European colonization brought smallpox to the Americas

Historians have believed that the collapse of Indigenous populations across the Americas was triggered largely by smallpox. The historical manuscripts and missionary chronicles provided detailed eyewitness reports of these devastating outbreaks. Molecular proof links colonial-era American epidemics directly to Old World viral strains remained elusive.

Now, a study published in the journal Science provides the definitive genetic confirmation researchers have sought for generations. It’s led by geneticists at Trinity College Dublin in collaboration with biological anthropologists at the Universidad de Chile. Researchers have successfully extracted and sequenced the oldest known smallpox viral genomes ever recovered in the Americas. The ancient viral DNA was retrieved from the naturally mummified remains of two individuals buried in northern Chile during the early Spanish colonial era.

The viral samples were recovered from bone fragments belonging to an adult woman (aged 30 to 35) and a young man (aged 18 to 20) buried near Camarones Cove. A coastal site in northern Chile that once marked the southern reaches of the Inca Empire. The individuals had been naturally preserved by the hyper-arid climate. They’re wrapped in camelid wool blankets and interred in traditional cloth bundles.

Scientists initially analyzed DNA from 13 individuals excavated at the site. They were searching for ancient bacterial infections such as tuberculosis. Instead, they discovered preserved traces of the variola virus. Guess what? It’s the deadly pathogen responsible for smallpox. Radiocarbon analysis alongside molecular clock estimates revealed that both individuals died between 1492 and 1631 CE. The violent era of Spanish conquest led by conquistadors like Francisco Pizarro.

Because the two viral genomes recovered from the mummies were virtually identical, geneticists concluded that both individuals likely succumbed to the same localized outbreak or were infected by the same circulating viral strain.

 Evolutionary Trajectory of a Global Killer

When researchers mapped the newly recovered genetic sequences onto a global evolutionary tree of smallpox, the results were unequivocal. The Chilean viral strain positioned directly between medieval European strains. The strains included those previously recovered from Viking-era human remains and later 17th- to 19th-century strains circulating in Europe. This placement provides molecular evidence that the virus was introduced to Indigenous American communities from the Old World.

The study yielded surprising insights into how pathogens evolve when introduced to vulnerable host populations. The variola virus originally evolved from a animal-host (zoonotic) pathogen. It was undergoing extensive genetic alteration up through the 16th century as it adapted to human hosts. Surprisingly, the virus’s rate of genetic change slowed dramatically during the peak colonial expansion of the 17th and 18th centuries. Researchers hypothesize that Indigenous populations lacked any pre-existing immunity. So, the virus had reached an evolutionary optimum. It could spread effortlessly without needing further genetic adaptation. The virus’s evolution accelerated once again in the late 18th and 19th centuries. It was after the introduction of Edward Jenner’s smallpox vaccine in 1796. Therefore, the evolutionary pressure forced the pathogen to adapt once more.

Why This Discovery Matters Today

Smallpox stands as one of the deadliest infectious diseases in human history. It has claimed hundreds of millions of lives over millennia before its official eradication in 1980 through global vaccination efforts. In the Americas, the disease inflicted physical casualties. The virus also shattered social structures and morale. The rapid disfigurement and death led communities to feel overwhelmed by forces they could neither treat nor comprehend.

This discovery demonstrates the immense power of ancient DNA research. Tracing how pathogen evolution interacts with human migration, population immunity, and public health interventions provides critical context for understanding modern infectious disease threats today.