Infectious diseases have had devastating effects on human populations throughout history. We created an archaeogenetic-based spatiotemporal map of human pathogens by screening shotgun sequencing data from 1,313 ancient humans, spanning 37,000 years of Eurasian history. We found a widespread presence of ancient bacterial, viral and parasite DNA, identifying 5,486 individual hits against 492 species from 136 genera. Among those hits, 3,384 involved known human pathogens, many of which had not previously been identified in ancient human remains. Moreover, we extended the findings of some pathogens back in time, e.g., hepatitis B virus (HBV) and Yersinia pestis (the cause of plague). We also observed changing epidemiological patterns for the spread of Yersinia pestis and Borrelia recurrentis (the cause of louse-borne relapsing fever) over time, which coincided with changes in the genomes of these pathogens. Grouping the ancient microbial species according to their likely reservoir and type of transmission, we found that while most groups were identified throughout the entire sampling period, zoonotic pathogens were only detected from around 6,500 years ago, peaking roughly 5,000 years ago, coinciding with the widespread domestication of livestock and the migration of pastoralist steppe people from the Pontic Steppe into Europe. Their migration caused a genetic upheaval in Europe and left a lasting genetic legacy, especially in the Northern and North-western parts of Europe, which was as great, or greater, than that of the Anatolian farmers and which shapes susceptibility to many current diseases, such as multiple sclerosis. Our studies on pathogens and multiple sclerosis offer insights into the co-evolution of human lifestyle and diseases, highlighting how cultural changes have influenced the infectious disease landscape over time and the impact infectious disease-associated selective pressures have had on our immune system setup and health today.

Astrid Iversen is a professor of virology and immunology at the University of Oxford. Her primary research interest is understanding the co-evolution of pathogens and the human immune response and how a better understanding of these interactions might lead to better treatment of infectious diseases and improved vaccine design. Moreover, she is involved in ancient DNA studies examining how the pathogenic challenges have changed during the last ~12,500 years, the impact this has had on our immune system setup, and the implications for current immune responses to old and new pathogens and autoimmune disease prevalence.