Ancient Smallpox DNA from Chilean Mummies Confirms European Introduction

Researchers recovered variola-virus DNA from two naturally mummified Indigenous individuals buried at the Camarones 9 site in northern Chile. The remains—an adult woman (?30–35 years) and a young man (?18–20 years)—date to the early colonial period (1492–1631 CE). Genomic analysis revealed two nearly identical small-pox genomes (>99.9 % identical) that belong to a previously unknown, now-extinct lineage (“CAM9”) positioned between medieval European strains and later variants that gave rise to 20th-century smallpox.

Discover MagazineChilean mummies preserve ancient smallpox genome that traces disease to European colonization – Popular Archeology Scientific AmericanScienceAlertPopular Science

European contact in the late 15th century introduced infectious diseases to the Americas, with smallpox causing catastrophic mortality among Indigenous peoples. Historical accounts have long suggested the disease arrived with the Spanish conquest, but direct molecular proof from the New World has been lacking. Prior to this work, the oldest smallpox genomes were from Europe; no ancient American genomes had been recovered.

Chilean mummies preserve ancient smallpox genome that traces disease to European colonization – Popular Archeology Popular ScienceReutersDiscover Magazine

• Chronology: The individuals lived in the early 16th century, aligning with the first documented Caribbean outbreak in 1518.

Discover Magazine

• Genomic similarity: The two CAM9 genomes are >99.9 % identical, indicating infection during the same outbreak or from a single circulating strain.

Scientific American

• Evolutionary placement: Phylogenetic analysis places CAM9 after early medieval European strains but before lineages that later dominated the 20th century, filling a gap in the virus’s evolutionary tree.

ScienceAlert

Study co-author Constanza de la Fuente Castro, a biological anthropologist at the University of Chile, noted that Chilean written records of smallpox appear much later than the genetic evidence. Geneticist Shigeki Nakagome highlighted the lineage’s value for tracing viral adaptations that occurred before the virus reached the Americas.

Scientific American

• Death tolls: Estimates vary—from “roughly 90 %” loss of Indigenous populations to “three to four million” deaths. The lack of uniform figures reflects differing methodological approaches and limited historical documentation.

Discover Magazine

• Infection timing: While the genomes are securely dated to the early colonial era, the precise year of infection cannot be pinpointed, leaving a range centered on the 16th century.

Chilean mummies preserve ancient smallpox genome that traces disease to European colonization – Popular Archeology

• Ancient genome scarcity: The CAM9 genomes remain among only a handful of pre-modern variola sequences worldwide, limiting broader conclusions about the virus’s global spread.

Scientific American

• “While two genomes might not sound like a lot, it’s a significant step in the total number of historical variola virus genomes available,” — Ana Duggan, Public Health Agency of Canada

Scientific American

• “Recovering ancient viral DNA is extremely challenging, so seeing clear evidence that these individuals were infected with smallpox was a remarkable moment for the entire team,” — Shigeki Nakagome, Trinity College Dublin

ScienceAlert

The authors advocate for increased funding and infrastructure in the Global South to enable local scientists to lead future ancient-DNA investigations. They suggest that the CAM9 lineage can serve as a reference point for modeling how major demographic shifts—colonization, epidemics, and vaccination—shape pathogen evolution, informing contemporary public-health strategies.

Popular Science