Molecular Epidemiology of Lassa virus in the Mano River Union area, West Africa

Abstract

Introduction: Lassa virus (LASV) is a single-stranded negative-sense RNA virus that belongs to the family of Arenaviridae. It causes the viral haemorrhagic fever known as Lassa fever (LF), which was first described in Nigeria in 1969. While endemic in several West African countries, frequent outbreaks occur in Nigeria and the Mano River Union (MRU) region (Sierra Leone, Guinea and Liberia). The Natal multimammate mouse, Mastomys natalensis and more recently, Mastomys erythroleucus, Hylomyscus pamfi and Mus baoulei have been implicated as reservoirs in the maintenance and transmission of LASV. According to molecular dating, the existing LASV variants originated in Nigeria over a thousand years ago, with the subsequent westward spread across West Africa during the last hundreds of years. Despite studies unveiling the evolution of LASV in various MRU regions, its spread remains unclearly understood in both Guinea and Sierra Leone, where M. natalensis, R. rattus and the House mouse, Mus musculus, mostly co-habit in human dwellings. Therefore, this study aims to reconstruct the evolution of LASV in the MRU area by performing a phylogeny to understand the spread of the virus in Sierra Leone and Guinea. To this end, the study shall provide information concerning the distribution of LASV in small mammal populations and examine the phylogeny of the virus in both countries. Methods: Standardized rodent trapping was performed in 41 localities in Sierra Leone and Guinea. In Sierra Leone, 26 villages were investigated. Six of these villages were longitudinally surveyed, with sampling carried out in various habitats and seasons for two years (2014–2016) in the Bo area and Southern region. The 20 other villages were surveyed in a transect (2017 – 2018) that started around Freetown in the Western area and passing through the North-West region up to the Northern province, with trapping conducted inside houses. In Guinea, 15 villages were also sampled in the transect (2013 – 2019), with trapping done inside houses. Small mammals trapped were morphologically and molecularly identified. Samples collected were tested for arenavirus IgG and LASV RNA, and the Bayesian phylogenetic analysis was performed on sequences generated by the PCR and NGS techniques.

Results: In Sierra Leone, 1490 small mammals were collected in the longitudinal survey, and 16 rodent species were identified. Here, M. natalensis (355, 24%) was found to be the most prevalent species, with a significantly higher abundance inside houses than surrounding vegetation and different trapping success between seasons (P < 0.0001). The transect survey collected 898 rodents, with 14 rodent species identified. Again, M. natalensis occurred the most, with a prevalence of 54.2% (487 in 898). For LASV/Arenavirus IgG in the longitudinal survey, 41 out of 1,473 (2.8%) samples tested IgG positive, and 31 of these were trapped in homes and 10 in the surrounding vegetation. Twenty-nine of 41 IgG positive rodents were M. natalensis. Four LASV-positive samples were detected by PCR in two villages, all found in M. natalensis. In the transect, 28 out of 864 samples tested positive for IgG, bringing the overall seroprevalence to about 3.2%. Twenty of the 28 seropositive rodents were M. natalensis. Nine LASV-positive individuals were detected in 3 of the 20 villages and were all M. natalensis. In Guinea, 696 rodents were collected, comprising five rodent taxa identified down to species level and two others at the genus level. Mastomys natalensis occurred at 90.8%. A total of 523 samples were tested for LASV/Arenavirus IgG. One hundred and thirteen samples, including 111 M. natalensis, were found positive, with an overall seroprevalence of about 21.6%. For LASV RNA, 40 samples, all M. natalensis, were PCR positive. Phylogenetic analysis shows that all sequences generated in this study belong to lineage IV and are distributed based on the location of the collection within distinct clades. The study showed that LASV evolved in the MRU region over 400 years ago. This concurs with the previously described route of entry, that is, through Cote d‘Ivoire/Mali, to Liberia, and subsequently to Guinea and Sierra Leone. Further analysis shows the ancestral strain for the study countries evolved about 257 years ago from around Nimba County in Libera, and subsequently spread to other regions of Guinea and Sierra Leone. Additionally, a Kodoko virus was also identified in a pygmy mouse, Mus minutoides, which marks the first non-Lassa arenavirus observed in Sierra Leone.

Conclusion: Several rodent species inhabit the various communities sampled, with M. natalensis being widespread. Also, there is widespread arenavirus infection circulating among the small mammal populations, evidenced by the LASV, KDKV and arenavirus IgG detected in various regions of Sierra Leone and Upper Guinea. The study, however, found a lower occurrence of M. natalensis and a lower circulation of LASV in rodents in villages in Sierra Leone. Findings in this study will serve as a point of reference for public health awareness and strategies for the treatment and control of LF in the MRU area.