbers; a letter or a number represents all the isolates in that branch.
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Figure 6: Phylogenetic trees showing the relationships between the different ISAV isolates; Combined RNA segments 5 and 6 showing the relationships between ISAV Genotype I isolates. For easy identification of the phylogenetic trees, some branches have been marked with letters or numbers; a letter or a number represents all the isolates in that branch.

Mentions: It is apparent that the phylogenetic trees for ISAV segments 5 and 6 (Figures 3 and 4; [see Additional files 1 and 2]) are different, and it is not known which tree reflects the evolutionary history of the ISAV species. Since the complete genomic information of all the isolates is not available, it can be reasonably expected that a phylogenetic tree generated based on the combination of segments 5 and 6 will provide a better approximation of genetic relatedness between virus isolates than the tree based on either segment 5 or 6 alone, not withstanding the possibility that these genes evolve independently. The present study produced a new sequence by concatenating the segment 5 sequence and the segment 6 sequence for each isolate with the rationalization that these new sequences would approximate the real phylogenetic relationship more closely. Figure 5 shows the phylogenetic tree for 106 of the ISAV isolates for which both segments 5 and 6 sequences were analyzed [see Additional file 1], and Figure 6 shows the detailed tree for the Genotype I portion of this tree. High bootstrapping values (more than 65%) are marked in Figures 5 and 6. For easy identification of the phylogenetic trees, some branches have been marked with letters or numbers. To our knowledge, this kind of concatenation and tree generation has not been done before. It is proposed that this tree, which incorporates an arbitrary numbering system of two unique first-order clades each (clades 1 and 2) in Genotypes I and II, be the basis for the nomenclature and genotyping for ISAV, and a proposed uniform nomenclature for ISAV species is illustrated in Figure 7.


Infectious salmon anaemia virus (ISAV) isolated from the ISA disease outbreaks in Chile diverged from ISAV isolates from Norway around 1996 and was disseminated around 2005, based on surface glycoprotein gene sequences.

Kibenge FS, Godoy MG, Wang Y, Kibenge MJ, Gherardelli V, Mansilla S, Lisperger A, Jarpa M, Larroquete G, AvendaƱo F, Lara M, Gallardo A - Virol. J. (2009)

Phylogenetic trees showing the relationships between the different ISAV isolates; Combined RNA segments 5 and 6 showing the relationships between ISAV Genotype I isolates. For easy identification of the phylogenetic trees, some branches have been marked with letters or numbers; a letter or a number represents all the isolates in that branch.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2710322&req=5

Figure 6: Phylogenetic trees showing the relationships between the different ISAV isolates; Combined RNA segments 5 and 6 showing the relationships between ISAV Genotype I isolates. For easy identification of the phylogenetic trees, some branches have been marked with letters or numbers; a letter or a number represents all the isolates in that branch.
Mentions: It is apparent that the phylogenetic trees for ISAV segments 5 and 6 (Figures 3 and 4; [see Additional files 1 and 2]) are different, and it is not known which tree reflects the evolutionary history of the ISAV species. Since the complete genomic information of all the isolates is not available, it can be reasonably expected that a phylogenetic tree generated based on the combination of segments 5 and 6 will provide a better approximation of genetic relatedness between virus isolates than the tree based on either segment 5 or 6 alone, not withstanding the possibility that these genes evolve independently. The present study produced a new sequence by concatenating the segment 5 sequence and the segment 6 sequence for each isolate with the rationalization that these new sequences would approximate the real phylogenetic relationship more closely. Figure 5 shows the phylogenetic tree for 106 of the ISAV isolates for which both segments 5 and 6 sequences were analyzed [see Additional file 1], and Figure 6 shows the detailed tree for the Genotype I portion of this tree. High bootstrapping values (more than 65%) are marked in Figures 5 and 6. For easy identification of the phylogenetic trees, some branches have been marked with letters or numbers. To our knowledge, this kind of concatenation and tree generation has not been done before. It is proposed that this tree, which incorporates an arbitrary numbering system of two unique first-order clades each (clades 1 and 2) in Genotypes I and II, be the basis for the nomenclature and genotyping for ISAV, and a proposed uniform nomenclature for ISAV species is illustrated in Figure 7.

