Phylogenomics of Lassa Virus Strains Circulating in Edo and Ondo States: Implications for Vaccine Antigen Design

Lassa fever is an acute viral hemorrhagic disease caused by Lassa virus (LASV), with Edo, Ondo, Bauchi, and Ebonyi States accounting for the majority of cases reported annually in Nigeria. Phylogenomic characterization of circulating LASV lineages is critical for understanding viral evolution and informing antigen selection for candidate vaccines under development. This study performed phylogenomic analysis of LASV strains from confirmed cases in Edo and Ondo States, South-South and Southwest Nigeria, respectively, over a two-year surveillance window. Full-length LASV genome sequences were generated from serum samples of 35 confirmed cases using a hybrid capture-based enrichment sequencing approach on the Illumina MiSeq platform. Genomes were assembled using iVar and analyzed using maximum likelihood phylogenetics in IQ-TREE2 with an SH-aLRT bootstrap approach. Clade assignment followed the established LASV lineage classification. Bayesian molecular clock analysis was conducted in BEAST2. Ninety-one percent of sequenced strains clustered within LASV lineage II (Nigerian), with two distinct sub-clades specific to Edo and Ondo sampling sites showing 3-7% nucleotide divergence in the glycoprotein (GPC) gene. Phylogeographic analysis identified probable rodent-to-human spillover hotspots in northern Edo and Ondo border communities. GPC amino acid variation at key B-cell epitope sites differed between the two state-specific sub-clades, with implications for cross-clade vaccine-induced neutralization. These findings inform antigen design considerations for LASV candidate vaccines targeting West African endemic populations. Keywords: Lassa virus, phylogenomics, lineage II, glycoprotein, Edo and Ondo States.