Smallpox DNA in ancient Inca mummies shows virus came from Europe

DNA samples collected from Inca mummies have confirmed the presence of a strain of smallpox that first emerged in Europe.

“We interpreted this as the first direct molecular evidence of smallpox introduction into the Americas through European colonisation,” says Shigeki Nakagome at Trinity College Dublin, Ireland.

Smallpox was the scourge of humanity for centuries until its eradication in the 1980s, through vaccination, from all but a few high-security medical laboratories. Severe strains of the virus had a mortality rate of up to a third and left survivors with scars from the blisters and scabs that cover the skin and fill with pus.

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The disease was particularly brutal in parts of the world colonised by Europeans, such as Australia and the Americas, where Indigenous populations had no natural immunity, resulting in millions of deaths.

In the Americas, historical reports record that smallpox began devastating Indigenous communities in the early 16th century, after the arrival of European colonists.

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Matthew Ward at the University of Dundee in the UK, who wasn’t involved in the new research, says the waves of epidemics, including smallpox, that spread across the Americas were some of the most important events in history. “These diseases killed perhaps 95 per cent of the Indigenous population of the Americas and allowed for European colonisation,” he says.

Nakagome and his colleagues studied samples of bone from mummies found at an archaeological site known as Camarones 9 in northern Chile, discovered in 1957. Over subsequent decades, 41 mummified bodies wrapped in blankets and buried with grave goods were recovered from the site.

“While the original aim was to study the human DNA, we also searched for DNA from ancient pathogens,” says Nakagome. “That is when we discovered fragments matching the smallpox virus in two individuals.”

The first was a woman who was 30 to 35 years old at the time of death, and the second, an 18-to-20-year-old man, was revealed by carbon dating to have died between 1492 and 1631.

By reconstructing the virus’s genomes and comparing them with other ancient and modern smallpox viruses, the team found that they belonged to a lineage of smallpox that includes early medieval and early modern European strains.

The discovery adds weight to the possibility that small skin lesions on the trunks of the mummies, previously attributed to chronic arsenic exposure, may in fact have been the distinctive pustules that scar the skin of smallpox victims.

“This finding allowed us to identify a small group of people impacted by the virus for which no historical record exists,” says team member Constanza de la Fuente Castro at the University of Chile in Santiago. Before the new research, the pathogen was known only from historical accounts of large-scale outbreaks, she says.

The work was particularly sensitive because of the disturbance of the original remains and the loss of material during analysis, both considered extremely controversial subjects to Indigenous people and the scientific community. “We never forget that behind every DNA extraction is a person, not a data point,” says de la Fuente Castro.

Ward welcomed the new research. “Understanding exactly what was killing native peoples and why they were so susceptible to epidemic disease is a vitally important issue,” he says.

Historians are now trying to understand how Europeans deliberately or inadvertently fuelled the spread of epidemics like smallpox, he says. “Without these epidemics, colonisation of the Americas would have been very different.”

Science DOI: 10.1126/science.aee6957