Two 500-year-old mummies confirm Europeans brought smallpox to the Americas: ‘It came from the Old World’
The oldest virus samples found on American soil had already fully adapted to humans
A woman in her thirties and a young man of about 20 died of smallpox in the first decades of Spanish colonization of the Americas. Exhumed decades ago from an Inca cultural site in northern Chile, DNA from the Variola virus has now been found in their remains. This constitutes the oldest evidence of the virus’s presence on American soil. The authors of the discovery, whose findings are published in the journal Science, also show that this lineage had already stopped losing genes. In other words, although of animal origin (zoonotic), it had found in humans its perfect host. The immune systems of Indigenous people, unable to confront the new disease, may have helped this maturation process. The analysis rules out the presence of the virus in the Americas before colonization.
While historians disagree about the size of the American population before Christopher Columbus’s arrival (about 13 million according to the most conservative estimates and roughly 90 million according to the most generous), they agree that disease reduced those numbers so drastically that by the late 16th century only about 10% remained — more destructive than warfare with Europeans or slavery. They also agree that among the various illnesses, including the mysterious Cocoliztli Epidemic, smallpox killed the most people. The first documented outbreak occurred in the Caribbean, on Hispaniola (now Santo Domingo) in 1518. Two years later it had spread to the mainland, decimating the Aztecs and reaching as far as the mouth of the Camarones inlet on the Pacific coast of present-day Chile.
“Camarones 9 is an archaeological site that is indeed in the Camarones ravine, reaching the coast,” says Constanza de la Fuente, a University of Chile researcher and co-author of the study. “It was excavated between the 1960s and 1980s, and many individuals were recovered who were bundled up, in a fetal position, and wrapped in various textiles,” she adds. They were moved and some were displayed at the San Miguel de Azapa Archaeological Museum. Since then, the arrival of ancient DNA technologies made it possible to study samples from 13 of them.
“Initially we were interested in finding bacteria, for example tuberculosis, for which ancient DNA samples are known in the Americas,” says Bruno Romero, a Trinity College Dublin researcher and co-author of the study. “We found none of that, but looking at the results, suddenly we found Variola. So we began analyzing the virus itself,” he adds. “These smallpox samples are the oldest ever found on the American continent,” De la Fuente emphasizes. Combining radiocarbon dating with the virus’s own molecular clock, the authors place the two samples in a time range from 1492 to 1631.
One factor that aided the finding is that both the woman and the young man from Camarones 9 were mummified. “The dry environment, lack of rain and high salinity of the Atacama Desert create conditions favorable for the preservation of bioanthropological and archaeological remains, organic and inorganic,” notes Bernardo Arriaza, an archaeologist at the Institute for Advanced Research of the University of Tarapacá (Chile) and a co-author of the paper.
The researchers compiled information on earlier smallpox samples from medieval Europe, such as the so-called Viking strains, and later samples from the 17th to 19th centuries up to the advent of vaccines. That allowed them to build a phylogenetic tree placing each sample, strain and lineage on the virus’s leaves, branches and trunk. This makes it possible to rule out the existence of smallpox in the Americas before Europeans arrived. “If the virus had been native to the Americas, it would have diverged from Eurasian samples long ago,” Romero notes. The reality is different: “The phylogenetic tree shows that this Variola strain occupies an intermediate position between the Viking strains and 17th-century strains from Lithuania, suggesting it came from the Old World,” the Trinity College researcher concludes.
For José Vicente Tuells, a professor at Universidad CEU Cardenal Herrera (Valencia) and an expert in the history of medicine, the work is highly significant because “it turns a widely accepted historical hypothesis into a direct genetic demonstration.” It is the first time that science — in this case genetics and ancient DNA — has provided evidence that “smallpox was a disease introduced from the Old World and that it circulated among Indigenous American populations during the early stage of colonization,” he adds. However, he also points out that because the sample size is small, the study does not resolve “the debate over the role of smallpox in the Indigenous demographic collapse.”
The two smallpox samples were, moreover, unusual. When analyzing the virus’s genetic machinery and its evolution, the researchers observed that several dozen genes had mutated; specifically, they were inactivated and did not express proteins with any function.
“We discovered that the virus underwent a long period of genetic change until the 16th century, but that its evolution slowed markedly during the zenith of colonial expansion and the major smallpox epidemics of the 17th and 18th centuries,” says Dr. Lara Cassidy of the School of Genetics and Microbiology at Trinity College Dublin, also a co-author of the study. “This suggests the virus may have reached an evolutionary optimum, allowing it to spread successfully with little additional adaptation, possibly aided by the lack of immunity in newly exposed populations.”
Antonio Alcamí is a virologist at the Severo Ochoa Molecular Biology Center (Madrid) and an expert in poxviruses, the family that includes human smallpox. He notes that “when viruses specialize in a host, they tend to lose genes.” Thus, the Viking strains, from around the year 1000, “were intermediate strains that had already lost some of those genes,” he adds. Modern smallpox — the 20th-century form prior to its eradication — “had lost 49 genes,” Alcamí says. That is the same number of genes that were inactivated in the strain found at Camarones.
Although that gene loss or inactivation is linked to specialization in a host, “there is a question to be answered,” the Spanish researcher says: “How does gene loss relate to an increase in virulence?” In fact, Viking smallpox was caused by an attenuated virus with low mortality. The virus that killed the woman and the young man from Camarones went on to kill millions of Americans.
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