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A Disease Older Than Empire: Leprosy's Ancient American Past
For decades, the prevailing narrative in medical archaeology held that leprosy—specifically, Hansen's disease—was a disease that came to the Americas with European colonizers. It left no detectable traces in Indigenous communities before the 16th century. But new genomic evidence from skeletal remains in northern Chile is challenging that view in a way that reshapes our understanding of ancient disease ecology and human-pathogen co-evolution in the Americas.
A recent study published in Nature Ecology & Evolution reconstructs two high-coverage genomes of Mycobacterium lepromatosis from archaeological human remains dated to approximately 4,000 years ago. These remains, unearthed at the La Herradura and El Cerrito sites near the Pacific Coast, belong to adult males whose bones bore signs of chronic infection. The findings mark the first ancient evidence of M. lepromatosis—a lesser-known bacterial cousin of M. leprae, the more commonly recognized cause of leprosy—anywhere in the world.
"This pathogen was not an Old World stowaway that arrived on colonial ships," said study co-author Kirsten Bos of the Max Planck Institute for Evolutionary Anthropology. "It was already here, entrenched in the pre-Columbian disease landscape."
A Rare and Elusive Pathogen
Since its discovery in 2008, M. lepromatosis has remained a microbiological mystery. Unlike M. leprae, which has been detected in numerous archaeological contexts across Europe and Asia, its newly described cousin has been found only in a few modern human cases and in red squirrels from the British Isles. The clinical form it causes—diffuse lepromatous leprosy (DLL) and the rare Lucio's phenomenon—is severe, often affecting skin, peripheral nerves, and internal organs.
In this study, researchers screened 54 skeletal elements from five archaeological sites using ancient DNA (aDNA) methods designed to detect a wide range of pathogens. Only two samples—one tibia and one tooth—showed strong genomic signals for M. lepromatosis. Both individuals also showed osteological changes suggestive of chronic infection, including nasal aperture modification and lesions on long bones and small hand bones.
Genetic Time Capsules
Once sequenced, the ancient bacterial genomes revealed astonishing levels of preservation—an uncommon feat for microbial DNA in tropical and semi-arid conditions. The reconstructed genomes, designated ECR001 and ECR003, showed more than 40-fold average genomic coverage. Comparisons with modern genomes of M. lepromatosis revealed a clear phylogenetic separation between ancient and modern lineages, with the ancient Chilean strains forming a sister clade to contemporary human-associated strains from Mexico.
"The genetic divergence suggests that M. lepromatosis has been evolving independently in the Americas for tens of thousands of years," said lead author Darío Ramirez of the University of Córdoba.
The team estimated the most recent common ancestor of all human-associated M. lepromatosis lineages to date back around 12,600 years, with the broader species likely emerging closer to 27,000 years ago. These dates suggest a deep evolutionary presence in the Americas—possibly even predating the peopling of South America itself.
Rethinking the Disease Landscape of the Americas
The implications are significant. For years, archaeological efforts to detect leprosy in pre-contact American contexts came up empty, reinforcing the idea that it was a European import. But if M. lepromatosis was already established in South America millennia before colonization, then the continent hosted at least one lineage of Hansen's disease long before Europeans arrived.
"The idea that this pathogen has a New World origin forces us to reassess not only the history of leprosy but the broader assumptions we make about Old World diseases in the Americas," said Rodrigo Nores, co-author and professor of anthropology at the University of Córdoba.
The study raises the possibility that M. lepromatosis was part of a deeper, endemic disease ecology in the Americas, one that has left little in the way of morphological signatures and has been overlooked due to the rarity and diagnostic ambiguity of skeletal lesions.
A Broader Host Range?
The modern distribution of M. lepromatosis is geographically limited, with confirmed cases largely clustered in Mexico and parts of Southeast Asia. Interestingly, it has also been found in red squirrels in Ireland and the UK, hinting at zoonotic potential. However, neither of the ancient Chilean individuals was found near modern armadillo ranges—currently considered a potential reservoir for leprosy-causing bacteria in the Americas.
This has led researchers to ask whether other, yet-undiscovered animal hosts might have played a role in maintaining the bacterium in the environment or facilitating its spread among humans.
The Next Frontier: Ancient Genomes and Disease Origins
This discovery joins a growing body of ancient pathogen research that is rewriting the timeline and geography of infectious diseases. Just as Yersinia pestis has been traced to the Eurasian steppe and Treponema pallidum (the syphilis family) to the Americas, M. lepromatosis now appears to have deep roots in the pre-Columbian New World.
Future work will require broader pathogen screening, better molecular diagnostics, and coordinated collaborations with local institutions during development projects—particularly in coastal and riverine contexts where ancient DNA preservation is more favorable.
"This study is a reminder that the pathogens we know today have histories we’ve only begun to chart," said Bos. *"And many of those histories are still buried—sometimes literally—in the archaeological record."
Suggested Further Reading
* Han XY et al. (2008). A new mycobacterium species causing diffuse lepromatous leprosy. Am J Clin Pathol, 130:856–864. https://doi.org/10.1309/AJCPQ6M3TH1EVW1L
* Avanzi C et al. (2016). Red squirrels in the British Isles are infected with leprosy bacilli. Science, 354:744–747. https://doi.org/10.1126/science.aah3783
* Pfrengle S et al. (2021). Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes. BMC Biol, 19:220. https://doi.org/10.1186/s12915-021-01158-8
* Barquera R et al. (2024). A deep history of treponemal disease in the Americas revealed through ancient genomic analyses. Nature, 640:186–193. https://doi.org/10.1038/s41586-024-07018-5
This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit www.anthropology.net/subscribe
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By Anthropology.netFor decades, the prevailing narrative in medical archaeology held that leprosy—specifically, Hansen's disease—was a disease that came to the Americas with European colonizers. It left no detectable traces in Indigenous communities before the 16th century. But new genomic evidence from skeletal remains in northern Chile is challenging that view in a way that reshapes our understanding of ancient disease ecology and human-pathogen co-evolution in the Americas.
