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Novel arenavirus sequences in Hylomyscus sp. and Mus (Nannomys) setulosus from Côte d'Ivoire: implications for evolution of arenaviruses in Africa.

Coulibaly-N'Golo D, Allali B, Kouassi SK, Fichet-Calvet E, Becker-Ziaja B, Rieger T, Olschläger S, Dosso H, Denys C, Ter Meulen J, Akoua-Koffi C, Günther S - PLoS ONE (2011)

Bottom Line: During 2003 through 2005, 1,228 small mammals representing 14 different genera were trapped in 9 villages in south, east, and middle west of Côte d'Ivoire.Arenavirus infection of Mus (Nannomys) setulosus was also demonstrated by serological testing.Reconstruction of possible virus-host co-phylogeny scenarios suggests that, within the African continent, signatures of co-evolution might have been obliterated by multiple host-switching events.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire des Arbovirus/Entérovirus, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire.

ABSTRACT
This study aimed to identify new arenaviruses and gather insights in the evolution of arenaviruses in Africa. During 2003 through 2005, 1,228 small mammals representing 14 different genera were trapped in 9 villages in south, east, and middle west of Côte d'Ivoire. Specimens were screened by pan-Old World arenavirus RT-PCRs targeting S and L RNA segments as well as immunofluorescence assay. Sequences of two novel tentative species of the family Arenaviridae, Menekre and Gbagroube virus, were detected in Hylomyscus sp. and Mus (Nannomys) setulosus, respectively. Arenavirus infection of Mus (Nannomys) setulosus was also demonstrated by serological testing. Lassa virus was not found, although 60% of the captured animals were Mastomys natalensis. Complete S RNA and partial L RNA sequences of the novel viruses were recovered from the rodent specimens and subjected to phylogenetic analysis. Gbagroube virus is a closely related sister taxon of Lassa virus, while Menekre virus clusters with the Ippy/Mobala/Mopeia virus complex. Reconstruction of possible virus-host co-phylogeny scenarios suggests that, within the African continent, signatures of co-evolution might have been obliterated by multiple host-switching events.

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Timing of speciation events in the Old World arenavirus clade.Phylogenies were inferred by BEAST software based on 122 partial nucleotide sequences of NP gene of viruses collected over a period of 70 years. The substitution rate was estimated from the data set. Posterior values are indicated on the branches. Blue bars indicate the smallest interval that contains 95% of the posterior probability density for a node age, i.e. the time to the most common recent ancestor of the respective clade. The year of collection is shown with the strains. The complete list of taxa with GenBank accession numbers and year of collection is provided in Table S1.
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pone-0020893-g004: Timing of speciation events in the Old World arenavirus clade.Phylogenies were inferred by BEAST software based on 122 partial nucleotide sequences of NP gene of viruses collected over a period of 70 years. The substitution rate was estimated from the data set. Posterior values are indicated on the branches. Blue bars indicate the smallest interval that contains 95% of the posterior probability density for a node age, i.e. the time to the most common recent ancestor of the respective clade. The year of collection is shown with the strains. The complete list of taxa with GenBank accession numbers and year of collection is provided in Table S1.

Mentions: Another piece of information on the evolutionary history of arenaviruses in Africa may be obtained by estimating the nucleotide substitution rate. The alignment of 122 partial NP sequences from OWAs, mainly collected between 1969 and 2008, contained sufficient temporal structure to estimate a global rate for the clade. The BEAST program calculated a rate of 5.1×10−4 substitutions×site−1×year−1 with good statistical precision: the smallest interval that contains 95% of the posterior probability density was 3.6–6.8×10−4 site−1×year−1. Nevertheless, it may be interpreted with caution, given that the difference in date between the samples is not large compared to the overall time scale of the reconstruction. The rate estimate for the OWA clade is in the same order of magnitude than estimates for other RNA viruses [31], [32]. It implies that the ancestors of contemporary OWAs are between 3000 and 7000 years old (Fig. 4). Speciation of Menekre and Gbagroube virus was calculated to have happened within the past 2000 years. All these times are orders of magnitudes too recent to match with the speciation times of the respective rodent hosts some millions of years ago [23], [25], [33].


