Ancient Yersinia pestis genomes of the second plague pandemic in the Baltic region

The second plague pandemic – starting with the Black Death in 1346-1353 and lasting at least until the 18th century – is historically well documented for the Baltic region. Yet, until 2020 it was a blank area with regards to ancient DNA evidence for its causative agent, Yersinia pestis. Here, we present five newly reconstructed, distinct Y. pestis genomes recovered from different sites in Estonia and western Russia, spanning from the late 14th century to the Plague of the Great Northern War (1702-1714), one of the last widespread outbreaks of plague in Europe. Together with recently published genomes from Latvia, Lithuania, Poland, and Sweden, they provide evidence for the persistent resurgence of plague in the Baltic region over several centuries and offer novel insights into the phylogeography of the Second Pandemic. Furthermore, the palaeogenetic identification of plague victims in different burial contexts including urban mass graves, single inhumations in rural cemeteries and emergency burials inform us about the struggle of past societies facing mortality crises.

Funding: ASTRA 2014-2020.4.01.16-0030, PRG243, PRG1027