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Evolution and phylogenetic analysis of full-length VP3 genes of Eastern Mediterranean bluetongue virus isolates.

Nomikou K, Dovas CI, Maan S, Anthony SJ, Samuel AR, Papanastassopoulou M, Maan NS, Mangana O, Mertens PP - PLoS ONE (2009)

Bottom Line: The BTV genome is composed of ten linear segments of double-stranded RNA (dsRNA), each of which codes for one of ten distinct viral proteins.The full-length nucleotide sequence of genome Seg-3 was determined for thirty BTV isolates recovered in the eastern Mediterranean region, the Balkans and other geographic areas (Spain, India, Malaysia and Africa).These analyses also show that the recent incursions into south-eastern Europe were caused by BTV strains belonging to two different major-lineages: representing an 'eastern' (BTV-9, -16 and -1) and a 'western' (BTV-4) group/topotype.

View Article: PubMed Central - PubMed

Affiliation: Arbovirus Molecular Research Group, Department of vector borne diseases, Institute for Animal Health, Pirbright Laboratory, Woking, Surrey, United Kingdom.

ABSTRACT
Bluetongue virus (BTV) is the 'type' species of the genus Orbivirus within the family Reoviridae. The BTV genome is composed of ten linear segments of double-stranded RNA (dsRNA), each of which codes for one of ten distinct viral proteins. Previous phylogenetic comparisons have evaluated variations in genome segment 3 (Seg-3) nucleotide sequence as way to identify the geographical origin (different topotypes) of BTV isolates. The full-length nucleotide sequence of genome Seg-3 was determined for thirty BTV isolates recovered in the eastern Mediterranean region, the Balkans and other geographic areas (Spain, India, Malaysia and Africa). These data were compared, based on molecular variability, positive-selection-analysis and maximum-likelihood phylogenetic reconstructions (using appropriate substitution models) to 24 previously published sequences, revealing their evolutionary relationships. These analyses indicate that negative selection is a major force in the evolution of BTV, restricting nucleotide variability, reducing the evolutionary rate of Seg-3 and potentially of other regions of the BTV genome. Phylogenetic analysis of the BTV-4 strains isolated over a relatively long time interval (1979-2000), in a single geographic area (Greece), showed a low level of nucleotide diversity, indicating that the virus can circulate almost unchanged for many years. These analyses also show that the recent incursions into south-eastern Europe were caused by BTV strains belonging to two different major-lineages: representing an 'eastern' (BTV-9, -16 and -1) and a 'western' (BTV-4) group/topotype. Epidemiological and phylogenetic analyses indicate that these viruses originated from a geographic area to the east and southeast of Greece (including Cyprus and the Middle East), which appears to represent an important ecological niche for the virus that is likely to represent a continuing source of future BTV incursions into Europe.

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Phylogenetic tree constructed using maximum likelihood analyses using the whole coding region of BTV Seg-3 and the GTR + I + Γ model.The viruses included are listed intables 1 and 2. Isolate abbreviations: Serotype/origin (GRE: Greece, ISR: Israel, ZIM: Zimbabwe, NIG: Nigeria, SUD: Sudan, MOR: Morocco, SPA: Spain, TUN: Tunisia, ITL: Italy, CORS: Corsica, USA: USA, CYP: Cyprus, BUL: Bulgaria, TUR: Turkey, IND: India, AUSAsia: Australasia, INDO: Indonesia, TAIW: Taiwan, MAY: Malaysia, AUS: Australia, ISA: Indonesia, RSA: Reference strain)/year of isolation or IAH dsRNA virus reference collection number. The tree is midpoint rooted for purposes of clarity. The numbers indicated on branches are non-parametric bootstrap (NPB) probabilities and only values with P>0.6 are shown.
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pone-0006437-g003: Phylogenetic tree constructed using maximum likelihood analyses using the whole coding region of BTV Seg-3 and the GTR + I + Γ model.The viruses included are listed intables 1 and 2. Isolate abbreviations: Serotype/origin (GRE: Greece, ISR: Israel, ZIM: Zimbabwe, NIG: Nigeria, SUD: Sudan, MOR: Morocco, SPA: Spain, TUN: Tunisia, ITL: Italy, CORS: Corsica, USA: USA, CYP: Cyprus, BUL: Bulgaria, TUR: Turkey, IND: India, AUSAsia: Australasia, INDO: Indonesia, TAIW: Taiwan, MAY: Malaysia, AUS: Australia, ISA: Indonesia, RSA: Reference strain)/year of isolation or IAH dsRNA virus reference collection number. The tree is midpoint rooted for purposes of clarity. The numbers indicated on branches are non-parametric bootstrap (NPB) probabilities and only values with P>0.6 are shown.

Mentions: Positive selection analysis at single amino acid sites was performed separately for the eastern (Australasian) and western (Nth American/Sth African) lineages. For each of these aligned data sets we estimated the rates of non-synonymous and synonymous changes at each site, using likelihood-based methods as implemented in the on-line Datamonkey server (http://www.datamonkey.org; [58], [59] (Figure 3). These analyses used: i) a conservative single-likelihood ancestor-counting (SLAC) method, which is related to that of Suzuki–Gojobori [60] and ii) a fixed-effects likelihood (FEL) method that was used to directly estimate non-synonymous and synonymous substitution rates at each site (this method is more appropriate for data sets with a moderate number of sequences) [58]. For these analyses an optimal model of nucleic acid selection was selected by the methods available on the Datamonkey website using neighbour joining phylogenetic trees. The SLAC method was also used to calculate the global ratio of non-synonymous substitutions per non-synonymous site (dN) to synonymous substitutions per synonymous site (dS) (expressed as dN/dS) and estimate the 95% confidence interval for each dataset.


