Spatio-temporal spread of Lassa virus and a new rodent host in the Mano River Union area, West Africa

ABSTRACT

The spread of Lassa virus (LASV) in Guinea, Liberia and Sierra Leone, which together are named the Mano River Union (MRU) area, was examined phylogeographically. To provide a reliable evolutionary scenario, new rodent-derived, whole LASV sequences were included. These were generated by metatranscriptomic next-generation sequencing from rodents sampled between 2003 and 2020 in 21 localities of Guinea and Sierra Leone. An analysis was performed using BEAST to perform continuous phylogeographic inference and EvoLaps v36 to visualize spatio-temporal spread. LASV was identified as expected in its primary host reservoir, the Natal multimammate mouse (Mastomys natalensis), and also in two Guinean multimammate mice (Mastomys erythroleucus) in northern Sierra Leone and two rusty-bellied brush-furred mice (Lophuromys sikapusi) in southern Sierra Leone. This finding is consistent with the latter two species being secondary host reservoirs. The strains in these three species were very closely related in LASV lineage IV. Phylogenetic analysis indicated that the most recent common ancestor of lineage IV existed 316–374 years ago and revealed distinct, well-supported clades from Sierra Leone (Bo, Kabala and Kenema), Guinea (Faranah, Kissidougou-Guekedou and Macenta) and Liberia (Phebe-Ganta). The phylogeographic scenario suggests southern Guinea as the point of origin of LASV in the MRU area, with subsequent spread to towards Mali, Liberia and Sierra Leone at a mean speed of 1.6 to 1.1 km/year.

KEYWORDS:

• Lassa virus
• spread
• phylogeography
• rodent
• Lophuromys sikapusi
• Guinea
• Sierra Leone
• West Africa

Acknowledgments

The authors thank Fanta Berete and Morlaye Sylla at the Projet des Fièvres Hémorragiques en Guinée, Mohamed Vandi and Mohamed Bah at the Sierra Leone Ministry of Health and Sanitation for participating in the field work, Father Joseph Turay and Mercy Mwaura for their support of the collaborative One Health surveillance programme in Sierra Leone. We also thank all the local authorities and individual household heads for allowing us to work in their communities. We are particularly indebted to Dr Matthias Borchert and Dr Almudena Mari Saez for their commitment in the LAROCS project. Finally, the production of maps and charts from the Evolaps platform would not have been possible without the advices of Dr François Chevenet.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Ethics approval

This study adopted the guidelines of the Declaration of Helsinki, and the approved Ethics of the following programs: TREAT-CONTROL-VHF: The Guinean National Ethics Committee for Health Research (2003/PFHG/05/GUI), LAROCS: The Guinean National Ethics Committee for Health Research (12/CNERS/12) and by the Ethics Committee of the Ministry of Health and Sanitation, Government of Sierra Leone (16 May 2012), PREEMPT: The University of California, Davis Institutional Animal Care and Use Committee (IACUC; protocol #22696 Field surveillance for rodent-borne pathogens in West Africa (Sierra Leone) in collaboration with the Sierra Leone Ministry of Health and Sanitation, and the Ministry of Agriculture and Forestry under permit #CONF/LSD/02/17).

Additional information

Funding

Funding for this study were provided by the European Union through the INCO-DEV grant (ICA4-CT2002-10050) and the PANDORA-ID-NET from the EDCTP Reg/(RIA2016E-1609), the Deutsche Forschungsgemainschaft (DFG – German Research Foundation) through the LAROCS project 2013–2019 (ref BO 3790/1&2-1, FI 1781/1&2-1), the Medical Research Council (MC_UU_00034/6), and the Defense Advanced Research Projects Agency (DARPA) through the PREEMPT project (D18AC00028).