Aude Lalis

Mastomys natalensis and Lassa fever, West Africa.

PCR screening of 1,482 murid rodents from 13 genera caught in 18 different localities of Guinea, West Africa, showed Lassa virus infection only in molecularly typed Mastomys natalensis. Distribution of this rodent and relative abundance compared with M. erythroleucus correlates geographically with Lassa virus seroprevalence in humans.

Taxonomy and biogeography of the African Pygmy mice, Subgenus Nannomys (Rodentia, Murinae, Mus) in Ivory Coast and Guinea (West Africa)

Abstract Recent investigations in Guinea and Ivory Coast showed that Mus (Nannomys) are hosts of new arenaviruses. However, the taxonomy and biogeography of the western pygmy mice are poorly known, as this genus contains many cryptic species. To improve our taxonomic knowledge on this subgenus and its distribution range in West Africa, we performed a molecular, cytogenetical and morphological study of all Mus (Nannomys) species in this part of Africa. This approach allowed us to detect five species in Guinea (Mus mattheyi, M. minutoides, M. setulosus, M. baoulei, M. musculoides) and four (M. minutoides, M. setulosus, M. baoulei, M. musculoides) in Ivory Coast. Our molecular results confirm the validity of M. baoulei and the extended distribution range of M. mattheyi. We also observed a high degree of genetic differentiation between and within these species, especially within the M. setulosus clade which may be a species complex. The canonical analyses on the craniometrical and external morphological features of the sequenced specimens are insufficient to perfectly separate the studied species. Nevertheless, our results confirm that M. setulosus and M. baoulei are the largest Mus species that occur in Guinea and Ivory Coast. M. baoulei can be distinguished by its short tail and M. setulosus by an enlarged and bilobated lower molar (M3). Among the smaller species, M. musculoides is difficult to identify using morphological data alone, but differences in tail length proportions, size of tympanic bullae, the length and shape of the upper dental row allow identification of this species with some confidence. Our results allow us to provide some conclusions about the distribution ranges of the studied Mus (Nannomys) spp. in both countries and to discuss their presence in relation to vegetation, habitat and human settlements.

The impact of human conflict on the genetics of Mastomys natalensis and Lassa virus in West Africa.

Environmental changes have been shown to play an important role in the emergence of new human diseases of zoonotic origin. The contribution of social factors to their spread, especially conflicts followed by mass movement of populations, has not been extensively investigated. Here we reveal the effects of civil war on the phylogeography of a zoonotic emerging infectious disease by concomitantly studying the population structure, evolution and demography of Lassa virus and its natural reservoir, the rodent Mastomys natalensis, in Guinea, West Africa. Analysis of nucleoprotein gene sequences enabled us to reconstruct the evolutionary history of Lassa virus, which appeared 750 to 900 years ago in Nigeria and only recently spread across western Africa (170 years ago). Bayesian demographic inferences revealed that both the host and the virus populations have gone recently through severe genetic bottlenecks. The timing of these events matches civil war-related mass movements of refugees and accompanying environmental degradation. Forest and habitat destruction and human predation of the natural reservoir are likely explanations for the sharp decline observed in the rodent populations, the consequent virus population decline, and the coincident increased incidence of Lassa fever in these regions. Interestingly, we were also able to detect a similar pattern in Nigeria coinciding with the Biafra war. Our findings show that anthropogenic factors may profoundly impact the population genetics of a virus and its reservoir within the context of an emerging infectious disease.

Complete genome sequence and molecular phylogeny of a newfound hantavirus harbored by the Doucet's musk shrew (Crocidura douceti) in Guinea.

Elucidation of the molecular phylogeny of shrew-borne hantaviruses in sub-Saharan Africa has been hampered by the lack of full-length viral genomes. In this report, we present the complete genome analysis of a newfound hantavirus, designated Bowé virus, detected in ethanol-fixed intercostal muscle of a Doucets musk shrew (Crocidura douceti), captured in southwestern Guinea in February 2012. Full-length amino acid sequence comparison of the S-, M- and L-segment gene products revealed that Bowé virus differed by 24.1-53.4%, 17.0-59.9% and 14.6-39.7%, respectively, from all other representative rodent-, shrew- and mole-borne hantaviruses. Phylogenetic analysis, using maximum-likelihood and Bayesian methods, under the GTR+I+Γ model of evolution, showed that Bowé virus shared a common ancestry with Tanganya virus, a hantavirus detected in the Thereses shrew (Crocidura theresae) in Guinea. Whole genome analysis of many more hantaviruses from sub-Saharan Africa are needed to better clarify how the radiation of African shrews might have contributed to the phylogeography of hantaviruses.

Molecular Phylogeny of Hantaviruses Harbored by Insectivorous Bats in Côte d’Ivoire and Vietnam

The recent discovery of genetically distinct hantaviruses in multiple species of shrews and moles prompted a further exploration of their host diversification by analyzing frozen, ethanol-fixed and RNAlater®-preserved archival tissues and fecal samples from 533 bats (representing seven families, 28 genera and 53 species in the order Chiroptera), captured in Asia, Africa and the Americas in 1981–2012, using RT-PCR. Hantavirus RNA was detected in Pomona roundleaf bats (Hipposideros pomona) (family Hipposideridae), captured in Vietnam in 1997 and 1999, and in banana pipistrelles (Neoromicia nanus) (family Vespertilionidae), captured in Côte d’Ivoire in 2011. Phylogenetic analysis, based on the full-length S- and partial M- and L-segment sequences using maximum likelihood and Bayesian methods, demonstrated that the newfound hantaviruses formed highly divergent lineages, comprising other recently recognized bat-borne hantaviruses in Sierra Leone and China. The detection of bat-associated hantaviruses opens a new era in hantavirology and provides insights into their evolutionary origins.

