Paleoepidemiology of infectious diseases across the Holocene EpidemioCene

The frequency of infectious disease emergence has increased over the last decades, a phenomenon attributed to modern global sociodemographic and environmental changes. However, major transformations of human lifestyles and technologies associated with large-scale repercussions on the planet's ecosystems have occurred since prehistory. Measuring the epidemiological impacts of these changes on large time scales could provide precious lessons to anticipate the consequences of ongoing processes. Recent advances in the field of paleogenetics have opened promising perspectives in this regard by allowing the identification of various pathogens from skeletal remains dating back several millennia. The use of ancient DNA evidence for quantitative assessments of past disease distribution and determinants has, however, largely been missing so far. With this project, my group will leverage tens of thousands of ancient DNA libraries and sequencing datasets produced during recent years at the host and partner institutions to undertake large-scale paleoepidemiological investigations covering the past 12,000 years of human history in western Eurasia. Novel laboratory, bioinformatic and statistical approaches will be developed to maximize pathogen detection sensitivity and estimate variations in disease frequency from ancient metagenomic data while accounting for expected sources of biases. This will be combined with epidemiological modelling and phylodynamic analyses of large sets of ancient pathogen genomes to unveil paleoepidemiological dynamics and their associations with sociocultural transitions and environmental changes throughout the Holocene. This project will provide unprecedented insights into the inseparable history of humans and their pathogens, a multi-millennial perspective on current global health challenges, and strong foundations for future paleoepidemiological studies.