A recent study published in Nature Ecology & Evolution reconstructs two high-coverage genomes of Mycobacterium lepromatosis from archaeological human remains dated to approximately 4,000 years ago. These remains, unearthed at the La Herradura and El Cerrito sites near the Pacific Coast, belong to adult males whose bones bore signs of chronic infection. The findings mark the first ancient evidence of M. lepromatosis—a lesser-known bacterial cousin of M. leprae, the more commonly recognized cause of leprosy—anywhere in the world.
"This pathogen was not an Old World stowaway that arrived on colonial ships," said study co-author Kirsten Bos of the Max Planck Institute for Evolutionary Anthropology. "It was already here, entrenched in the pre-Columbian disease landscape."
A Rare and Elusive Pathogen
Since its discovery in 2008, M. lepromatosis has remained a microbiological mystery. Unlike M. leprae, which has been detected in numerous archaeological contexts across Europe and Asia, its newly described cousin has been found only in a few modern human cases and in red squirrels from the British Isles. The clinical form it causes—diffuse lepromatous leprosy (DLL) and the rare Lucio's phenomenon—is severe, often affecting skin, peripheral nerves, and internal organs.
In this study, researchers screened 54 skeletal elements from five archaeological sites using ancient DNA (aDNA) methods designed to detect a wide range of pathogens. Only two samples—one tibia and one tooth—showed strong genomic signals for M. lepromatosis. Both individuals also showed osteological changes suggestive of chronic infection, including nasal aperture modification and lesions on long bones and small hand bones.
Genetic Time Capsules
Once sequenced, the ancient bacterial genomes revealed astonishing levels of preservation—an uncommon feat for microbial DNA in tropical and semi-arid conditions. The reconstructed genomes, designated ECR001 and ECR003, showed more than 40-fold average genomic coverage. Comparisons with modern genomes of M. lepromatosis revealed a clear phylogenetic separation between ancient and modern lineages, with the ancient Chilean strains forming a sister clade to contemporary human-associated strains from Mexico.
"The genetic divergence suggests that M. lepromatosis has been evolving independently in the Americas for tens of thousands of years," said lead author Darío Ramirez of the University of Córdoba.
The team estimated the most recent common ancestor of all human-associated M. lepromatosis lineages to date back around 12,600 years, with the broader species likely emerging closer to 27,000 years ago. These dates suggest a deep evolutionary presence in the Americas—possibly even predating the peopling of South America itself.
Rethinking the Disease Landscape of the Americas
The implications are significant. For years, archaeological efforts to detect leprosy in pre-contact American contexts came up empty, reinforcing the idea that it was a European import. But if M. lepromatosis was already established in South America millennia before colonization, then the continent hosted at least one lineage of Hansen's disease long before Europeans arrived.
"The idea that this pathogen has a New World origin forces us to reassess not only the history of leprosy but the broader assumptions we make about Old World diseases in the Americas," said Rodrigo Nores, co-author and professor of anthropology at the University of Córdoba.
The study raises the possibility that M. lepromatosis was part of a deeper, endemic disease ecology in the Americas, one that has left little in the way of morphological signatures and has been overlooked due to the rarity and diagnostic ambiguity of skeletal lesions.
A Broader Host Range?
The modern distribution of M. lepromatosis is geographically limited, with confirmed cases largely clustered in Mexico and parts of Southeast Asia. Interestingly, it has also been found in red squirrels in Ireland and the UK, hinting at zoonotic potential. However, neither of the ancient Chilean individuals was found near modern armadillo ranges—currently considered a potential reservoir for leprosy-causing bacteria in the Americas.
This has led researchers to ask whether other, yet-undiscovered animal hosts might have played a role in maintaining the bacterium in the environment or facilitating its spread among humans.
The Next Frontier: Ancient Genomes and Disease Origins
This discovery joins a growing body of ancient pathogen research that is rewriting the timeline and geography of infectious diseases. Just as Yersinia pestis has been traced to the Eurasian steppe and Treponema pallidum (the syphilis family) to the Americas, M. lepromatosis now appears to have deep roots in the pre-Columbian New World.
Future work will require broader pathogen screening, better molecular diagnostics, and coordinated collaborations with local institutions during development projects—particularly in coastal and riverine contexts where ancient DNA preservation is more favorable.
"This study is a reminder that the pathogens we know today have histories we’ve only begun to chart," said Bos. *"And many of those histories are still buried—sometimes literally—in the archaeological record."
Suggested Further Reading
* Han XY et al. (2008). A new mycobacterium species causing diffuse lepromatous leprosy. Am J Clin Pathol, 130:856–864. https://doi.org/10.1309/AJCPQ6M3TH1EVW1L
* Avanzi C et al. (2016). Red squirrels in the British Isles are infected with leprosy bacilli. Science, 354:744–747. https://doi.org/10.1126/science.aah3783
* Pfrengle S et al. (2021). Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes. BMC Biol, 19:220. https://doi.org/10.1186/s12915-021-01158-8
* Barquera R et al. (2024). A deep history of treponemal disease in the Americas revealed through ancient genomic analyses. Nature, 640:186–193. https://doi.org/10.1038/s41586-024-07018-5
This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit www.anthropology.net/subscribe