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Lassa virus circulating in Liberia: a retrospective genomic characterisation
Michael R Wiley1, Lawrence Fakoli2, Andrew G Letizia3
1Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA; Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
The Lancet. Infectious Diseases
|October 8, 2019
Summary
Genomic sequencing reveals significant Lassa fever virus diversity in Liberia, highlighting the need for diagnostics and therapeutics tailored to local strains. This study provides crucial data for West African public health initiatives.
Area of Science:
- Virology
- Genomics
- Epidemiology
Background:
- Lassa fever cases are rising in West Africa, with Liberia reporting the highest per capita incidence.
- Genomic data on circulating Lassa fever virus strains in Liberia is limited, hindering targeted interventions.
- This study aimed to expand the genomic database to support the development of diagnostics and therapeutics.
Purpose of the Study:
- To characterize the genomic diversity of Lassa fever virus strains circulating in Liberia.
- To compare Liberian Lassa virus strains with those found in other West African regions.
- To inform the development of effective diagnostics, therapeutics, and vaccines for Lassa fever.
Main Methods:
- Near-complete genomes of Lassa fever virus were generated from clinical samples from Liberia and Guinea using targeted-enrichment sequencing.
- Additional Lassa virus sequences were generated from viral stocks from Liberia, Guinea, Nigeria, and Sierra Leone.
- Phylogenetic and phylogeographic analyses were conducted, comparing new genomes with existing data and evaluating diagnostic assay performance.
Main Results:
- Twenty-three new Lassa fever virus genomes from Liberia were identified, falling into clades IV.A and IV.B and showing genetic divergence from strains elsewhere in West Africa.
- Phylogeographic analysis suggests Liberia was an early entry point for Lassa virus into the Mano River Union region approximately 300-350 years ago.
- High genetic diversity was observed among Liberian Lassa virus genomes, with significant divergence from commonly used diagnostic assays.
Conclusions:
- The substantial novel genomic diversity of Lassa fever virus in Liberia necessitates diagnostic tools that match locally circulating strains.
- Evaluating cross-lineage protection is crucial for developing effective Lassa fever vaccines and therapeutics.
- This research underscores the importance of localized genomic surveillance for Lassa fever control.