Novel arenavirus sequences in Hylomyscus sp. and Mus (Nannomys) setulosus from Côte d'Ivoire: implications for evolution of arenaviruses in Africa.

Coulibaly-N'Golo D, Allali B, Kouassi SK, Fichet-Calvet E, Becker-Ziaja B, Rieger T, Olschläger S, Dosso H, Denys C, Ter Meulen J, Akoua-Koffi C, Günther S - PLoS ONE (2011)

Timing of speciation events in the Old World arenavirus clade.Phylogenies were inferred by BEAST software based on 122 partial nucleotide sequences of NP gene of viruses collected over a period of 70 years. The substitution rate was estimated from the data set. Posterior values are indicated on the branches. Blue bars indicate the smallest interval that contains 95% of the posterior probability density for a node age, i.e. the time to the most common recent ancestor of the respective clade. The year of collection is shown with the strains. The complete list of taxa with GenBank accession numbers and year of collection is provided in Table S1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3111462&req=5

pone-0020893-g004: Timing of speciation events in the Old World arenavirus clade.Phylogenies were inferred by BEAST software based on 122 partial nucleotide sequences of NP gene of viruses collected over a period of 70 years. The substitution rate was estimated from the data set. Posterior values are indicated on the branches. Blue bars indicate the smallest interval that contains 95% of the posterior probability density for a node age, i.e. the time to the most common recent ancestor of the respective clade. The year of collection is shown with the strains. The complete list of taxa with GenBank accession numbers and year of collection is provided in Table S1.
Mentions: Another piece of information on the evolutionary history of arenaviruses in Africa may be obtained by estimating the nucleotide substitution rate. The alignment of 122 partial NP sequences from OWAs, mainly collected between 1969 and 2008, contained sufficient temporal structure to estimate a global rate for the clade. The BEAST program calculated a rate of 5.1×10−4 substitutions×site−1×year−1 with good statistical precision: the smallest interval that contains 95% of the posterior probability density was 3.6–6.8×10−4 site−1×year−1. Nevertheless, it may be interpreted with caution, given that the difference in date between the samples is not large compared to the overall time scale of the reconstruction. The rate estimate for the OWA clade is in the same order of magnitude than estimates for other RNA viruses [31], [32]. It implies that the ancestors of contemporary OWAs are between 3000 and 7000 years old (Fig. 4). Speciation of Menekre and Gbagroube virus was calculated to have happened within the past 2000 years. All these times are orders of magnitudes too recent to match with the speciation times of the respective rodent hosts some millions of years ago [23], [25], [33].

Bottom Line: During 2003 through 2005, 1,228 small mammals representing 14 different genera were trapped in 9 villages in south, east, and middle west of Côte d'Ivoire.Arenavirus infection of Mus (Nannomys) setulosus was also demonstrated by serological testing.Reconstruction of possible virus-host co-phylogeny scenarios suggests that, within the African continent, signatures of co-evolution might have been obliterated by multiple host-switching events.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire des Arbovirus/Entérovirus, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire.

ABSTRACT
This study aimed to identify new arenaviruses and gather insights in the evolution of arenaviruses in Africa. During 2003 through 2005, 1,228 small mammals representing 14 different genera were trapped in 9 villages in south, east, and middle west of Côte d'Ivoire. Specimens were screened by pan-Old World arenavirus RT-PCRs targeting S and L RNA segments as well as immunofluorescence assay. Sequences of two novel tentative species of the family Arenaviridae, Menekre and Gbagroube virus, were detected in Hylomyscus sp. and Mus (Nannomys) setulosus, respectively. Arenavirus infection of Mus (Nannomys) setulosus was also demonstrated by serological testing. Lassa virus was not found, although 60% of the captured animals were Mastomys natalensis. Complete S RNA and partial L RNA sequences of the novel viruses were recovered from the rodent specimens and subjected to phylogenetic analysis. Gbagroube virus is a closely related sister taxon of Lassa virus, while Menekre virus clusters with the Ippy/Mobala/Mopeia virus complex. Reconstruction of possible virus-host co-phylogeny scenarios suggests that, within the African continent, signatures of co-evolution might have been obliterated by multiple host-switching events.

Show MeSH
Related in: MedlinePlus