Researchers have extracted ancient DNA fragments of the variola virus—the pathogen responsible for smallpox—from the naturally mummified remains of two Indigenous individuals buried in northern Chile. Publishing their findings in studies covered by outlets including the Irish Examiner, scientific teams pinpointed the genetic material between roughly 1492 and 1631, securing new molecular evidence on how the disease spread during the turbulent transition from Inca rule to the Spanish colonial period.
Mapping a Century of Transition
Smallpox remains the sole human infectious disease eradicated on a global scale. The World Health Organization (WHO) declared the pathogen eradicated in 1980 after a campaign of vaccination, surveillance, and containment. Yet historical records have long traced devastating epidemics to the dawn of European contact in the Americas, marking the first documented outbreak on the island of Hispaniola in 1518.
The newly recovered genetic fragments from Chile directly tie these strains to viruses that once circulated in Europe. Phylogenetic analysis reveals that the two Chilean viruses belonged to a now-extinct lineage branching away from other known variola groups around 1296. This date reflects an estimated evolutionary divergence rather than the precise arrival of smallpox in South America.
The limits of ancient DNA
The scientific findings show that the retrieved material consists solely of damaged, short genetic fragments preserved across the centuries. No intact virus particles survived within the mummified remains.
Time degrades ancient DNA into small pieces while driving chemical changes. Scientists sequence these surviving fragments and rely on computers to piece the genomes back together computationally. Building a functional poxvirus particle demands an intact genome paired with specific proteins and enzymes capable of reproducing inside a living cell. Because the ancient Chilean fragments lack this complete viral machinery, they cannot spontaneously cause smallpox or offer a viable route for the disease to return.
While researchers successfully assembled a synthetic horsepox virus in a laboratory setting back in 2018 using specialized procedures and helper viruses, the Chilean study focused strictly on sequencing naturally degraded DNA via computer modeling. No physical viral agents were generated.
Lesions, arsenic, and modern security
The mummified remains analyzed in the study displayed small skin lesions. Earlier investigations led by bioarchaeologist and study co-author Bernardo Arriaza tied these marks to chronic arsenic exposure, highlighting elevated arsenic levels in the tissues caused by local rivers carrying natural minerals from the surrounding geology into regional food and water supplies.
The newly extracted variola DNA confirms that both individuals contracted smallpox. Even so, researchers stress that the genetic data cannot definitively determine what caused those specific skin lesions, nor can it prove whether smallpox ultimately caused the death of either person. Today, live variola virus is securely stored exclusively inside two WHO-designated high-security laboratories for strictly approved research purposes.
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