Phylogenetic and motif-based genomic analysis of Mokola virus: implications for regional divergence and data gaps

Abstract

Mokola virus (MOKV), a member of the Lyssavirus genus, is an understudied zoonotic pathogen endemic to Africa, with sporadic detections in humans and animals. Despite its public health relevance and resistance to rabies vaccines and post-exposure prophylaxis, comprehensive genomic data remain limited. This study explores the evolutionary diversity and phyloepidemiology of MOKV using all eleven complete genomes available as of May 2025. Complete genomes and five canonical genes (G, M, N, P, L) were analyzed through Neighbor-Joining phylogenies (1,000 bootstraps), ANI/AAI comparisons, motif discovery, and ORF annotation. Across loci, a well-supported monophyletic cluster of South African isolates was recovered (bootstrap ≥ 94%), whereas isolates from the United Kingdom and France appeared intermixed across multiple weakly to moderately supported lineages, providing no evidence for country or continent-specific monophyly. ANI/AAI heatmaps showed high intra-cluster similarity within the South African lineage and greater divergence among European isolates, with the polymerase (L) and nucleoprotein (N) being more conserved than the phosphoprotein (P) and portions of the glycoprotein (G). De novo motif discovery revealed conserved regulatory signatures within coding regions and genome termini, while ORF analysis confirmed the canonical lyssavirus gene organization across all isolates. These findings highlight the evolutionary stability of African lineages and genetic heterogeneity of European isolates, underscoring the need for expanded genomic surveillance in Africa and the application of phyloepidemiological approaches to monitor emerging lyssaviruses. Not applicable.