Not Imported: Leprosy Was Already Thriving in Ancient America By David Freeman - July 3, 2025
Buried beneath the dry coastal soil of northern Chile, two ancient skeletons have just upended what scientists thought they knew about the origin of leprosy in the Americas. New genomic evidence has confirmed the presence of Mycobacterium lepromatosis, one of the two bacteria responsible for Hansen’s disease, in human remains dating back 4,000 years. The discovery, made at the archaeological sites of La Herradura and El Cerrito near modern-day Coquimbo, marks the first time this pathogen has been identified in the Americas prior to European contact.
Until now, the dominant assumption in medical history held that leprosy was brought to the Americas by colonizers after 1492. Most genetic studies focused on Mycobacterium leprae, the more well-known of the two leprosy-causing bacteria, which has deep historical roots in Eurasia. But this new study, published in Nature Ecology & Evolution, provides definitive DNA-based proof that M. lepromatosis had already taken hold in Indigenous populations of the South American coast more than 4,000 years ago.
Leprosy was already endemic in the New World millennia before the arrival of Europeans, potentially making it one of the only globally recognized diseases with ancient origins rooted in the Americas. It raises the possibility of reservoirs in native fauna or sustained human-to-human transmission long before trans-oceanic contact. Unlike the better-known M. leprae, which has been documented in ancient European, Asian, and Oceanic populations, M. lepromatosis was until now absent from archaeological findings, its presence inferred only from modern DNA samples in Mexico and Southeast Asia.
To better understand the historical spread of the disease, researchers analyzed skeletal remains from 41 individuals across five precolonial sites in the semi-arid Elqui River valley. Both male individuals from La Herradura and El Cerrito showed physical changes associated with chronic disease. The individual from El Cerrito (ECR003) was around 40 to 44 years old at death. The La Herradura individual (ECR001) was slightly younger, estimated to be 35 to 40. Examination revealed skeletal pitting, abnormal foramina in the small bones of the hands, periostosis in the lower leg bones, and erosion consistent with infection-induced bone remodeling.
While such damage is not exclusive to leprosy, and can overlap with other chronic infectious diseases or metabolic conditions, the molecular evidence is what sets this discovery apart. Both skeletons contained thousands of DNA fragments belonging to M. lepromatosis. Using hybrid capture and next-generation sequencing, researchers were able to reconstruct high-quality genomes of the bacterium. Genomic coverages reached 45x for ECR001 and 74x for ECR003, levels rarely achieved in ancient pathogen studies.
To ensure the findings were authentic and not the result of contamination or post-burial bacterial intrusion, the team used multiple authentication steps. DNA damage patterns matched those expected from ancient material. Radiocarbon dating of the skeletons placed them firmly in the range of 3,900 to 4,100 years ago. Mitochondrial analysis confirmed that both individuals were of Indigenous American origin, removing the possibility that they were post-contact cases introduced through European or Asian vectors.
Comparative analysis against 16 modern M. lepromatosis genomes, including those isolated from humans in Mexico and red squirrels in the UK and Ireland, revealed that the Chilean genomes form a sister lineage to the existing human strains. The phylogenetic tree indicates a divergence within the human-associated strains roughly 12,600 years ago. For context, the divergence of the squirrel-associated lineage appears much more recent, likely beginning about 440 years ago. That recency fits with the possibility that the presence of the disease in European wildlife resulted from colonial-era introductions.
Crucially, the evolutionary split between M. lepromatosis and M. leprae appears to go back even further, with a common ancestor estimated to have existed approximately 27,000 years ago. This points to a long, separate evolutionary path, which reinforces the hypothesis that leprosy was not solely an Old World import. Instead, M. lepromatosis may have developed its human association independently in the Americas, potentially through a now-extinct reservoir species or through long-standing low-level transmission among Indigenous populations.
The study’s authors highlight that while M. leprae infections often leave clearer skeletal markers, M. lepromatosis may not. This difference could explain why the disease remained invisible in the archaeological record until now. In the absence of molecular tools, signs of infection would have been overlooked, misattributed, or not recognized at all. Many earlier South American skeletal collections may warrant reexamination using modern paleogenomic methods.
