Scientists have decoded the genetic blueprints of a rare leprosy bacterium preserved in 4,000-year-old Chilean skeletons, opening a surprising new chapter in the story of Hansen’s disease.
- Researchers reconstructed two complete genomes of Mycobacterium lepromatosis, an uncommon cousin of the main leprosy germ.
- The discovery pushes the timeline of Hansen’s disease in the Americas back by millennia, long before European contact.
- Finding the pathogen in ancient South American remains shows that two related leprosy bacteria, M. lepromatosis in the Americas and M. leprae in Eurasia, evolved on separate continents for thousands of years.
- The work demonstrates how modern DNA tools can pull hidden disease histories out of ancient bones, rewriting our understanding of global health past and present.
Global Reach & Ancient Roots
Leprosy, also known as Hansen’s disease, is a chronic infection that can cause serious physical complications if left untreated. Today, it still exists in more than 100 countries. While modern treatments can cure the disease, access to healthcare often depends on a person’s economic and social conditions.
Historical records show that leprosy once had a major impact on communities across Europe and Asia. Its long presence is also confirmed in the bones of people who lived thousands of years ago. Archaeologists have found skeletal signs of leprosy as far back as 5,000 years in Europe, Asia, and Oceania. However, these signs have not been found in pre-colonial remains from the Americas, suggesting that the disease likely arrived with European colonizers. After that point, it spread not only to people but also, intriguingly, to animals like armadillos.
At the genetic level, Hansen’s disease is caused by two closely related bacteria. The more common one is Mycobacterium leprae, while a rarer cousin, Mycobacterium lepromatosis, was identified more recently. DNA from ancient European skeletons shows that M. leprae likely emerged in Eurasia around 7,000 years ago, during the Neolithic period. This timeline aligns with the origins of other well-known infectious diseases such as plague and tuberculosis. Meanwhile, ancient samples of the rarer M. lepromatosis are still rare, but unlocking its history could offer valuable insights into how leprosy evolved and spread across the globe.
Hidden Illness in Pre-Contact Americas
We know comparatively little about the infectious disease experience of the diverse communities of people living in the Americas before the colonial period. This accounts for almost 20,000 years of human history, and the diverse ecosystems into which humans integrated across the continent would have presented challenges to the immune system not otherwise encountered in other parts of the world. We know very little about these diseases, as they were overshadowed by the onslaught of pathogens that Europeans later introduced. Archaeological studies of human bones from the pre-contact Americas confirm that the time was far from disease-free, but often the traces seen on the bones aren’t specific enough to be assigned to a known disease.
“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. She and her team have been studying pathological bone from the American context for over a decade. Some diseases that the group has found were expected – just last year, they found evidence that the family of diseases closely related to syphilis had its roots in the Americas, which many had suspected. “The advanced techniques now used to study ancient pathogen DNA allow us to look beyond the suspects and into other diseases that might not be expected from the context,” she adds.
Unearthing Ancient Leprosy Genomes
Bos’s team worked closely with researchers from Argentina and Chile to both identify bones suitable for analysis and to carry out the meticulous work of isolating the DNA of ancient pathogens. Doctoral candidate Darío Ramirez of the University of Córdoba, Argentina, worked extensively with such material, and was the first to identify a genetic signature related to leprosy in some 4000-year-old skeletons from Chile. “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.”
This provided the first clue that M. lepromatosis and M. leprae, though nominally both pathogens that cause Hansen’s Disease, might have very different histories. Reconstruction of the genome was key in looking into this. While putting the molecular puzzle of an ancient genome back together is never an easy task, these pathogens in particular had “amazing preservation, which is uncommon in ancient DNA, especially from specimens of that age,” comments Lesley Sitter, a postdoctoral researcher in Bos’s team who carried out the analysis.
Mystery Origins & Future Clues
The pathogen is related to all known modern forms of M. lepromatosis, but as there are so few genomes available for comparison, there is still much to be learned about it. This work has shown that a pathogen considered rare in a modern context caused disease for thousands of years in the Americas.
Rodrigo Nores, professor of Anthropology at the University of Córdoba, Argentina is convinced that more cases, both ancient and modern, will be identified in the coming years: “this disease was present in Chile as early as 4000 years ago, and now that we know it was there, we can specifically look for it in other contexts.”
Once more genomes surface, we’ll be able to piece out further details of its history and better understand its global distribution today. The pathogen has recently been discovered in squirrel populations from the United Kingdom and Ireland, but in the Americas it has yet to be found in any species other than humans. With such little data, mystery still surrounds its origin.
“It remains to be determined if the disease originated in the Americas, or if it joined some of the first settlers from Eurasia,” adds Bos. “So far the evidence points in the direction of an American origin, but we’ll need more genomes from other time periods and contexts to be sure.”
Reference: “4,000-year-old Mycobacterium lepromatosis genomes from Chile reveal long establishment of Hansen’s disease in the Americas” by Darío A. Ramirez, T. Lesley Sitter, Sanni Översti, María José Herrera-Soto, Nicolás Pastor, Oscar Eduardo Fontana-Silva, Casey L. Kirkpatrick, José Castelleti-Dellepiane, Rodrigo Nores and Kirsten I. Bos, 30 June 2025, Nature Ecology & Evolution.
DOI: 10.1038/s41559-025-02771-y
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