Smallpox DNA Hidden for Centuries in Mummies Found in Chile Suggests European Colonists Brought the Virus to the Americas

Researchers say they found the first direct, molecular proof of the deadly trajectory the virus took

Sarah Kuta | Daily Correspondent

August 3, 2026 11:27 a.m.

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Historians have long suspected European colonists brought the smallpox-causing Orthopoxvirus variola virus to the Americas, where it decimated Indigenous populations. Now, scientists say they have discovered the first direct, molecular evidence supporting that hypothesis.

They report their findings in a new paper published July 30 in Science.

“Nobody would ever question that smallpox came to this hemisphere from colonization, but this proves it,” Patricia Foster, a biologist at Indiana University who was not involved with the research, tells the Associated Press’ Adithi Ramakrishnan.

Researchers recently revisited the naturally mummified remains of two individuals, who were likely Inca, buried in what is now northern Chile during the early Spanish colonial period. One was a 30- to 35-year-old woman, while the other was an 18- to 20-year-old man. After they died, they were swaddled in blankets and buried alongside various grave goods in an Indigenous site now known as Camarones 9.

Hidden within their skeletons for centuries were fragments of ancient smallpox DNA, which proved to be most closely related to European strains. Additionally, the team’s analysis revealed that the northern Chile outbreak occurred sometime between 1492 and 1631 C.E. This timeline further supports the hypothesis that the virus arrived with the Spanish, who captured and killed the Inca emperor in what is now Peru in the early 1530s.

Smallpox was one of humanity’s deadliest diseases, killing an estimated 500 million people before it was eradicated in 1980. Yet despite its enormous consequences, scientists still know surprisingly little about its origins, spread and evolution.

The researchers weren’t looking for smallpox DNA when they re-examined the remains from the archaeological site, initially discovered in 1957. They were hoping to recover and sequence human DNA from bone samples collected in the 1990s, so they could trace the individuals’ ancestries and relationships. But the human ancient DNA was badly degraded.

They were also looking for tuberculosis DNA, but were surprised to find smallpox instead. No historical records indicate that a smallpox epidemic raged in northern Chile at that time, but there the proof was, “literally written into biological evidence that we can still recover and read today,” study co-author Constanza de la Fuente Castro, a biological anthropologist at the University of Chile, tells the Associated Press.

Unlike the human DNA, the smallpox DNA was well-preserved. And the samples taken from the woman and the man were nearly identical, suggesting they had been killed by the same strain. Once the researchers realized what they’d found, “a lot of things started making sense in the site,” de la Fuente Castro tells Science’s Lizzie Wade. Some of the individuals buried in the cemetery had skin lesions, which had previously been attributed to chronic arsenic exposure. But one of smallpox’s hallmark symptoms was the formation of deep, painful, pus-filled sores that spread across victims’ bodies before eventually scabbing over.

Using the newly recovered DNA from northern Chile, as well as previously collected samples of the virus from other times and places, the scientists sketched out a smallpox family tree. Overall, the virus appears to have originated roughly 1,500 years ago, likely jumping to humans from some animal, though it’s still not clear which one. From there, scientists think it then split off into distinct branches.

The strain found in northern Chile appears to have emerged around 1296 C.E. and died out sometime before the early 20th century. Other strains, including some circulating during the Viking Age, also appear to have gone extinct. However, some—including those spreading through Lithuania in the 1600s and England in the 1700s—appear to have persisted for centuries, because they’re very closely related to modern strains.

The virus also seems to have morphed and changed as time went on—most notably, losing one or two genes per century, per the New York Times’ Carl Zimmer. Those adaptations may have made smallpox deadlier to humans over time.

Regardless, when the virus arrived in the Americas, it “killed perhaps 95 percent of the Indigenous population,” which helped pave the way for European colonization, Matthew Ward, a historian at the University of Dundee, who was not involved in the study, tells NewScientist’s James Woodford.

Indigenous people living in the Americas—including the Aztecs in what is now Mexico, the Maya in Central America and the Inca in western South America—had no natural immunity to smallpox. Other colonial-era hardships, such as famine, poverty, enslavement and other diseases, likely further weakened their ability to fend off smallpox.

But beyond causing sickness and death, smallpox also delivered a “psychological blow” to many Indigenous people, who saw it as a sign that their “traditional gods had ⁠forsaken them or were impotent against whatever spiritual force assisted the Spanish invaders,” as Will Dunham writes for Reuters.

Without smallpox and other viral epidemics, the colonization of the Americas likely “would have been very different,” Ward tells NewScientist.

Sarah Kuta is a writer and editor based in Longmont, Colorado. She covers history, science, travel, food and beverage, sustainability, economics and other topics.