So far, studies estimating the substitution rate mainly relied on LASV sequences obtained from human infections scattered over a large geographic area. Timing of the phylogenetic divergence events in LASV evolution depends on estimation of the molecular clock rate of the virus. Geographical pattern of the lineages indicates that the virus has spread from east to west 7. Phylogenetic analyses showed that LASV currently consists of five lineages, with three lineages found in Nigeria, one in Sierra Leone, Guinea and Liberia, and one in Mali and Côte d’Ivoire 7, 8, 9. The large RNA segment (L-RNA) encodes the RNA-dependent RNA polymerase (L) and the matrix protein Z 6. The small RNA segment (S-RNA) encodes the nucleoprotein (NP) and the glycoprotein precursor (GPC). LASV is a member of the family Arenaviridae containing two genome segments of single-stranded RNA. It is transmitted to humans through the multimammate mouse, Mastomys natalensis, which is living commensally in rural areas of West Africa 4, 5. The disease caused by LASV, Lassa fever, is endemic in two distinct endemic areas, one in Nigeria and the second in Sierra Leone-Guinea-Liberia-Mali 3. The virus is estimated to cause about 200,000 infections with up to 5,000 deaths each year in West Africa 2. Lassa virus (LASV) was discovered in 1969 in Nigeria 1. The latter feature is relevant for rodent control strategies, as it implies that recurrence of the virus from neighbouring villages may occur in villages where the virus has previously been eradicated. In conclusion, our data indicate that the temporal and spatial pattern of LASV evolution in the natural reservoir is characterized by a combination of stationary circulation within a village and virus movement between villages. We observed, however, there are monophyletic clusters at village and sub-village level at specific points in time. Second, viruses circulating in a specific village are diverse and polyphyletic. First, the virus evolves in the reservoir with a molecular clock rate of 9 (7–11) × 10 –4 position –1 year –1 implying that contemporary LASV lineages circulate in the Faranah area since less than 100 years. This study reveals two main features of LASV evolution in M. natalensis trapped in 12 villages around Faranah, Upper Guinea, over a period of 12 years. To this end, we generated 132 partial nucleoprotein sequences of LASV from M. This study aimed at reconstructing the spatial and temporal evolution of Lassa virus (LASV) in the natural host population.
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