A woman in her early 30s and a young man around 20 were naturally mummified and buried in bundles in northern Chile. When researchers sampled their remains centuries later, they were looking for human DNA, not disease. Yet fragments of each person’s thigh bone held nearly identical traces of smallpox.

The two Indigenous people were buried at Camarones 9, a site used during the Inca and early colonial periods. A study published in Science reports that they likely lived between 1492 and 1631. The viral DNA preserved in their remains represents the oldest smallpox genomes found in the Americas.

Because the genomes were more than 99.9 percent identical, the two people may have been infected during the same outbreak or by the same strain moving through their community. Their DNA linked them to Indigenous people in the Americas and showed no detectable European ancestry. The virus, however, belonged to a lineage connected to the Old World.

Smallpox epidemics are estimated to have killed three to four million people across the Americas, possibly more, according to the study. Colonial records tell part of that story, but less is known about how the disease moved through Indigenous communities. The Chilean genomes provide evidence from two people who experienced it.

Read More: The First Global Vaccination Expedition Set Sail in 1803

Ancient DNA Reveals Smallpox in Two Chilean Mummies

In all, researchers screened bone samples from 13 people at Camarones 9. Only the woman and young man tested positive for variola virus, which causes smallpox.

Some naturally mummified people from Camarones 9 do have small skin lesions, particularly around the torso. Those marks had previously been blamed on long-term arsenic exposure, which was already known to have affected people in the region.

The discovery raises the possibility that some lesions instead came from smallpox. That doesn’t show that the disease caused every mark or killed either person. The community may have faced both arsenic exposure and outbreaks of the virus.

An Extinct Smallpox Lineage Connects Chile to the Old World

Researchers named the newly identified lineage CAM9 after the burial site. When they placed it on smallpox’s evolutionary family tree, it fell between strains found in early medieval Europe and those that later gave rise to more recent forms of the disease.

The lineage appears to have disappeared before the 20th century. Researchers still can’t say exactly where it came from because ancient smallpox genomes remain limited outside Europe. Even so, its place on the family tree and the age of the remains point to smallpox reaching South America through European colonization.

Historical records place a smallpox outbreak in the Caribbean in 1518, followed by outbreaks in Mexico by 1520 and along the northern Inca frontier by 1525. Chile’s earliest reported epidemics may date between 1554 and 1556, although historians can’t confirm that smallpox caused them. An outbreak recorded in northern Chile in 1561 is widely treated as the first confirmed appearance of the disease there.

Smallpox Was Changing as Colonial Epidemics Spread

The better-preserved genome also captured the virus partway through its evolution. Researchers identified 49 genes that were missing or no longer working, signs that smallpox had already adapted more closely to humans.

The pattern shows that this gene loss continued until around the late 1500s or early 1600s, as colonial expansion and smallpox epidemics transformed populations. Viral change then slowed for roughly two centuries before speeding up again, potentially around the spread of vaccination.

The DNA can’t tell us exactly when the two people became sick or whether smallpox killed them. What it can show is that the same strain reached a young man and a woman in one northern Chilean community, bringing a history of colonization and disease down to two individual lives.

Read More: How the U.S. Stays Prepared for a Possible Smallpox Outbreak

Article Sources

Our writers at Discovermagazine.com use peer-reviewed studies and high-quality sources for our articles, and our editors review for scientific accuracy and editorial standards. Review the sources used below for this article:

• This article references information from a study published in Science:The genomic identity of early smallpox in South America