Lassa fever in Benin: description of the 2014 and 2016 epidemics and genetic characterization of a new Lassa virus

ABSTRACT

We report two outbreaks of Lassa fever that occurred in Benin in 2014 and 2016 with 20 confirmed cases and 50% (10/20) mortality. Benin was not previously considered to be an endemic country for Lassa fever, resulting in a delay to diagnose the disease and its human transmission. Molecular investigations showed the viral genomes to be similar to that of the Togo strain, which is genetically very different from other known strains and confirms the existence of a new lineage. Endemic circulation of Lassa virus in a new territory and the genetic diversity thus confirm that this virus represents a growing threat for West African people. Given the divergence of the Benin strain from the prototypic Josiah Sierra Leone strain frequently used to generate vaccine candidates, the efficacy of vaccine candidates should also be demonstrated with this strain.

KEYWORDS:

• Lassa fever
• Lassa virus
• genome
• Benin
• outbreak
• phylogeny
• new lineage
• serology

Acknowledgements

We thank Yahannon Martial and Mama Yaya Abdou Matinou for facilitating access to the epidemiological data from the department of Borgou. We are grateful to Anne Bocquin and Héloïse Thomasset from INSERM – Jean Mérieux BSL4Laboratory and Institut Pasteur for their technical assistance. AY, CP, SG, SB, and EFC conceived the study; CP, SB, and EFC wrote the manuscript; CP, TR, and DC acquired genome data by NGS and Sanger sequencing; TR and DT performed virus isolation on Vero cells; LO, BBZ, AJ, SMe, SMu, and CP performed the identification of LASV from the samples by RT-PCR and ELISA; TR, LO, DP, and SB validated the results of the diagnosis; MP managed the data and supported the logistics in Benin and Germany; ECK and EOJ coordinated the collection of samples and epidemiological data in Tchaourou and Parakou; AY, FL, HB, FG coordinated the shipment of samples to Europe; LK, RS, CGK, MDS, SK, ALK, and PM coordinated the outbreak response within the country; and EFC gathered the field data and performed the phylogenetic analysis.

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

Correction Statement

This article has been republished with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

This research was funded by the German Research Foundation [grant numbers DFG FI 1781/2-1 and GU 883/4-1], the European Commission through the Horizon 2020 project EVAg (European Virus Archive goes global [grant number 653316], and the Global Health protection programme supported by the Federal Ministry of Health [grant number ZMVI1-2516-GHP-704]. Institut Pasteur and INSERM – Jean Mérieux BSL4 Laboratory were funded by Santé Publique France.