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Significance The spread and evolution of plague have been under debate in the past few years. However, very little is known of the dynamics of the plague pathogen,Yersinia pestis , during the last phase of the Second Plague Pandemic in Europe (18th and 19th century). We present nine ancientY. pestis genomes from the Second Plague Pandemic. CHE1 is the first Second Plague Pandemic genome from the Caucasus region, an area that houses plague wildlife reservoirs to this day, making it a key strain to help elucidate the origin of Medieval and Early Modern plague. Our study documents the importance of a noneurocentric approach to historical plague dynamics and proposes an origin of plague introductions outside of Europe.

A genomic and historical synthesis of plague in 18th century Eurasia