The First Direct Genetic Evidence That Europeans Brought Smallpox to the Americas

For centuries, historians have attributed the catastrophic post-Columbian population decline in the Americas — estimated at 50 to 90 percent in some regions — in part to smallpox. Yet until a landmark study published July 30, 2026, in Science, no direct molecular evidence had ever linked the disease to European colonization. That changed when researchers recovered ancient viral DNA from two naturally mummified individuals from northern Chile, providing the first genetic proof that smallpox crossed the Atlantic with European colonizers.

The First Direct Genetic Evidence

Two naturally mummified individuals exhumed from the Inca archaeological site Camarones 9 in northern Chile — a woman in her 30s and a young man about 20 years old — yielded ancient DNA fragments of the Variola major virus . These are the first ancient smallpox genomes ever recovered from the Americas and the first direct molecular evidence that Europeans introduced smallpox to the New World .

The mummies date to the early Spanish colonial period, with radiocarbon calibration placing their deaths between 1492 and 1631 CE . Their remains were preserved naturally by the extreme aridity of the Atacama Desert. The bone samples had originally been collected to study human DNA — the smallpox discovery was a surprising secondary finding .

The viral genomes recovered from both individuals were nearly identical, suggesting they died during the same outbreak or were infected by the same circulating strain . Researchers designated the newly discovered strain CAM9, named after the Camarones 9 site .

What the CAM9 Strain Reveals

Evolutionary History

The CAM9 genomes belong to a now-extinct variola virus lineage that is distinct from all modern (20th-century) smallpox strains . Phylogenetic analysis shows this ancient strain is basal to the lineage that later gave rise to the 20th-century "alastrim" (mild) smallpox clade — meaning it represents a branch of the virus that circulated during the early colonial period but has since disappeared . The strain shares a common ancestry with Old World variola viruses, confirming its European origin .

Researchers found that the CAM9 lineage sits evolutionarily between strains known from medieval Europe and those that circulated in later centuries, effectively bridging the gap in variola's family tree .

Timing of Arrival

By comparing the ancient genomes with known modern strains, the researchers estimated that the viral lineage diverged from its European ancestor around the 15th–16th centuries, consistent with arrival during the earliest phase of Spanish colonization . The radiocarbon dates of the mummies themselves (as early as ~1492) place smallpox in South America within the first generation after Columbus .

Historical accounts describe a devastating smallpox epidemic in the Andes in the 1520s–1530s, often linked to the Spanish conquest of the Inca. These genomes provide the first physical evidence matching that timeline .

A Now-Extinct Lineage

The CAM9 strain belongs to a divergent, extinct viral lineage that was circulating in the 16th century but did not survive into the modern era. Today's globally circulating smallpox strains — eradicated in 1980 — belong to a different, more recently evolved branch. This suggests that multiple smallpox lineages were introduced from Europe, and only some of them became the dominant strains of later centuries .

Researchers also found that the CAM9 lineage had already stopped losing genes — meaning that although the virus was ultimately of animal origin (zoonotic), it had fully adapted to humans as its perfect host by the time it reached the Americas .

Broader Implications for Colonial-Era Epidemics

• Confirms a long-held assumption. Historians have long attributed the catastrophic post-Columbian Indigenous population decline — estimated at 50–90% in some regions — in part to smallpox. This study provides the first molecular proof for that narrative . Pathogen geneticist and study co-author Shigeki Nakagome stated: "This discovery provides the first molecular confirmation that smallpox was carried to the Americas during the colonial period" .

• Viral evolution in real time. The lineage's extinction shows that smallpox evolution in the Americas was not a single linear introduction; multiple viral variants arrived and competed, with only some persisting into the 20th century .

• Methodological breakthrough. The successful recovery of ancient viral DNA from arid-climate mummies opens the door to tracing other Old World pathogens — such as measles or tuberculosis — that colonial contact may have introduced .

• Human cost. The researchers emphasize that these two individuals are direct witnesses to the disease that killed untold millions of Indigenous people who had no prior immunity . Reuters described the findings as "the first direct molecular evidence of the smallpox unwittingly carried from the Old World to the New World that wiped out untold millions" .

The Smoking Gun

In short, the CAM9 genomes are the smoking gun — the first genetic proof that smallpox crossed the Atlantic with European colonizers and sparked one of the deadliest demographic catastrophes in human history. The evidence confirms what historians have long suspected but could never prove: that the disease arrived after 1492, not before, and that its introduction was a direct consequence of European colonization.