Inca bones confirm smallpox reached the Americas with Europeans

Smallpox genomes recovered from mummified remains in northern Chile provide the oldest molecular evidence of the disease in the Americas and support the historical view that European explorers and colonists brought the devastating pathogen to the New World, ERR reported.

The remains were found in the Camarones 9 cemetery. Researchers from Ireland, Japan and Chile originally set out to study the ancestry of people who lived in the region long ago, but the human genetic material in samples collected decades earlier had deteriorated too severely. The virus genome, however, was unexpectedly well preserved.

Smallpox was one of the deadliest diseases to affect humanity for thousands of years. It was responsible for nearly 300 million deaths in the 20th century alone, before becoming the only infectious disease eradicated through deliberate human action.

For Indigenous people living in the Americas during the era of European exploration, smallpox was even more deadly because they were believed to have had no immunity to the unfamiliar pathogen. Until now, knowledge of how the epidemics spread had been based mainly on written accounts by colonists.

The study, published in the journal Science, examined two victims buried at Camarones 9. Researchers extracted virus genomes from the thigh bones of a woman aged between 30 and 35 and a young man aged between 18 and 20.

The naturally mummified individuals lived during the period when the Inca Empire was collapsing and Spanish conquerors were taking control of the region. The pathogen DNA from the two remains was almost identical, suggesting that both died during the same outbreak.

Genetic analysis also showed that neither victim had any detectable European ancestry. The researchers therefore identified both as genetically belonging to the Indigenous peoples of the Americas. Their mitochondrial DNA haplogroups, A2 and B2, remain widespread in the region.

The absence of European ancestry indicates that smallpox spread rapidly through local Inca villages and that direct contact with Europeans was not necessary for infection.

The South American smallpox genome was biologically different from the strains studied extensively by medical researchers in the 20th century. In the virus family tree, the Chilean sample fell between European pathogens from the early Middle Ages and those from later centuries. Molecular data indicate that this virus line separated from its ancestors around 1296.

To estimate the age of the ancient virus, the researchers combined radiometric dating with molecular clock models. Samples taken from the female mummy hair helped narrow down the timing of the outbreak. The team also accounted for the local marine-based diet when analysing the carbon dating.