Ancient Smallpox Case Found in Isolated Northern Spain Cave Challenges Disease Spread Theories

Researchers have uncovered the oldest genetically confirmed case of smallpox in southern Europe within a remote cave community in northern Spain. The site, known as Las Gobas in Burgos province, was home to a small rural population living in rock-cut caves between the 7th and 11th centuries. Despite the Iberian Peninsula experiencing significant demographic shifts and conquests during this early medieval period, this community maintained near-complete genetic isolation, reproducing mainly within close family groups.

The study, led by Ricardo Rodríguez-Varela from the Centre for Palaeogenetics in Stockholm and published in Science Advances, combined traditional archaeology with advanced genomic sequencing. Analysis of 48 skeletal remains from a rock-cut cemetery allowed reconstruction of genomes from 33 individuals. The population showed a marked gender imbalance with twice as many males as females and extremely low Y-chromosome diversity, indicating a single paternal lineage and no genetic exchange with outsiders, even after the Muslim conquest altered neighboring populations.

Genomic data revealed that about 63% of the individuals had long stretches of identical DNA inherited from both parents, consistent with frequent close-kin marriages such as between cousins. The skeletal remains also showed evidence of severe physical trauma, including unhealed skull fractures and puncture wounds likely inflicted by sharp weapons near death, pointing to lethal interpersonal violence within the community.

Metagenomic analysis identified a bacterial pathogen transmitted from animals to humans through open wounds, supporting the community’s reliance on livestock. Most notably, the team detected smallpox virus DNA in a 10th-century burial, representing the earliest confirmed case in southern Europe. This strain closely matches medieval variants previously found in Scandinavia, Germany, and Russia, contradicting prior theories that smallpox entered Iberia from North Africa via southern Muslim trade routes. Instead, the findings suggest the disease spread southward through northern European networks.

This discovery reshapes understanding of medieval disease transmission and highlights the complex social and genetic dynamics of isolated populations during turbulent historical periods in the Iberian Peninsula.