Figure 1.
Map of Côte d'Ivoire showing the capture sites.
Latitude North and longitude West coordinates are given below the name of the villages.
Table 1.
Small mammals from Côte d'Ivoire tested by pan-Old World arenavirus RT-PCR, Lassa virus-specific RT-PCR, and Old World arenavirus immunofluorescence assaya.
Table 2.
Sequences generated in this study.
Table 3.
Genetic distance of Gbagroube and Menekre virus to other Old World arenaviruses.
Figure 2.
Phylogenetic analysis of Old World arenaviruses including Gbagroube and Menekre virus.
Phylogenies were inferred by BEAST software based on nucleotide sequences of complete GPC and NP gene, and partial L gene. Posterior values are indicated on the branches. For GPC and NP genes, the phylogeny was verified by using PhyML software (trees not shown). Branches which are not or poorly supported by PhyML (bootstrap values <0.5) are indicated with an asterisk; all other branches are supported with bootstrap values >0.5. For clarity of presentation, some distal branches were collapsed. The LCM virus main clade includes strains CH-5692, CH-5871, Armstrong, WE, Traub, MX, Pasteur, UBC-aggressive, and Marseille 12. The origin of Lassa virus strains is indicated by a prefix: SL, Sierra Leone; LIB, Liberia; GUI, Guinea; IC, Ivory Coast; NIG, Nigeria. Lassa virus lineages are indicated by roman numerals. The complete list of taxa with GenBank accession numbers is provided in Table S1.
Figure 3.
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].
Figure 4.
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.