Morphological identification of sibling species: the case of West African Mastomys (Rodentia: Muridae) in sympatry

In this study, we investigate skull size and shape differentiation between sibling species of Mastomys with the aim to characterize and discriminate three sympatric species found in West Africa: M. huberti, M. erythroleucus and M. natalensis. A total of 133 genetically determined specimens were used for the morphometric analyses. Statistical analyses clearly demonstrated that the three species largely overlapped in centroid size (M. erythroleucus tends to be larger on average than the M. huberti and M. natalensis) but they exhibited large differences in skull shape. The current study focused on skull shape, and allowed us to discriminate three morphological groups that are congruent with the three species suggested by molecular identification (90% of the individuals are correctly assigned by cross-validated classifications). In the Mastomys, the evolution of cranial length and shape may be influenced by competitive pressure between closely related species separated by ecological segregation. This source of variability could possibly induce character displacement between species of Mastomys.

Cranial morphometric and fine scale genetic variability of two adjacentMastomys natalensis (Rodentia: Muridae) populations

The objective of this multidisciplinary project was to study the intra-specific morphometric and genetic variability between two adjacent populations ofMastomys natalensis Smith, 1834 living in different environments. The study of micro-evolutionary processes at work by using geometrical morphometrics allowed us to define two groups, characterized by different features of the skull shape. Using molecular microsatellites analysis, we showed that the two populations exchanged high gene flow and could be considered as a single panmictic unit. These results suggest that this widely-distributed species exhibits a local population-level differentiation in shape variation of skulls, probably due to different ecological situations. We speculate that the variability in the cranial characteristics (connected with the feeding ability) could reveal a local adaptation preferentially based on the food availability. We propose an explanation linking the shape differences to the fitness gain in the exploitation of resources available in the two environments. Since we suggest a potential differentiation process between populations, we believe that the two groups constitute even better models to understand the factors involved in the early stages of local adaptations.

Genetic Variation in a North African Rodent Pest, Meriones shawi: Microsatellite Polymorphism

Meriones shawi is an ubiquitous and endemic rodent in northern African. This species is considered as an economically important pest because it often damages crops. Moreover, the gerbillines are known to function as reservoirs for a variety of serious human epidemic diseases. Ten polymorphic microsatellite loci were identified using 454 GS-FLX Titanium pyrosequencing and a multiplex PCR assay was developed. The utility of these markers was evaluated in 30 individuals from three different Moroccan populations. Number of alleles per locus ranged from 2 to 7, with observed and expected heterozygosities ranging from 0.033 to 0.967 and from 0.033 to 0.729, respectively. Departures from Hardy-Weinberg equilibrium were observed at two loci. These markers will be useful resources for future population genetics studies for this rodent and pest-borne disease management.

A set of 18 polymorphic microsatellite loci in the Algerian mouse, Mus spretus Lataste 1883 (Rodentia: Muridae)

A multiplex PCR assay was developed for the identification of polymorphic microsatellite loci (18) for the Algerian mouse, Mus spretus, using 454 GS-FLX Titanium pyrosequencing. The utility of these markers was evaluated in 184 individuals from for different Moroccan populations. Number of alleles per locus ranged from 10 to 39, with expected and observed heterozygosities ranging from 0.256 to 0.947 and from 0.259 to 0.926 respectively. None departures from Hardy–Weinberg equilibrium were observed at all loci. These markers will be valuable tools for population genetic studies in conservation management.

Mice and Men: an Evolutionary History of Lassa Fever

Abstract: Lassa fever is a hemorrhagic viral disease caused by the Lassa virus (LASV), a member of the Arenaviridae family from the Arenavirus genus, and is transmitted to humans by some rodents. Although the Lassa fever was described for the first time in the 1950s, the virus responsible was only isolated in 1969 during an epidemic in Lassa village in Nigeria. Lassa fever is endemic in West Africa and outbreaks occur in two distinct geographical areas, the Mano river region (SL, L and G) and Nigeria. However, serological studies suggest that the LASV has recently emerged in various African countries (Senegal 1988; Mali 2009; Burkina Faso 2010; Ivory Coast 2000, 2013; Benin 1977, 2014; Cameroon 2011; Ghana 2011; Democratic Republic of Congo 2011; Uganda 2017). LASV is also the hemorrhagic fever most frequently exported to countries of the Global North, with more than thirty cases documented since 1969: in England (1971, 1972, 1975, 1976, 1981, 1982, 1984, 1985, 2000, 2003), the Netherlands (1980, 2000), Germany (1974, 2000, 2006, 2016), Sweden (2016), Israel (1987), the United States (1969, 1975, 1976, 1989, 2004, 2015), Canada (1989) and Japan (1987).