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Genomic diversity and evolution of the lyssaviruses.

Delmas O, Holmes EC, Talbi C, Larrous F, Dacheux L, Bouchier C, Bourhy H - PLoS ONE (2008)

Bottom Line: To date, genomic and evolutionary studies have most often utilized partial genome sequences, particularly of the nucleoprotein and glycoprotein genes, with little consideration of genome-scale evolution.In doing so we significantly increase the extent of genome sequence data available for these important viruses.A phylogenetic analysis reveals strong geographical structuring, with the greatest genetic diversity in Africa, and an independent origin for the two known genotypes that infect European bats.

View Article: PubMed Central - PubMed

Affiliation: Institut Pasteur, UPRE Lyssavirus Dynamics and Host Adaptation, World Health Organization Collaborating Centre for Reference and Research on Rabies, Paris, France.

ABSTRACT
Lyssaviruses are RNA viruses with single-strand, negative-sense genomes responsible for rabies-like diseases in mammals. To date, genomic and evolutionary studies have most often utilized partial genome sequences, particularly of the nucleoprotein and glycoprotein genes, with little consideration of genome-scale evolution. Herein, we report the first genomic and evolutionary analysis using complete genome sequences of all recognised lyssavirus genotypes, including 14 new complete genomes of field isolates from 6 genotypes and one genotype that is completely sequenced for the first time. In doing so we significantly increase the extent of genome sequence data available for these important viruses. Our analysis of these genome sequence data reveals that all lyssaviruses have the same genomic organization. A phylogenetic analysis reveals strong geographical structuring, with the greatest genetic diversity in Africa, and an independent origin for the two known genotypes that infect European bats. We also suggest that multiple genotypes may exist within the diversity of viruses currently classified as 'Lagos Bat'. In sum, we show that rigorous phylogenetic techniques based on full length genome sequence provide the best discriminatory power for genotype classification within the lyssaviruses.

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Related in: MedlinePlus

Phylogenetic relationships of 22 complete coding regions of LYSSAV genomes representatives of the 7 genotypes.The phylogeny was inferred using an ML procedure, and all horizontal branches are scaled according to the number of substitutions per site. Boot strap values (>95%) are shown for key nodes. The tree is mid-point rooted for purposes of clarity only.
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pone-0002057-g002: Phylogenetic relationships of 22 complete coding regions of LYSSAV genomes representatives of the 7 genotypes.The phylogeny was inferred using an ML procedure, and all horizontal branches are scaled according to the number of substitutions per site. Boot strap values (>95%) are shown for key nodes. The tree is mid-point rooted for purposes of clarity only.

Mentions: There have been several attempts to estimate the evolutionary relationships among lyssaviruses, with most utilizing only one or two genes [1], [7], [21], [26], [30]–[34]. We therefore undertook a phylogenetic analysis of 22 genomes representative of the seven genotypes of LYSSAV based on a multiple alignment of concatenated coding sequences. Our phylogenetic analysis reveals the separation of LYSSAV into two major branches previously defined as different ‘phylogroups’ [7] and 7 component lineages defined as genotypes [5], [35]. Phylogroup 1 comprised GT1, 4, 5, 6 and 7, while phylogroup 2 contains only GT2 and GT3 (Figure 2). Notably, phylogroup 2 contains viruses of sampled exclusively from Africa – LBV and MOKV – while a third African genotype (DUVV) is found within phylogroup 1 [32], [36]. Also of note was the observation that although GT5 and GT6 both circulate in European insectivorous bats [32], the former is more closely related to the African GT4 viruses [32]. Hence, there has clearly been an independent origin of genotypes 5 and 6 in European bats, as previously documented in analyses of the N and G genes in isolation [32]. Finally, that bats appear as the principle host species across such a large phylogeographic range indicates that the association between lyssaviruses and bats is likely to be the ancestral condition (with a secondary loss of bat transmission in GT3), such that the movement of bats is likely to be responsible for the global dissemination of these viruses [7].


