Geographic distribution and genetic characterization of Lassa virus in sub-Saharan Mali

Abstract

Background: Lassa fever is an acute viral illness characterized by multi-organ failure and hemorrhagic manifestations. Lassa fever is most frequently diagnosed in Nigeria, Sierra Leone, Liberia, and Guinea, although sporadic cases have been recorded in other West African countries, including Mali. The etiological agent of Lassa fever is Lassa virus (LASV), an Arenavirus which is maintained in nature and frequently transmitted to humans by Mastomys natalensis. The purpose of this study was to better define the geographic distribution of LASV-infected rodents in sub-Saharan Mali.

Methodologies/principal findings: Small mammals were live-trapped at various locations across Mali for the purpose of identifying potential zoonotic pathogens. Serological and molecular assays were employed and determined LASV infected rodents were exclusively found in the southern Mali near the border of Côte d'Ivoire. Overall, 19.4% of Mastomys natalensis sampled in this region had evidence of LASV infection, with prevalence rates for individual villages ranging from 0 to 52%. Full-length genomic sequences were determined using high throughput sequencing methodologies for LASV isolates generated from tissue samples of rodents collected in four villages and confirmed the phylogenetic clustering of Malian LASV with strain AV.

Conclusions/significance: The risk of human infections with LASV is greatest in villages in southern Mali. Lassa fever should be considered in the differential diagnosis for febrile individuals and appropriate diagnostic techniques need to be established to determine the incidence of infection and disease in these regions.

Figure 1. Map of Mali depicting the various locations where small mammals were trapped.

Sera and tissue samples were collected at some locations (blue dots) whereas at other locations only sera were collected (green dots). The major cities of Mali are represented by black markers. Inset is an expanded view of southern Mali where the occurrence of Lassa virus infected rodents was documented. The sampled villages are named, and red markers indicate villages where Lassa virus infected rodents were documented. The maps were generated using ESRI ArcMap 10.1; the map of Mali utilizes an ESRI satellite imagery basemap and the inset utilizes an ESRI basemap with the imagery and transportation layers activated, both supplied with the GIS software.

Figure 2. Phylogenetic analysis was conducted on full-length sequences for the nucleocapsid protein using the Jukes-Cantor Neighbor-joining method with 10,000 bootstrap replicates.

Sequences from the five Malian isolates were compared to the following arenavirus sequences: Tacaribe (NC_004293), Lujo (NC_012776), Lymphocytic choriomeningitis virus (LCMV, strain Armstrong, AY847350), Ippy (NC_007905), Mobala (AY342390), Morogoro (NC_013057), Mopeia (NC_006575) and Lassa virus strains Josiah (AY628203), CSF (AF333969), NL (AY179173), AV (AF246121), Z148 (AY628205), Macenta (AY628201), BA366 (GU830839), Nig08-A18 (GU481070), Nig08-A47 (GU481078), 803213 (AF181854), Pinneo (AY628207), GA391 (X52400), Acar 3080 (AY628208) and Weller (AY628206).

Figure 3. Phylogenetic analysis was conducted on full-length sequences for the glycoproteins using the Jukes-Cantor Neighbor-joining method with 10,000 bootstrap replicates.

Sequences from the five Malian isolates were compared to the arenavirus sequences outlined in figure legend 2.

Figure 4. Phylogenetic analysis was conducted on full-length sequences for the polymerase using the Jukes-Cantor Neighbor-joining method with 10,000 bootstrap replicates.

Sequences from the five Malian isolates were compared to the following arenavirus sequences: Tacaribe (NC_004292), Lujo (NC_012777), Lymphocytic choriomeningitis virus (LCMV, strain Armstrong, J04331), Ippy (NC_007906), Mobala (NC_007904), Morogoro (NC_013058), Mopeia (NC_006574) and Lassa virus strains Josiah (NC_004297), CSF (AY179174), NL (AY179172), AV (AY179171), Z148 (AY628204), Macenta (AY628200), BA366 (GU979513), Nig08-A18 (GU481071), Nig08-A47 (GU481079).