Inca Mummy DNA Offers First Molecular Proof That Colonizers Brought Smallpox to the Americas

Genomes recovered from two Chilean Inca mummies provide the first direct DNA evidence that European colonizers introduced smallpox to the Americas, a study in Science reports.

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Researchers have recovered the oldest known smallpox genomes in the Americas from two Inca mummies in Chile, providing the first direct molecular evidence that European colonizers brought the disease to the New World. The findings, published in the journal Science on 30 July 2026, fill a gap between historical accounts and biological proof.

The two mummies — an adult female aged 30–35 and an adult male aged 18–20 — lived between 1492 and 1631. They were excavated from the Camarones 9 archaeological site in northern Chile, a burial ground discovered in 1957 that yielded 41 mummified bodies. The viral genomes they carried are nearly identical, suggesting both individuals were struck by the same outbreak or a circulating strain.

The ancient genomes belong to a lineage that split from another European strain around 1296, predating modern smallpox strains. This lineage includes early medieval and early modern European strains, linking the mummies' infection directly to the colonizers' arrival.

"None of us expected to find variola virus DNA from the sample that they collected, so it was completely a surprise," said Shigeki Nakagome, a researcher involved in the study. He added: "I don't think there was any historical record documenting smallpox in this particular community, so no one expected the smallpox evidence."

The team initially set out to study human DNA from the mummies. "While the original aim was to study the human DNA, we also searched for DNA from ancient pathogens," Nakagome said. "That is when we discovered fragments matching the smallpox virus in two individuals."

The study provides "the first molecular evidence of smallpox introduction to the Americas through colonization," Nakagome said. Previous evidence had been limited to two 16th-century toddlers in Peru with bone lesions suggestive of smallpox. "We interpreted this as the first direct molecular evidence of smallpox introduction into the Americas through European colonisation," he added.

Smallpox, caused by the variola virus, was declared eradicated globally in 1980, and today only high-security laboratories retain samples. In severe strains, the disease killed up to one-third of those infected, and survivors were often left scarred.

Historical records document the first smallpox outbreak in the Americas in 1518, during the Spanish conquest of the Caribbean. Experts estimate the disease killed 3–4 million Indigenous people who had no prior immunity. Combined with violence, slavery, and other diseases, smallpox contributed to the death of about 90% of the original inhabitants of the Americas by 1600.

"This paper is really lovely because we know from the historical record that smallpox had a huge impact on Indigenous populations in the Americas," said Anne Stone, a researcher not involved in the study. "This paper gives us the first description of the pathogen during the colonial period," she added. "It's always useful to study ancient pathogens."

The mummies also bore skin lesions on their trunks, previously attributed to chronic arsenic exposure. The new findings suggest these may actually be smallpox pustules. "This finding allowed us to identify a small group of people impacted by the virus for which no historical record exists," said Constanza de la Fuente Castro, another author. She stressed the human dimension: "We never forget that behind every DNA extraction is a person, not a data point."

The study also offers broader context. "Understanding exactly what was killing native peoples and why they were so susceptible to epidemic disease is a vitally important issue," said Matthew Ward, a historian. "Without these epidemics, colonisation of the Americas would have been very different." He added, "These diseases killed perhaps 95 per cent of the Indigenous population of the Americas and allowed for European colonisation."

The research highlights how the variola virus evolved to target only humans, as Bruno Romero González noted: "Because of that, variola started to focus on targeting only humans." The study is published under DOI 10.1126/science.aee6957.