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Piscine Reovirus: Genomic and Molecular Phylogenetic Analysis from Farmed and Wild Salmonids Collected on the Canada/US Pacific Coast.

Siah A, Morrison DB, Fringuelli E, Savage P, Richmond Z, Johns R, Purcell MK, Johnson SC, Saksida SM - PLoS ONE (2015)

Bottom Line: Identical sequence types were found in fish sampled in 2001, 2005 and 2014.Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4.In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period.

View Article: PubMed Central - PubMed

Affiliation: British Columbia Centre for Aquatic Health Sciences, Campbell River, British Columbia, Canada.

ABSTRACT
Piscine reovirus (PRV) is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US), British Columbia (Canada) and Washington State (US). Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II), distinct from other Norwegian and Chilean sequences (groups I, III and IV). Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period.

No MeSH data available.


Related in: MedlinePlus

Amino acid alignment of open reading frame consensus sequences encoding the Piscine reovirus σ3 and μ1 protein.Secondary structure and transmembrane domains were predicted using EMBOSS 6.6.7 (Geneious software v6.1). Predicted secondary structure of alpha helix, beta strand, coil and turn are presented in purple cylinders, yellow arrows, grey sinusoids and blue curved arrow. Sequences are identified using the GenBank accession numbers. A/ represents ORF sequences encoding PRV σ3 amino acid alignment. Red stars are conserved Zn-finger motifs. B/ represents ORF sequences encoding PRV μ1 amino acid alignment. Red cross is myristoylation site in the MRV protein and green line is post-translational cleavage site in MRV and ARV [7].
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pone.0141475.g006: Amino acid alignment of open reading frame consensus sequences encoding the Piscine reovirus σ3 and μ1 protein.Secondary structure and transmembrane domains were predicted using EMBOSS 6.6.7 (Geneious software v6.1). Predicted secondary structure of alpha helix, beta strand, coil and turn are presented in purple cylinders, yellow arrows, grey sinusoids and blue curved arrow. Sequences are identified using the GenBank accession numbers. A/ represents ORF sequences encoding PRV σ3 amino acid alignment. Red stars are conserved Zn-finger motifs. B/ represents ORF sequences encoding PRV μ1 amino acid alignment. Red cross is myristoylation site in the MRV protein and green line is post-translational cleavage site in MRV and ARV [7].

Mentions: The PRV S1 and M2 segments have open reading frame (ORF) that encode the major outer capsid σ3 and μ1 proteins, respectively. These proteins play key roles in membrane penetration and infectivity of mammalian reoviruses [7]. Amino acids alignment showed high similarities of sequences between the different sequences for both ORF encoding proteins (Fig 6). Zn-finger motifs of σ3 protein are conserved among the different sequences (Fig 6A) as well as myristoylation and post-translational cleavage sites described in mammalian and avian reoviruses (Fig 6B). However, our alignment highlighted some amino acid differences between PRV sequences from Norway (HW125610)/Chile (KC795571) and West coast of North America. For example, at a position 174 of σ3 protein sequences, glutamic acid (E) in Norwegian/Chilean is substituted by lysine (K) in Canadian/US. This substitution leads to a secondary structure modification from “alpha helix” structure in Norwegian/Chilean to a “turn” structure in Canadian/US sequences (Fig 6A). Alignment of μ1 amino acids showed a substitution of serine (S) from Norwegian/Chilean to alanine (A) from Canadian/US at position 262 which leads to a shift from β strand in Norwegian/Chilean structure to α helix structure in Canadian/US sequences (Fig 6B).


Piscine Reovirus: Genomic and Molecular Phylogenetic Analysis from Farmed and Wild Salmonids Collected on the Canada/US Pacific Coast.

Siah A, Morrison DB, Fringuelli E, Savage P, Richmond Z, Johns R, Purcell MK, Johnson SC, Saksida SM - PLoS ONE (2015)

Amino acid alignment of open reading frame consensus sequences encoding the Piscine reovirus σ3 and μ1 protein.Secondary structure and transmembrane domains were predicted using EMBOSS 6.6.7 (Geneious software v6.1). Predicted secondary structure of alpha helix, beta strand, coil and turn are presented in purple cylinders, yellow arrows, grey sinusoids and blue curved arrow. Sequences are identified using the GenBank accession numbers. A/ represents ORF sequences encoding PRV σ3 amino acid alignment. Red stars are conserved Zn-finger motifs. B/ represents ORF sequences encoding PRV μ1 amino acid alignment. Red cross is myristoylation site in the MRV protein and green line is post-translational cleavage site in MRV and ARV [7].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4633109&req=5

pone.0141475.g006: Amino acid alignment of open reading frame consensus sequences encoding the Piscine reovirus σ3 and μ1 protein.Secondary structure and transmembrane domains were predicted using EMBOSS 6.6.7 (Geneious software v6.1). Predicted secondary structure of alpha helix, beta strand, coil and turn are presented in purple cylinders, yellow arrows, grey sinusoids and blue curved arrow. Sequences are identified using the GenBank accession numbers. A/ represents ORF sequences encoding PRV σ3 amino acid alignment. Red stars are conserved Zn-finger motifs. B/ represents ORF sequences encoding PRV μ1 amino acid alignment. Red cross is myristoylation site in the MRV protein and green line is post-translational cleavage site in MRV and ARV [7].
Mentions: The PRV S1 and M2 segments have open reading frame (ORF) that encode the major outer capsid σ3 and μ1 proteins, respectively. These proteins play key roles in membrane penetration and infectivity of mammalian reoviruses [7]. Amino acids alignment showed high similarities of sequences between the different sequences for both ORF encoding proteins (Fig 6). Zn-finger motifs of σ3 protein are conserved among the different sequences (Fig 6A) as well as myristoylation and post-translational cleavage sites described in mammalian and avian reoviruses (Fig 6B). However, our alignment highlighted some amino acid differences between PRV sequences from Norway (HW125610)/Chile (KC795571) and West coast of North America. For example, at a position 174 of σ3 protein sequences, glutamic acid (E) in Norwegian/Chilean is substituted by lysine (K) in Canadian/US. This substitution leads to a secondary structure modification from “alpha helix” structure in Norwegian/Chilean to a “turn” structure in Canadian/US sequences (Fig 6A). Alignment of μ1 amino acids showed a substitution of serine (S) from Norwegian/Chilean to alanine (A) from Canadian/US at position 262 which leads to a shift from β strand in Norwegian/Chilean structure to α helix structure in Canadian/US sequences (Fig 6B).

Bottom Line: Identical sequence types were found in fish sampled in 2001, 2005 and 2014.Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4.In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period.

View Article: PubMed Central - PubMed

Affiliation: British Columbia Centre for Aquatic Health Sciences, Campbell River, British Columbia, Canada.

ABSTRACT
Piscine reovirus (PRV) is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US), British Columbia (Canada) and Washington State (US). Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II), distinct from other Norwegian and Chilean sequences (groups I, III and IV). Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period.

No MeSH data available.


Related in: MedlinePlus