Genomic diversity and evolution of the lyssaviruses.

Delmas O, Holmes EC, Talbi C, Larrous F, Dacheux L, Bouchier C, Bourhy H - PLoS ONE (2008)

Phylogenetic relationships of 22 complete coding regions of LYSSAV genomes representatives of the 7 genotypes.The phylogeny was inferred using an ML procedure, and all horizontal branches are scaled according to the number of substitutions per site. Boot strap values (>95%) are shown for key nodes. The tree is mid-point rooted for purposes of clarity only.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2327259&req=5

pone-0002057-g002: Phylogenetic relationships of 22 complete coding regions of LYSSAV genomes representatives of the 7 genotypes.The phylogeny was inferred using an ML procedure, and all horizontal branches are scaled according to the number of substitutions per site. Boot strap values (>95%) are shown for key nodes. The tree is mid-point rooted for purposes of clarity only.
Mentions: There have been several attempts to estimate the evolutionary relationships among lyssaviruses, with most utilizing only one or two genes [1], [7], [21], [26], [30]–[34]. We therefore undertook a phylogenetic analysis of 22 genomes representative of the seven genotypes of LYSSAV based on a multiple alignment of concatenated coding sequences. Our phylogenetic analysis reveals the separation of LYSSAV into two major branches previously defined as different ‘phylogroups’ [7] and 7 component lineages defined as genotypes [5], [35]. Phylogroup 1 comprised GT1, 4, 5, 6 and 7, while phylogroup 2 contains only GT2 and GT3 (Figure 2). Notably, phylogroup 2 contains viruses of sampled exclusively from Africa – LBV and MOKV – while a third African genotype (DUVV) is found within phylogroup 1 [32], [36]. Also of note was the observation that although GT5 and GT6 both circulate in European insectivorous bats [32], the former is more closely related to the African GT4 viruses [32]. Hence, there has clearly been an independent origin of genotypes 5 and 6 in European bats, as previously documented in analyses of the N and G genes in isolation [32]. Finally, that bats appear as the principle host species across such a large phylogeographic range indicates that the association between lyssaviruses and bats is likely to be the ancestral condition (with a secondary loss of bat transmission in GT3), such that the movement of bats is likely to be responsible for the global dissemination of these viruses [7].

Bottom Line: To date, genomic and evolutionary studies have most often utilized partial genome sequences, particularly of the nucleoprotein and glycoprotein genes, with little consideration of genome-scale evolution.In doing so we significantly increase the extent of genome sequence data available for these important viruses.A phylogenetic analysis reveals strong geographical structuring, with the greatest genetic diversity in Africa, and an independent origin for the two known genotypes that infect European bats.

View Article: PubMed Central - PubMed

Affiliation: Institut Pasteur, UPRE Lyssavirus Dynamics and Host Adaptation, World Health Organization Collaborating Centre for Reference and Research on Rabies, Paris, France.

ABSTRACT
Lyssaviruses are RNA viruses with single-strand, negative-sense genomes responsible for rabies-like diseases in mammals. To date, genomic and evolutionary studies have most often utilized partial genome sequences, particularly of the nucleoprotein and glycoprotein genes, with little consideration of genome-scale evolution. Herein, we report the first genomic and evolutionary analysis using complete genome sequences of all recognised lyssavirus genotypes, including 14 new complete genomes of field isolates from 6 genotypes and one genotype that is completely sequenced for the first time. In doing so we significantly increase the extent of genome sequence data available for these important viruses. Our analysis of these genome sequence data reveals that all lyssaviruses have the same genomic organization. A phylogenetic analysis reveals strong geographical structuring, with the greatest genetic diversity in Africa, and an independent origin for the two known genotypes that infect European bats. We also suggest that multiple genotypes may exist within the diversity of viruses currently classified as 'Lagos Bat'. In sum, we show that rigorous phylogenetic techniques based on full length genome sequence provide the best discriminatory power for genotype classification within the lyssaviruses.

Show MeSH
Related in: MedlinePlus