A 5,000-year-old hunter-gatherer already plagued by Yersinia pestis

A 5,000-year-old Yersinia pestisgenome (RV 2039) is reconstructed from a hunter-fisher-gatherer (5300–5050 cal BP) buried at Riņņukalns, Latvia. RV 2039 is the first in a series of ancient strains that evolved shortly after the split of Y. pestisfrom its antecessor Y. pseudotuberculosis∼7,000 years ago. The genomic and phylogenetic characteristics of RV 2039 are consistent with the hypothesis that this very early Y. pestisform was most likely less transmissible and maybe even less virulent than later strains. Our data do not support the scenario of a prehistoric pneumonic plague pandemic, as suggested previously for the Neolithic decline. The geographical and temporal distribution of the few prehistoric Y. pestiscases reported so far is more in agreement with single zoonotic events.