In a discovery that overturns old suppositions about the origin of leprosy, researchers have recovered two extremely well-preserved genomes of Mycobacterium lepromatosis—a rare and severe form of bacteria that causes Hansen’s disease—from 4,000-year-old Chilean human skeletons. The finding is the first ancient genetic evidence of this form of leprosy in the Americas and suggests that the disease emerged on the continent independently, centuries before the arrival of Europeans.

Cranium of a leper, showing deformed eye sockets, nose, jaw, and chin. On display at the Ribes Vikinger Museum, Denmark. Credit: Cnyborg / CC BY-SA 3.0

The skeletons, unearthed at Chile’s Atacama Desert archaeological sites of El Cerrito and La Herradura, belonged to two adult males who lived around 2000 BCE. The skeletons bore signs of leprosy, such as widened nasal cavities and thickening of the hand bones. When scientists studied the skeletons, they were surprised to find highly intact M. lepromatosis genomes, with better DNA preservation than in many modern samples.

While Mycobacterium leprae has long been known to be the dominant cause of Hansen’s disease—and is found in archaeological remains all over Europe and Asia dating back 5,000 years—M. lepromatosis was only identified in 2008 and is still rare today. This form of leprosy is ᴀssociated with the most severe manifestations of the disease, such as diffuse lepromatous leprosy (DLL) and the potentially fatal Lucio’s phenomenon.

The two recovered genomes indicate that M. lepromatosis split from M. leprae approximately 26,800 years ago, with the American lineages diverging around 12,600 years ago—presumably coinciding with early human migration into South America. Importantly, the ancient Chilean strain has 94 unique mutations not found in modern genomes, suggesting long-standing isolated evolution.

Children sitting beside a collection of human remains at Paco Leper Cemetery, Manila, Philippines. Credit: National Museum of Health and Medicine / CC BY 2.0

This deep divergence means that Hansen’s disease did not arrive with European colonists to the Americas, as previously believed, but perhaps originated or was independently introduced much earlier. “So far, the evidence points in the direction of an American origin,” said Kirsten Bos, group leader for Molecular Paleopathology at the Max Planck Insтιтute for Evolutionary Anthropology, “but we’ll need more genomes from other time periods and contexts to be sure.”

The study also raises broader questions about disease evolution and the limitations of our historical knowledge.

Today, M. lepromatosis remains rare, largely confined to Mexico and the Caribbean, but it has also been found in red squirrels in Ireland and the UK, highlighting possible zoonotic transmission routes. Although new cases are limited, finding it in ancient Chile provides evidence that the pathogen also circulated more widely and might have played a significant role in pre-Columbian health.

This finding showcases the ability of ancient DNA studies to reveal the lost epidemics of the past—pathogens that shaped civilizations and disappeared without a trace, until now.

More information: Max Planck SocietyPublication: Ramirez, D. A., Sitter, T. L., Översti, S., Herrera-Soto, M. J., Pastor, N., Fontana-Silva, O. E., … Bos, K. I. (2025). 4,000-year-old Mycobacterium lepromatosis genomes from Chile reveal long establishment of Hansen’s disease in the Americas. Nature Ecology & Evolution. doi:10.1038/s41559-025-02771-y