Ancient pathogen genomics in Africa: Current evidence and future directions

Ancient pathogen genomics has redefined how infectious disease histories are reconstructed, revealing unexpected origins, transmission routes, and lineage turnovers that are invisible from modern genomes alone. Yet, this perspective remains heavily biased toward Eurasia, leaving Africa-central to human evolution and home to diverse ecological settings relevant to zoonotic and vector-borne disease emergence-largely unexplored. In this review, we assess the current state of ancient pathogen research in Africa and synthesize insights from bacterial, parasitic, and viral perspectives. We identify Africa as a pivotal frontier for the field and outline strategic priorities for moving from isolated detections toward continent-scale reconstructions of past disease landscapes, with potential relevance for understanding long-term patterns of endemicity, emergence, and epidemic risk.