Limits...
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 p13 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. Detailed information of individual sequences are presented in S2 Table.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4633109&req=5

pone.0141475.g004: Amino acid alignment of open reading frame consensus sequences encoding the Piscine reovirus p13 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. Detailed information of individual sequences are presented in S2 Table.

Mentions: The PRV S1 segment has an internal open reading frame (ORF) that encodes the p13 protein, which is hypothesized to play a key role in the cytotoxicity of the virus [9]. Amino acids alignment was performed on the 143 sequences listed in S2 Table. Nine consensus sequences have been identified including six from Norway (GU994022p13_E, HG329869p13_E, HG329842p13_E, HG329882p13_E, HG329893p13_E, HG329850p13_E) and three from the Canada/US Pacific coast (KR478642p13_NA, KC473453p13_NA, KR872635p13_NA). Interestingly, the Norwegian consensus GU994022p13_E, HG329842p13_E and HG329850p13_E include sequences from fish with HSMI and with no lesions (S2 Table). Alignment of consensus sequences showed that Norwegian GU994022p13_E has 8 amino acids variants in comparison to the other consensus sequences, while identified nucleic acid variants are silent and have no frame shift effect on the proteins (Fig 4). However, the secondary structure of p13 amino acid sequences predicted using EMBOSS 6.6.7 [16] implemented by the Geneious software (version 6.1.) showed some differences.


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 p13 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. Detailed information of individual sequences are presented in S2 Table.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0141475.g004: Amino acid alignment of open reading frame consensus sequences encoding the Piscine reovirus p13 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. Detailed information of individual sequences are presented in S2 Table.
Mentions: The PRV S1 segment has an internal open reading frame (ORF) that encodes the p13 protein, which is hypothesized to play a key role in the cytotoxicity of the virus [9]. Amino acids alignment was performed on the 143 sequences listed in S2 Table. Nine consensus sequences have been identified including six from Norway (GU994022p13_E, HG329869p13_E, HG329842p13_E, HG329882p13_E, HG329893p13_E, HG329850p13_E) and three from the Canada/US Pacific coast (KR478642p13_NA, KC473453p13_NA, KR872635p13_NA). Interestingly, the Norwegian consensus GU994022p13_E, HG329842p13_E and HG329850p13_E include sequences from fish with HSMI and with no lesions (S2 Table). Alignment of consensus sequences showed that Norwegian GU994022p13_E has 8 amino acids variants in comparison to the other consensus sequences, while identified nucleic acid variants are silent and have no frame shift effect on the proteins (Fig 4). However, the secondary structure of p13 amino acid sequences predicted using EMBOSS 6.6.7 [16] implemented by the Geneious software (version 6.1.) showed some differences.

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