Armadillos have long been known to carry M. leprae in the Americas and are believed to transmit it to humans through direct contact or consumption. There is growing concern that M. lepromatosis may also circulate in armadillo populations, though confirmation is pending. In modern Brazil, for instance, more than 10 percent of Hansen’s disease cases now test positive for M. lepromatosis. Two Mexican patients confirmed with the infection reported previous contact with wild armadillos. While the ancient Chilean individuals lived outside the modern range of these animals, the geographic spread of armadillo species in the past remains underexplored.
The discovery invites more than just academic interest. It raises public health questions. Despite significant progress in diagnosis and treatment, Hansen’s disease still affects hundreds of thousands globally. Over 174,000 new cases were reported in 2022. Poverty, overcrowding, and immunosuppression remain primary risk factors. Understanding the reservoirs, spread patterns, and long-term history of both causative species is crucial for better disease management today.
Surveillance of potential animal hosts is uneven. While red squirrels in the British Isles have been confirmed carriers of both M. leprae and M. lepromatosis, surveys in mainland Europe have so far come up empty. Similar studies are only just beginning in Latin America. The risk of zoonotic transfer is not theoretical. Historical infections in both humans and animals show that cross-species transmission has occurred repeatedly across centuries.
Efforts to track the environmental presence of these bacteria have also identified ticks and even free-living amoebae as possible carriers. The ability of the pathogen to survive in the environment for extended periods opens the door to transmission routes that bypass direct human or animal contact. This makes it even more vital to map out ecological risks alongside human case clusters.
The Chilean findings also add to the growing realization that the Americas may have hosted more infectious disease diversity before 1492 than previously acknowledged. Another recent genomic study confirmed ancient treponemal infections (a broader family that includes syphilis) going back thousands of years on the continent. Together, these studies argue against the outdated belief that the New World was mostly free of epidemic disease before colonization.
This new evidence of ancient leprosy, revealed through paleogenomics, signals a turning point. It reinforces how much of the continent’s true disease history has gone unrecorded by traditional archaeology. More than that, it suggests that M. lepromatosis may be one of the only known pathogens with an entirely pre-contact, Indigenous American origin story. If validated by additional ancient finds in Central and North America, this could fundamentally shift how we view the global history of leprosy.
The two Chilean skeletons now stand as the earliest physical proof of M. lepromatosis in the Western Hemisphere. But they are likely just the beginning. As DNA techniques become more accessible to researchers working across Latin America, more such discoveries will surface. Every new genome helps refine the timeline, track the migration, and identify overlooked hosts. In the process, they may also guide new diagnostic techniques and contribute to a fuller understanding of one of the world’s oldest diseases.
What was once hidden in bone has now been read in code. And the story it tells changes everything.
Source: Nature
Ramirez, D. A., Sitter, T. L., Översti, S., Herrera-Soto, M. J., Pastor, N., Fontana-Silva, O. E., Kirkpatrick, C. L., Castelleti-Dellepiane, J., Nores, R., & 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. https://doi.org/10.1038/s41559-025-02771-y
The gold scarab is depicted in Egyptian art as sacred. However the genus model Egyptians used is central American. Plusiotis or Chrysina. The name is undergoing change.
Chrysina and Plusiotis scarabs
Thor Heyerdahl proved Egyptian mariners could have reached Central and South America thousands of years before Christ in papyrus reed ships. It is well known a healthy trade between the Americas existed that long ago, proven by artifacts found in teash dumps in places like Chaco Canyon. Both east and west ceremonially built pyramids about the same time. Egyptian knowledge of the beetle support the cultures had some sort of visitation and maybe even trade exchange.
Leprosy was written about in ancient Egyptian language. Maybe it came from there to the Americas and our armadillos?
Pity they didn't see Chile's silver butterfly
You can look away from a painting, but you can't listen away from a symphony
The kind of thing we used to learn in Physical Anyhropology. Leprosy shows up in skeletal remains, and so can be traced better than some diseases - venereal disease as well.
In fact there used to be lots of argumentation over whether VD originated here or in the Old World, with both sides kind of taking an 'it wasn't our fault' stance..-greenman
on July 3, 2025, 5:05 pm
