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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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Related in: MedlinePlus

Historical associations between Old World arenaviruses and their rodent hosts.(A) Juxtaposition of host and virus tree. The rodent tree was compiled from published data [23], [24], [25], [26], [27]. The positions of Gbagroube and Menekre virus in the virus tree correspond to those in the NP gene tree shown in Fig. 2. Primary virus–host associations are indicated by dotted lines [2], [3], [4], [5], [6], [8], [28], [29]. (B) Reconciliation of virus tree (solid lines) with host tree (dotted lines) by CoRe-PA 0.3 [22]. One of several best-fit scenarios proposed by the program is shown, which includes 5 co-speciations, 4 host-switches, and 3 sorting events [30].
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pone-0020893-g003: Historical associations between Old World arenaviruses and their rodent hosts.(A) Juxtaposition of host and virus tree. The rodent tree was compiled from published data [23], [24], [25], [26], [27]. The positions of Gbagroube and Menekre virus in the virus tree correspond to those in the NP gene tree shown in Fig. 2. Primary virus–host associations are indicated by dotted lines [2], [3], [4], [5], [6], [8], [28], [29]. (B) Reconciliation of virus tree (solid lines) with host tree (dotted lines) by CoRe-PA 0.3 [22]. One of several best-fit scenarios proposed by the program is shown, which includes 5 co-speciations, 4 host-switches, and 3 sorting events [30].

Mentions: The identification of arenaviruses in rodents so far not implicated as OWA host species led us to investigate how the new data fit with current hypotheses on arenavirus–host co-evolution [1], [21]. The phylogenies of the OWAs were compared and reconciled with those of their hosts using the CoRe-PA 0.3 program [22]. As the virus phylogeny calculated with NP gene sequences was most stable and inferred by both BEAST and PhyML, it was used for the co-phylogeny analysis. The host tree was compiled from literature data [23], [24], [25], [26], [27]. All rodents known to be associated with an OWA were included [2], [3], [4], [5], [6], [8], [28], [29]. Juxtaposition of virus and host trees showed no obvious congruence between them (Fig. 3A). Reconciliation of the virus tree with the host tree revealed that a maximum of 5 co-speciation events (joint divergence of both host and virus) might have happened during evolution. The maximum of 5 co-speciations was found by CoRe-PA irrespective of whether a pre-defined cost model was used or optimal co-phylogenies were searched for with automatically calculated cost values. In addition to 5 co-speciations, best-fit scenarios included 4 host switches (transfer of virus from one host to another host that is not itself the immediate descendant of the source host) and 3 sorting events (apparent absence of virus in the descendants of a host that had previously been associated with virus) [30]. One of several possible co-phylogeny scenarios is shown in Fig. 3B. To test if the observed frequency of 5 co-speciations is biologically meaningful, randomization tests implemented in CoRe-PA were performed. Reconciliation of randomized virus trees with the host tree showed that 5 or more co-speciations occur just by chance in 63% of the random co-phylogenies; the average was 4.8 events. Thus, co-speciation between OWAs and their respective hosts — the hallmark of co-evolution — was not observed at a frequency above statistical noise. In conclusion, the currently available data do not lend support to the hypothesis that arenaviruses co-evolved with their hosts in Africa. Host-switching and adaptation might have been involved in evolution.


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)

Historical associations between Old World arenaviruses and their rodent hosts.(A) Juxtaposition of host and virus tree. The rodent tree was compiled from published data [23], [24], [25], [26], [27]. The positions of Gbagroube and Menekre virus in the virus tree correspond to those in the NP gene tree shown in Fig. 2. Primary virus–host associations are indicated by dotted lines [2], [3], [4], [5], [6], [8], [28], [29]. (B) Reconciliation of virus tree (solid lines) with host tree (dotted lines) by CoRe-PA 0.3 [22]. One of several best-fit scenarios proposed by the program is shown, which includes 5 co-speciations, 4 host-switches, and 3 sorting events [30].
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020893-g003: Historical associations between Old World arenaviruses and their rodent hosts.(A) Juxtaposition of host and virus tree. The rodent tree was compiled from published data [23], [24], [25], [26], [27]. The positions of Gbagroube and Menekre virus in the virus tree correspond to those in the NP gene tree shown in Fig. 2. Primary virus–host associations are indicated by dotted lines [2], [3], [4], [5], [6], [8], [28], [29]. (B) Reconciliation of virus tree (solid lines) with host tree (dotted lines) by CoRe-PA 0.3 [22]. One of several best-fit scenarios proposed by the program is shown, which includes 5 co-speciations, 4 host-switches, and 3 sorting events [30].
Mentions: The identification of arenaviruses in rodents so far not implicated as OWA host species led us to investigate how the new data fit with current hypotheses on arenavirus–host co-evolution [1], [21]. The phylogenies of the OWAs were compared and reconciled with those of their hosts using the CoRe-PA 0.3 program [22]. As the virus phylogeny calculated with NP gene sequences was most stable and inferred by both BEAST and PhyML, it was used for the co-phylogeny analysis. The host tree was compiled from literature data [23], [24], [25], [26], [27]. All rodents known to be associated with an OWA were included [2], [3], [4], [5], [6], [8], [28], [29]. Juxtaposition of virus and host trees showed no obvious congruence between them (Fig. 3A). Reconciliation of the virus tree with the host tree revealed that a maximum of 5 co-speciation events (joint divergence of both host and virus) might have happened during evolution. The maximum of 5 co-speciations was found by CoRe-PA irrespective of whether a pre-defined cost model was used or optimal co-phylogenies were searched for with automatically calculated cost values. In addition to 5 co-speciations, best-fit scenarios included 4 host switches (transfer of virus from one host to another host that is not itself the immediate descendant of the source host) and 3 sorting events (apparent absence of virus in the descendants of a host that had previously been associated with virus) [30]. One of several possible co-phylogeny scenarios is shown in Fig. 3B. To test if the observed frequency of 5 co-speciations is biologically meaningful, randomization tests implemented in CoRe-PA were performed. Reconciliation of randomized virus trees with the host tree showed that 5 or more co-speciations occur just by chance in 63% of the random co-phylogenies; the average was 4.8 events. Thus, co-speciation between OWAs and their respective hosts — the hallmark of co-evolution — was not observed at a frequency above statistical noise. In conclusion, the currently available data do not lend support to the hypothesis that arenaviruses co-evolved with their hosts in Africa. Host-switching and adaptation might have been involved in evolution.

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