Phylodynamic Analysis of HCV Genotype 1 and Genotype 2 Transmission Chains in Nigeria: Implications for Elimination Targets

Hepatitis C virus (HCV) elimination by 2030 is a WHO target that requires understanding transmission network dynamics to design effective interruption strategies. In Nigeria, which has among the highest HCV burdens in Africa with an estimated 2.2 million chronically infected individuals, the phylodynamic characterisation of dominant genotype 1 and genotype 2 transmission chains is absent from current literature. This study performs comprehensive phylodynamic analysis of HCV genotype 1 and genotype 2 transmission chains across Nigeria using specimens from six geopolitical zones. Blood donors, patients at liver clinics, and people who inject drugs at harm reduction programmes in Lagos, Kano, Abuja, Enugu, Kaduna, and Port Harcourt will contribute NS5B gene sequences for phylogenetic analysis. Time-scaled Bayesian phylodynamics (BEAST2) will estimate effective population size dynamics and introduction events. Transmission network analysis using phylogenetic clustering tools (ClusterPicker, HIV-TRACE adapted for HCV) will identify active transmission clusters, and associated epidemiological risk factors will be characterised. Spatiotemporal analysis will determine whether genotype distribution patterns are evolving geographically. This study produces an original theoretical contribution to HCV epidemiology in sub-Saharan Africa by generating the first national-scale HCV phylodynamic dataset from Nigeria, directly informing the prioritisation of elimination interventions across population groups and geographic zones most critical to HCV transmission interruption. Keywords: HCV phylodynamics, genotype 1, genotype 2, elimination, Nigeria