Ancient DNA recovered from two 4,000‑year‑old skeletons in northern Chile shows that a rare cause of Hansen’s disease was present in the Americas long before European contact. Researchers reconstructed high‑coverage genomes of Mycobacterium lepromatosis—the less common leprosy bacillus—demonstrating for the first time that this pathogen afflicted pre‑colonial populations on the Pacific coast.
These genomes, sequenced from a tibia and a tooth (individuals ECR001 and ECR003), were enriched using in‑solution capture and field‑emission TEM to isolate pathogen DNA from bone powder. The resulting data yielded average coverages of 45× and 74×, respectively, allowing confident assignment to M. lepromatosis rather than its close relative M. leprae.
“Ancient DNA has become a great tool that allows us to dig deeper into diseases that have had a long history in the Americas,” says Kirsten Bos, group leader for Molecular Paleopathology at the Max Planck Institute for Evolutionary Anthropology.
By comparing these ancient genomes to modern M. lepromatosis strains from humans and red squirrels, the team found that the two Chilean genomes form a distinct sister clade, indicating a deep split from Eurasian lineages. Radiocarbon dating and Bayesian phylogenetic analyses suggest the most recent common ancestor of the human‑associated strains dates back roughly 12,600 years, hinting at either an early introduction by the first peoples or an endemic reservoir now lost to history.
“We were initially suspicious, since leprosy is regarded a colonial-era disease, but more careful evaluation of the DNA revealed the pathogen to be of the lepromatosis form.”
The discovery rewrites the narrative of Hansen’s disease in the New World, showing that M. lepromatosis caused human infections millennia before records linked leprosy to European colonists. It also raises the possibility of past animal or environmental reservoirs in the Americas, underscoring the need for broader palaeogenomic and ecological surveys to trace its full history and modern distribution.
Ultimately, by uncovering a single, unexpected branch on the leprosy family tree, researchers are piecing together how ancient pathogens moved with people and animals—insights that may inform understanding of disease emergence, transmission, and control today.
The study has been published in Nature Ecology & Evolution.
