Late infection diagnosis: Rudolf Virchow's skull collection indicates 5000-year-old hunter-gatherer already plagued by Yersinia pestis

A 5000-year-old Yersinia pestis genome (RV 2039) from a hunter-fisher-gatherer (5350-5150 cal BP) buried at the site of Rinnukalns, Latvia, was reconstructed. The remains had been stored in the Anthropological Rudolf Virchow Collection in Berlin for 145 years. RV 2039 was the first in a series of ancient strains that evolved shortly after the split of Y. pestis from its antecessor Y. pseudotuberculosis about 7000 years ago. The genomic and phylogenetic characteristics of RV 2039 are consistent with the hypothesis that this very early Y. pestis form was likely less transmissible and maybe even less virulent than later strains. Our data do not support the scenario of a prehistoric plague pandemic as suggested previously for the Neolithic decline. The geographical and temporal distribution of the few prehistoric Y. pestis cases reported so far is more in agreement with the scenario of single zoonotic events.