Evolution and phylogenetic analysis of full-length VP3 genes of Eastern Mediterranean bluetongue virus isolates.

Nomikou K, Dovas CI, Maan S, Anthony SJ, Samuel AR, Papanastassopoulou M, Maan NS, Mangana O, Mertens PP - PLoS ONE (2009)

Phylogenetic tree constructed using maximum likelihood analyses using the whole coding region of BTV Seg-3 and the GTR + I + Γ model.The viruses included are listed intables 1 and 2. Isolate abbreviations: Serotype/origin (GRE: Greece, ISR: Israel, ZIM: Zimbabwe, NIG: Nigeria, SUD: Sudan, MOR: Morocco, SPA: Spain, TUN: Tunisia, ITL: Italy, CORS: Corsica, USA: USA, CYP: Cyprus, BUL: Bulgaria, TUR: Turkey, IND: India, AUSAsia: Australasia, INDO: Indonesia, TAIW: Taiwan, MAY: Malaysia, AUS: Australia, ISA: Indonesia, RSA: Reference strain)/year of isolation or IAH dsRNA virus reference collection number. The tree is midpoint rooted for purposes of clarity. The numbers indicated on branches are non-parametric bootstrap (NPB) probabilities and only values with P>0.6 are shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2713410&req=5

pone-0006437-g003: Phylogenetic tree constructed using maximum likelihood analyses using the whole coding region of BTV Seg-3 and the GTR + I + Γ model.The viruses included are listed intables 1 and 2. Isolate abbreviations: Serotype/origin (GRE: Greece, ISR: Israel, ZIM: Zimbabwe, NIG: Nigeria, SUD: Sudan, MOR: Morocco, SPA: Spain, TUN: Tunisia, ITL: Italy, CORS: Corsica, USA: USA, CYP: Cyprus, BUL: Bulgaria, TUR: Turkey, IND: India, AUSAsia: Australasia, INDO: Indonesia, TAIW: Taiwan, MAY: Malaysia, AUS: Australia, ISA: Indonesia, RSA: Reference strain)/year of isolation or IAH dsRNA virus reference collection number. The tree is midpoint rooted for purposes of clarity. The numbers indicated on branches are non-parametric bootstrap (NPB) probabilities and only values with P>0.6 are shown.
Mentions: Positive selection analysis at single amino acid sites was performed separately for the eastern (Australasian) and western (Nth American/Sth African) lineages. For each of these aligned data sets we estimated the rates of non-synonymous and synonymous changes at each site, using likelihood-based methods as implemented in the on-line Datamonkey server (http://www.datamonkey.org; [58], [59] (Figure 3). These analyses used: i) a conservative single-likelihood ancestor-counting (SLAC) method, which is related to that of Suzuki–Gojobori [60] and ii) a fixed-effects likelihood (FEL) method that was used to directly estimate non-synonymous and synonymous substitution rates at each site (this method is more appropriate for data sets with a moderate number of sequences) [58]. For these analyses an optimal model of nucleic acid selection was selected by the methods available on the Datamonkey website using neighbour joining phylogenetic trees. The SLAC method was also used to calculate the global ratio of non-synonymous substitutions per non-synonymous site (dN) to synonymous substitutions per synonymous site (dS) (expressed as dN/dS) and estimate the 95% confidence interval for each dataset.

Bottom Line: The BTV genome is composed of ten linear segments of double-stranded RNA (dsRNA), each of which codes for one of ten distinct viral proteins.The full-length nucleotide sequence of genome Seg-3 was determined for thirty BTV isolates recovered in the eastern Mediterranean region, the Balkans and other geographic areas (Spain, India, Malaysia and Africa).These analyses also show that the recent incursions into south-eastern Europe were caused by BTV strains belonging to two different major-lineages: representing an 'eastern' (BTV-9, -16 and -1) and a 'western' (BTV-4) group/topotype.

View Article: PubMed Central - PubMed

Affiliation: Arbovirus Molecular Research Group, Department of vector borne diseases, Institute for Animal Health, Pirbright Laboratory, Woking, Surrey, United Kingdom.

ABSTRACT
Bluetongue virus (BTV) is the 'type' species of the genus Orbivirus within the family Reoviridae. The BTV genome is composed of ten linear segments of double-stranded RNA (dsRNA), each of which codes for one of ten distinct viral proteins. Previous phylogenetic comparisons have evaluated variations in genome segment 3 (Seg-3) nucleotide sequence as way to identify the geographical origin (different topotypes) of BTV isolates. The full-length nucleotide sequence of genome Seg-3 was determined for thirty BTV isolates recovered in the eastern Mediterranean region, the Balkans and other geographic areas (Spain, India, Malaysia and Africa). These data were compared, based on molecular variability, positive-selection-analysis and maximum-likelihood phylogenetic reconstructions (using appropriate substitution models) to 24 previously published sequences, revealing their evolutionary relationships. These analyses indicate that negative selection is a major force in the evolution of BTV, restricting nucleotide variability, reducing the evolutionary rate of Seg-3 and potentially of other regions of the BTV genome. Phylogenetic analysis of the BTV-4 strains isolated over a relatively long time interval (1979-2000), in a single geographic area (Greece), showed a low level of nucleotide diversity, indicating that the virus can circulate almost unchanged for many years. These analyses also show that the recent incursions into south-eastern Europe were caused by BTV strains belonging to two different major-lineages: representing an 'eastern' (BTV-9, -16 and -1) and a 'western' (BTV-4) group/topotype. Epidemiological and phylogenetic analyses indicate that these viruses originated from a geographic area to the east and southeast of Greece (including Cyprus and the Middle East), which appears to represent an important ecological niche for the virus that is likely to represent a continuing source of future BTV incursions into Europe.

Show MeSH
Related in: MedlinePlus