Bottom Line: This paper describes the genetic characterization of a large number of ISAV strains associated with extensive outbreaks in Chile starting in June 2007, and their phylogenetic relationships with selected European and North American isolates that are representative of the genetic diversity of ISAV.This is considered a manifestation of ISAV quasispecies HE protein sequence diversity.This is the first comprehensive report tracing ISAV from Europe to South America.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pathology and Microbiology, OIE Reference Laboratory for ISA, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada. kibenge@upei.ca

ABSTRACT

Background: Infectious salmon anaemia (ISA) virus (ISAV) is a pathogen of marine-farmed Atlantic salmon (Salmo salar); a disease first diagnosed in Norway in 1984. For over 25 years ISAV has caused major disease outbreaks in the Northern hemisphere, and remains an emerging fish pathogen because of the asymptomatic infections in marine wild fish and the potential for emergence of new epidemic strains. ISAV belongs to the family Orthomyxoviridae, together with influenza viruses but is sufficiently different to be assigned to its own genus, Isavirus. The Isavirus genome consists of eight single-stranded RNA species, and the virions have two surface glycoproteins; fusion (F) protein encoded on segment 5 and haemagglutinin-esterase (HE) protein encoded on segment 6. However, comparison between different ISAV isolates is complicated because there is presently no universally accepted nomenclature system for designation of genetic relatedness between ISAV isolates. The first outbreak of ISA in marine-farmed Atlantic salmon in the Southern hemisphere occurred in Chile starting in June 2007. In order to describe the molecular characteristics of the virus so as to understand its origins, how ISAV isolates are maintained and spread, and their virulence characteristics, we conducted a study where the viral sequences were directly amplified, cloned and sequenced from tissue samples collected from several ISA-affected fish on the different fish farms with confirmed or suspected ISA outbreaks in Chile. This paper describes the genetic characterization of a large number of ISAV strains associated with extensive outbreaks in Chile starting in June 2007, and their phylogenetic relationships with selected European and North American isolates that are representative of the genetic diversity of ISAV.

Results: RT-PCR for ISAV F and HE glycoprotein genes was performed directly on tissue samples collected from ISA-affected fish on different farms among 14 fish companies in Chile during the ISA outbreaks that started in June 2007. The genes of the F and HE glycoproteins were cloned and sequenced for 51 and 78 new isolates, respectively. An extensive comparative analysis of ISAV F and HE sequence data, including reference isolates sampled from Norway, Faroe Islands, Scotland, USA, and Canada was performed. Based on phylogenetic analysis of concatenated ISAV F and HE genes of 103 individual isolates, the isolates from the ISA outbreaks in Chile grouped in their own cluster of 7 distinct strains within Genotype I (European genotype) of ISAV, with the closest relatedness to Norwegian ISAVs isolated in 1997. The phylogenetic software program, BACKTRACK, estimated the Chile isolates diverged from Norway isolates about 1996 and, therefore, had been present in Chile for some time before the recent outbreaks. Analysis of the deduced F protein sequence showed 43 of 51 Chile isolates with an 11-amino acid insert between 265N and 266Q, with 100% sequence identity with Genotype I ISAV RNA segment 2. Twenty four different HE-HPRs, including HPR0, were detected, with HPR7b making up 79.7%. This is considered a manifestation of ISAV quasispecies HE protein sequence diversity.

Conclusion: Taken together, these findings suggest that the ISA outbreaks were caused by virus that was already present in Chile that mutated to new strains. This is the first comprehensive report tracing ISAV from Europe to South America.

Show MeSH
Related in: MedlinePlus