By synthesizing palaeogenomic, archaeological, and historical records, this study investigates disease dynamics in 13th-century North China. We screened ancient metagenomic data from 15 individuals from a 13th-century mortuary context at the Xiyang site (Shanxi, North China). Authentic Salmonella enterica subsp. enterica serovar Paratyphi C (SPC) reads were detected in 5/15 individuals, of which three met criteria for downstream analyses. Ancient authenticity was supported by deamination signatures, short fragment lengths, mapping stringency, and negative controls. Human genomic profiles show affinities consistent with contemporaneous North China agricultural populations. Archaeological context reveals these 15 individuals derived from six multi-individual burials with no biological kinship ties across burials, indicating multi-household exposure rather than a single-family cluster. Pathogen detections represent a conservative lower bound; the true number of infections likely exceeded five. Historical records from 1213–1232 CE document a severe epidemic with fever, headache, diarrhea, and bloody stool—symptoms consistent with SPC. Wartime environmental degradation likely facilitated faecal-oral pathogen spread. SPC detection aligns temporally with this epidemic. Together, archaeological, palaeogenomic, and textual evidence support the hypothesis that SPC contributed to outbreaks, while acknowledging it was not necessarily the sole agent. Limitations include modest sample size (n=15; positives=5), uncertain within-tomb simultaneity, and incomplete chronological precision. These findings extend SPC’s range to 13th-century North China and motivate targeted capture, direct dating, and broader screening to evaluate scale, timing, and aetiological heterogeneity.

First Author: Jiayu He

Co-Authors: Li Yu, Fan Zhang, Ge Song

Keywords:
Ancient DNA
Epidemic
East Asian
Salmonella Paratyphi C