Continent-wide Multi-Segment Phylogenomic Study of Host and Geographic Structuring of African Hantaviruses

Background: African hantaviruses remain among the least characterized members of the family Hantaviridae , with fragmented genomic data limiting our understanding of their evolutionary relationships, host associations, and geographic structuring. Here, we investigated the integrated continent-wide phylogenomic structure of African hantaviruses using all three coding genomic segments. Methods: We compiled and curated 281 full-length and partial coding sequences representing the L segment ( n = 166), M segment ( n = 48), and S segment ( n = 67) from 13 African countries, alongside representative global reference strains. Temporal signal was evaluated using root-to-tip regression analysis. Segment-specific phylogenetic reconstructions were performed to characterize host-associated and geographic structuring. Additionally, pairwise tanglegram comparisons of the L, M, and S phylogenies were constructed to evaluate topological congruence and identify potential signals of genetic reassortment. Results Root-to-tip regressions revealed weak temporal signal across the L ( R ² = 0.069), M ( R ² = 0.021), and S ( R ² = 0.046) datasets, precluding reliable molecular-clock inference. Phylogenetic analyses demonstrated pronounced host-associated and geographic structuring across all three segments. Rodent, shrew, and bat-associated hantaviruses formed distinct evolutionary clades, with bat and shrew-borne lineages occupying basal, divergent positions relative to rodent-associated viruses. Endemic African hantaviruses exhibited marked regional clustering, forming distinct Malagasy, East African, and West African assemblages, whereas Senegalese, Beninese, and Malian sequences clustered within globally distributed, Rattus -associated Seoul orthohantavirus lineages. Comparative analyses highlighted complementary phylogenetic signals: the L segment provided a robust framework for resolving deep evolutionary relationships, the M segment offered clear discrimination among closely related host and geographic groups, and the S segment consistently recovered primary lineage boundaries. Pairwise tanglegrams demonstrated substantial topological concordance among segments highest between L and M with localized incongruences primarily in the L–S comparison restricted to closely related terminal taxa, consistent with but not definitive evidence of reassortment Conclusions African hantaviruses display strong host-associated and geographic structuring, with major evolutionary relationships broadly conserved across all three genomic segments. These findings provide an integrated continent-wide phylogenomic framework, establishing a foundation for future genomic surveillance, evolutionary studies, and One Health strategies across Africa.