Figure 1.
A) Mano River region map with the location of 25 trapping sites.
Sites where only Mastomys erythroleucus or M. natalensis were trapped are shown in white and black dots respectively; sites where both species were captured are colored in gray. Regions where Lassa virus-positive rodents were caught are marked with large black circles (Districts of Faranah: villages of Gbetlaya (GB), Bantou (BA), Tanganya (TA) and Guéckédou: Denguedou (DGD). The reddish rectangular inset corresponds to the area represented in part B. B) Maps of Geneland spatial assignments to clusters for K = 2. The highest membership values are in light yellow and the isolines (grey curves) illustrate the spatial changes in assignment values. The plot is based on the highest-probability run for K = 2 (the same split and similar posterior probabilities were obtained for all 20 replicates).
Figure 2.
A) M. natalensis populations clustering based on Structure Bayesian inference (K = 2 to 4); Burn-in period = 150,000; MCMC repeat length = 200,000).
Each color represents one assumed population cluster K. Multiple colored bars display an individual's estimated membership proportion in more than one population (q), i.e. the admixture level. The labels correspond to the sampling location indicated in table S1. It should be noted that PCR-positive and PCR-negative rats collected in a same location belong to the same source population according to structure. B) Neighbor-joining (NJ) phenogram summarizing Cavalli-Sforza & Edwards' (1967) DCE chord distances among 15 populations of M. natalensis collected in Guinea. Values on the nodes represent the percentage of bootstrap replicates over individuals (n = 100). Branch lengths are proportional to the genetic distance between the different populations and the scale bar represents a distance DCE of 0.05. Population codes are defined according to Table S1. C) The same phylogenetic reconstruction as shown in (B) but with a partition of the LASV positive and negative rats into sub-populations. The Bamakama sample was used as an out-group.
Table 1.
Summary statistics of Multivariate Analysis of Variance (MANOVA): The mixed – effects (Lassa Virus infection, Locality, Year and Season) on three parameters of genetic diversity (Inbreeding coefficient, Fis, Observed heterozygosity, Ho and Allelic richness, A) of four Mastomys natalensis populations where both LASV-PCR negative and LASV-PCR positive individuals coexisted.
Figure 3.
Maximum clade credibility tree representing the genealogy of the LASV strains by analyzing 627 nucleotides of the nucleoprotein gene using a Bayesian method.
The tree has a proportional relationship between branch length and time. The main lineages are highlighted. The numbers represent posterior probabilities of the most important internal nodes. Color code: Green: Nigeria; blue: Liberia; Red: Sierra Leone and Pink: Guinea. Strains abbreviation and characteristics are described in Tables S4.
Figure 4.
Beast Bayesian skyline plots obtained by analyzing LASV nucleoprotein sequences from 18 Nigerian and 72 Mano River region strains sampled at different times.
The black solid line represents the median and the grey area the 95% HPD of the Ne(t) estimates. The orange columns highlight civil war peaks in the concerned regions and illustrate the concordance between civil war, virus population decline and viral diversity loss.
Table 2.
Beast Bayesian analyses for the 90 Lassa virus strains under different coalescent tree priors: constant population size, exponential growth, and skyline plots.