DUBLIN – The two mummified individuals had lain in the desert at the northern edge of Chile for centuries, their skin carrying visible marks that archaeologists had long attributed to arsenic poisoning from the region’s mineral-rich soil. A new study published in Science corrects that interpretation: the marks were smallpox lesions, and the viral DNA retrieved from their remains has now produced the first molecular proof that European colonists carried the disease to the Americas.
Bruno Romero González, a doctoral student at Trinity College Dublin who led the research, and his co-authors extracted and sequenced fragments of the variola virus genome from skeletal tissue recovered from the Camarones 9 site in northern Chile, where the mummies were originally found in 1990. “This discovery provides the first molecular confirmation that smallpox was carried to the Americas during the colonial period,” said Shigeki Nakagome, a co-author also at Trinity College Dublin. Patricia Foster of Indiana University put the significance more plainly: “Nobody would ever question that smallpox came to this hemisphere from colonization, but this proves it.”
The mummies – a woman in her 30s and a man in his 20s – are believed to have been Inca. Researchers estimate both died between the late fifteenth and early seventeenth centuries, a range that places them in the colonial period that followed the Spanish arrival in the Americas. The nearly identical viral DNA found in both individuals points to a shared outbreak rather than two separate infections.
The strain recovered from the Camarones 9 mummies shared its closest genetic relationship with European smallpox strains from the same era, offering direct molecular evidence for a transmission path that historians had inferred but never confirmed at the genomic level. The research team, which also included Constanza de la Fuente Castro of the University of Chile and Lara Cassidy of Trinity College Dublin, performed the ancient DNA extraction from material that had never been collected with molecular analysis in mind, a feat they describe as recovering a record “literally written into biological evidence that we can still recover and read today,” in de la Fuente Castro’s words.
The study’s second major finding concerns how the virus behaved after it arrived. The variola strain found in the Camarones 9 mummies lost approximately one to two genes per century following its introduction to the Americas – a rate of evolutionary change that slowed measurably when the pathogen encountered populations that had no prior exposure to the disease. The researchers believe this decelerated evolution may have increased the virus’s lethality among Indigenous communities. In the absence of an evolutionary arms race between host immune systems and pathogen, the most harmful viral variants faced less selective pressure to moderate their effects.
The demographic consequences were extraordinary. Smallpox is estimated to have killed approximately 95 percent of Indigenous populations across the Americas following European contact, a figure that encompasses the Aztec, Maya, and Inca civilizations as well as hundreds of smaller societies across the continent. The Ebola epidemic currently unfolding in the Democratic Republic of the Congo, now the second-largest in history, has killed more than 1,500 people – a measure of how devastatingly unusual a 95-percent fatality rate across an entire hemisphere truly was. The Inca emperor Huayna Capac died of smallpox before Francisco Pizarro reached Peru; his empire, already fractured by the succession crisis that followed, fell in part to a disease the invaders carried without knowing it.
The study in Science, as Smithsonian Magazine reported, also places the variola virus’s origins earlier than the colonial period. The strain recovered from the Chilean mummies is linked to a lineage that researchers estimate diverged approximately 1,500 years ago, likely through a transmission event from an animal reservoir to a human host. Some early strains – including what the team identifies as Viking Age variants – eventually went extinct. Lithuanian and English lineages persisted and continued to evolve into the form of the virus that circulated until its global eradication in 1980.
The pattern of slowing evolution did not last. The researchers found that the American strain’s evolutionary pace did not resume at its earlier rate until after Edward Jenner introduced his smallpox vaccine in the late eighteenth century. Vaccination campaigns created the kind of population-level immune response that drives pathogen adaptation, effectively restarting a selective pressure that had been absent since the virus arrived on a continent where no one had ever encountered it.
The Camarones 9 individuals, recovered from the Atacama Desert more than three decades ago, had their remains catalogued and stored as archaeological specimens without any indication that they might carry traces of a pathogen responsible for one of history’s most destructive epidemics. Ancient DNA work has made that kind of retrospective retrieval increasingly feasible, recovering genetic information from material that was collected before the molecular tools to analyze it existed. The study adds another chapter to a growing body of work using archaeological remains to trace the movement of diseases that long predated any written record of their passage.
What the paper cannot yet resolve is the precise timing within the 1492-to-1631 range, or the number of separate introduction events that may have occurred as smallpox spread across the continent. The Camarones 9 site offers one data point from one outbreak in one region. The full story of how the virus traveled from its European origins to the Inca heartland and then outward remains incomplete – but for the first time, a molecular thread runs from a laboratory in Dublin to two individuals who died in the Chilean desert centuries before their remains could tell anyone what had killed them.
