Definitive proof of smallpox was found in the remains of two people who lived in the Inca Empire during the start of Spanish colonization.
Smallpox is caused by the variola virus, a member of the orthopoxvirus family, which are DNA viruses. It was one of the most devastating diseases in human history before a massive global vaccination effort eradicated it globally in 1977.
Scientists and historians widely agree that Europeans brought smallpox to the Americas, which caused profound levels of death among Indigenous communities. But most of the evidence from the conquest of the Inca and early colonial period is found in historical records written by Spanish colonizers. These give a one-sided account that may not fully capture the devastation caused by the virus.
Research published yesterday in the journal Science offers a new witness to history: The first direct molecular evidence that variola was present during the early colonial era and that the virus came from Europe was found in a cemetery in northern Chile.
Discrete smallpox strain found in Chile
The researchers analyzed mummified bone fragments from 13 individuals buried in an Inca-period site called Camarones 9. The site is located in the arid Camarones Valley, and radiocarbon dating of the site's faunal and botanical material dates between the years 1320 and 1680.
Of the 13 fragments, variola DNA was found in the femurs belonging to two people: One was a woman who was between the ages of 30 and 35 when she died, and the other was a man aged 18 to 20 years.
Smallpox was not only a disease that caused widespread death; it also disrupted the transmission of knowledge, language, leadership, and community life.
Genomic sequencing shows that this discrete strain, which researchers named CAM9 smallpox genome, split from a branch of European variola virus around 1296. When comparing CAM9 to other variola strains, the authors described its evolutionary lineage as "intermediate," sitting between Viking-era strains and modern ones that circulated during the 20th century.
Regarding the other individuals buried at Camarones 9, it's possible that they died before the arrival of smallpox. Or they could have been contemporaries of the two people who did have it but didn't contract the illness at all.
However, environmental preservation of the mummies buried at Camarones 9 wasn't great, senior author Shigeki Nakagome, PhD, a geneticist specializing in ancient genomics at Trinity College Dublin, told CIDRAP News. It's plausible that some people buried there had smallpox even if the DNA analysis was negative for variola.
Because the variola virus was still evolving in Europe and people kept coming to the Americas in waves, Nakagome would like to see this type of analysis performed on other individuals in the archaeological record to track how different strains and species of disease shaped the colonial period.
“We don't know yet which strain was brought from the Old World to the New World each time,” he said.
This research helps document the profound human cost of colonization while complementing Indigenous historical memory, said Soledad Chango, a linguist earning her PhD in anthropology at Columbia University and a native Kichwa speaker, one of the languages spoken during the Incan Empire.
"Smallpox was not only a disease that caused widespread death; it also disrupted the transmission of knowledge, language, leadership, and community life,” said Chango, who was not involved in the research. "Entire generations of knowledge keepers and local authorities were lost, leaving consequences that continue to shape our communities today."
Smallpox role in Spanish conquest is debated
At its height, the Inca ruled over the largest pre-Columbian empire in the Americas. The realm spanned some 770,000 square miles in the western half of South America and was connected by a sophisticated highway system of roads and bridges. The Inca had no written language and instead used a complex knot system called quipu, in which different colors and patterns indicated numerical value, and potentially other information.
It's widely agreed that smallpox, along with measles and influenza, contributed to the decimation of Indigenous populations after the Spanish conquest.
But there are debates on the timing, prevalence, and severity of these diseases, particularly in the case of smallpox, said Melissa S. Murphy, PhD, a bioarcheologist at the University of Wyoming whose research includes work on the effects of imperialism and colonialism in pre-Hispanic and colonial Peru.
Murphy did not contribute to the findings in Science, which she said is an important discovery because it provides direct evidence that smallpox was present.
It's very odd to have that level of death, and then just like no information on it other than colonial historical accounts.
Khrystyne Tschinkel, PhD, a bioarchaeologist at Hamline University and one of the reviewers of the paper, agrees with Murphy and said part of the problem is that the archaeological record is a bit of a black hole. While it's assumed that millions of people died from diseases because of evidence of a demographic collapse, these individuals have not been found.
“Where are they? What happened to them?” she said. “It's very odd to have that level of death, and then just like no information on it other than colonial historical accounts.”
It's hard to know when the first major outbreak of smallpox occurred since many of the quipu were likely destroyed. But some of the demographic collapse was likely driven by forced labor, food insecurity, and brutality inflicted by Europeans onto Indigenous communities. These conditions create breeding grounds for epidemics, noted R. Alan Covey, PhD, an archaeologist at the University of Texas at Austin specializing in the Inca empire and early colonial Peru. Covey did not contribute to the Science paper.
“You can see from the census data in the 1570s, the population goes down by about 50% in about 30 years," he said.
So far, the only other publication showing the presence of smallpox in South America during the 16th century is Tschinkel's 2024 paper that analyzed the skeletons of two toddlers who belonged to the Chimú people, a group that was colonized by the Inca about 60 years before the arrival of the Spanish.
You can see from the census data in the 1570s, the population goes down by about 50% in about 30 years.
Their bones have lesions indicative of smallpox, which allowed Tschinkel to diagnose the disease. However, smallpox infection doesn't always leave lesions, so DNA provides another avenue for analysis.
Smallpox might have infiltrated the Inca realm prior to the arrival of the Spanish
Some historians speculate that variola was introduced to South America during earlier Spanish expeditions in northern and eastern parts of the continent: The virus then traveled faster than the colonizers through communities that had never encountered smallpox and had no immunity.
One of those early smallpox deaths might have been the Incan Emperor Huayna Capac. While campaigning in what is now Colombia, he contracted and died of a disease that might have been smallpox in 1527—though the evidence of this is inconclusive.
Soon after Huayna Capac's eldest son, Ninan Cuyochi, died from disease, also possibly smallpox.
“If you think of it, first contact in the Andes was not made by Pizarro, but a pathogen," said bioarchaeologist Haagen D. Klaus, PhD, of George Mason University, who did not contribute to the research.
Francisco Pizarro led the Spanish conquest of the Inca. Arriving in 1531, he found a realm roiled with violence, political upheaval, and possibly disease.
If you think of it, first contact in the Andes was not made by Pizarro, but a pathogen.
The deaths of Huayna Capac and Ninan Cuyochi created a power vacuum that led to a civil war. At the same time, rebellion sprang up in provinces that had been colonized by the Inca and forcibly incorporated into the empire.
Pizarro capitalized on this instability by aligning himself with factions who opposed the Emperor Atahualpa, another son of Huayna Capac and the last Incan ruler. Pizarro captured and then executed Atahualpa in 1533, marking the beginning of nearly 300 years of Spanish colonial rule.
Chango said she encourages scientists to work with Indigenous communities on future research, as this not only supports ethical practices, but recognizes the resilience and continuity of a culture, despite centuries of colonial violence
