A minimal hybridization capture system for the parallel enrichment and cost-effective detection of ancient human pathogens

Abstract

13 The preservation of ancient DNA in archaeological remains enables identification of past disease 14 agents. However, pathogen DNA is typically highly diluted by host and environmental DNA, 15 limiting detection. Here, we present a proof-of-concept study using in-solution hybridization 16 capture to improve detectability of a pre-defined set of 12 pathogens. We validate the method by 17 detecting Yersinia pestis, the plague agent, in six individuals from 17th and 18th century French 18 plague cemeteries with minimal sequencing. Expanding our probe set to target biomarkers of 19 virtually any pathogen of interest offers a powerful tool for tracking the prevalence of infectious 20 diseases in ancient populations. 21 Keywords: 3 to ten keywords : Ancient DNA, hybridization capture, target enrichment, 22 pathogen, plague Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université 1 bioRxiv preprint doi: https://doi.org/10.1101/2025.06.02.657376; this version posted June 3, 2025. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license. 23