Ancient DNA recovered from Chilean mummies provides genetic evidence that European colonization brought smallpox to the Americas. Published in the journal Science, researchers analyzed bone fragments from an adult man and woman, linking the extinct viral strain directly to European medieval lineages and confirming centuries of historical records.
When Spanish conquistadors landed in the New World centuries ago, they carried muskets, armor, and horses, but the most devastating blow arrived unseen. Infectious diseases ravaged Indigenous populations who had never previously been exposed. While administrative records and missionary reports meticulously documented how millions perished, direct molecular proof remained elusive.
Uncovering Viral DNA in Northern Chile
Researchers examining bone fragments originally collected from an archaeological site at Camarones in northern Chile made an unexpected discovery. While testing DNA analysis software intended to study human history at the site, scientists noticed traces of an unknown smallpox variant. The investigation focused on 13 bone samples from the region, ultimately identifying infections in the leg bone fragments of two naturally mummified individuals: an adult woman aged 30 to 35 and an adult man between 18 and 20 years old.
According to the study published in the journal Science, the individuals were buried in bundles, wrapped in camelid wool blankets, and accompanied by grave goods. Researchers noted that the practice of bundle burial predated the Inca Empire and was common across earlier periods.
“The individuals were naturally mummified and buried in bundles, wrapped in camelid wool blankets and accompanied by various grave goods.”
Constanza de la Fuente Castro, Universidad de Chile biological anthropologist
Tracing the European Origins of the Strain
By dating the remains and sequencing the viral genes, scientists concluded that the two people likely died between 1492 and 1631. Genetic analysis of the variola virus showed that the strains belonged to a now-extinct lineage situated evolutionarily between medieval European versions and later centuries of the pathogen.
This molecular link confirms that the smallpox variants infecting populations in the Americas evolved directly from Old World strains introduced during colonization.
“Nobody would ever question that smallpox came to this hemisphere from colonization, but this proves it.”
Patricia Foster, Indiana University biologist
The study authors emphasize that precisely which European population or voyage brought the pathogen across the Atlantic remains unclear. Settlers arrived in multiple waves following Christopher Columbus’s 1492 explorations in the Caribbean and Amerigo Vespucci’s voyages along the South American coast. Furthermore, researchers point out that the disease could also have passed through Africa as part of the expanding transatlantic slave trade.
Evolutionary Pause and Historical Impact
The discovery of smallpox infections in a remote southern area with no prior record of the outbreak raises new questions about how the virus traveled so far. Researchers suggest the pathogen may have spread rapidly along established Indigenous trading networks that predated European arrival. The two viral genomes recovered were nearly identical, indicating that both individuals contracted the disease during the same outbreak or from the exact same circulating strain.
Analysis of the pathogen’s genome revealed a surprising evolutionary pattern. The virus underwent significant genetic changes up until the 16th century, after which evolution decelerated markedly during the major epidemics accompanying Spanish colonization. Scientists explain that this plateau suggests the virus had achieved an optimal genetic state for infecting immunologically naive populations, picking up evolutionary speed again only after the introduction of the first vaccine in 1796.
Beyond epidemiology, the viral intrusion altered the course of history. Historical records indicate that smallpox ravaged the Inca Empire around 1524 to 1528, killing millions and decimating leadership before Francisco Pizarro captured the last Incan emperor, Atahualpa, in 1532. The catastrophic loss of life and severe physical disfigurement also inflicted a psychological wound, leaving many Indigenous communities vulnerable to conquest.
“It wasn’t just cultural or demographic. It’s literally written into biological evidence that we can still recover and read today.”
Constanza de la Fuente Castro, University of Chile biological anthropologist
