Ancient smallpox genomes reveal how European colonization brought the disease to the Americas
Researchers from Trinity College Dublin have recovered and analyzed the first ancient smallpox virus genomes ever identified in the Americas, providing the strongest direct evidence to date that the disease was introduced through European colonization.
Smallpox, caused by variola virus, played a major role in the catastrophic population decline experienced by Indigenous peoples after the arrival of Europeans. Such was the extent of those declines that many claim smallpox and other introduced diseases entirely reshaped societies, killing hundreds of millions of people.
Until now, however, there had been no direct genetic evidence linking colonial-era outbreaks in the Americas to strains circulating in the Old World.
The study, just published in the journal Science, analyzed ancient viral DNA recovered from two individuals from a local community buried in northern Chile between the late 15th and early 17th centuries. The researchers found that the viruses belonged to a now-extinct lineage of variola virus that sits evolutionarily between medieval European strains and strains that circulated in later centuries.
"This discovery provides the first molecular confirmation that smallpox was carried to the Americas during the colonial period, but beyond tracing the disease's arrival, our study also sheds new light on how smallpox evolved," said Dr. Shigeki Nakagome of Trinity's School of Medicine.
"We found that the virus underwent a long period of genetic change up to the 16th century, but that its evolution slowed markedly during the height of colonial expansion and major smallpox epidemics in the 17th and 18th centuries," said Dr. Lara Cassidy of Trinity's School of Genetics and Microbiology.
"This suggests that the virus may have reached an evolutionary optimum, allowing it to spread successfully with little further adaptation—possibly aided by the lack of immunity that newly exposed populations had."
The team also found evidence that this period of evolutionary stability may have ended in the 19th century, when vaccination became increasingly widespread. As immunity levels rose, the pace of viral evolution appears to have increased again.
Potential impact of the research
Bruno Romero González, a doctoral student in Trinity's School of Medicine, said, "Taken together, the findings show how major historical events, including colonization, population change and vaccination, likely shaped the evolution of one of humanity's most devastating infectious diseases, while also demonstrating the power of ancient DNA to address longstanding historical questions."
Specifically, the work provides the first direct genetic evidence that Old World smallpox strains were present in Indigenous communities in the Americas during the colonial period, offering molecular support for historical accounts of smallpox introduction through European colonization.
The study also reveals how human societies shape pathogen evolution. The researchers suggest that when a pathogen can spread easily through large, susceptible populations, evolutionary pressures may favor maintaining a successful form rather than driving further genetic changes. Conversely, the apparent rebound in evolutionary rates after vaccination became widespread hints that public health interventions can alter the evolutionary landscape of pathogens.
The findings could inform modern infectious disease research, highlighting how population movement, immunity and public health measures can influence pathogen evolution. Related questions remain highly relevant for modern diseases such as influenza, COVID-19 and mpox.
For archaeological studies, the work expands the field of ancient pathogen genomics, demonstrating how ancient DNA can uncover aspects of disease history that are invisible in historical records alone. This opens new opportunities to study past epidemics and their impacts on global human populations.
How was smallpox eradicated?
Scientist Edward Jenner developed a vaccine in 1796. Widespread vaccination campaigns dramatically reduced transmission during the 19th and 20th centuries, although by the 20th century, smallpox was still causing an estimated 300–500 million deaths globally.
Then, a coordinated international eradication campaign was led by the World Health Organization, which ultimately succeeded in eliminating the disease. The last naturally occurring case was recorded in 1977 in Somalia, and in 1980 the WHO officially declared smallpox eradicated.
This makes smallpox the first and, so far, only human infectious disease to have been successfully eradicated worldwide.
Publication details
Bruno Romero González et al, The genomic identity of early smallpox in South America, Science (2026). DOI: 10.1126/science.aee6957. www.science.org/doi/10.1126/science.aee6957
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Citation: Ancient smallpox genomes reveal how European colonization brought the disease to the Americas (2026, July 30) retrieved 30 July 2026 from https://phys.org/news/2026-07-ancient-smallpox-genomes-reveal-european.html
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