Ancient plague genomes of the Second Pandemic from Estonia and Western Russia

Keller, Marcel; Guellil, Meriam; Saag, Lehti; Malve, Martin; Valk, Heiki; Kriiska, Aivar; Slavin, Philip; Metspalu, Mait; Tambets, Kristiina; Scheib, Christiana L. (20 May 2022). Ancient plague genomes of the Second Pandemic from Estonia and Western Russia (Unpublished). In: Plague and Plagues. Transdisciplinary and diachronic perspectives on the history of plague. Palma de Mallorca.

Until 2020, the Baltic region was a blank spot on the map of ancient Yersinia pestis genomes of the so-called Second Pandemic (14th-18th century). Since then, publications of genomes from Sweden, Poland, Lithuania, and Latvia partially filled this gap, offering valuable insights into the involvement and role of the Baltic region in this pandemic. However, they still need to be integrated into a single phylogenetic tree and coherent narrative.
As part of an ongoing palaeogenetic project on Medieval Estonia, we screened several regular burial sites as well as mass graves and multiple burials for pathogens and were able to identify plague victims in five sites in Estonia and one in Western Russia (Pskov oblast), dating to the 14th to 18th centuries. Taken together with the previously published data, we can observe how plague waves repeatedly ravaged through the Baltic region, complementing our knowledge from written sources. The rapid spread of single bacterial lineages suggests furthermore the importance of maritime and inland trade through the Hanseatic League. Nevertheless, also rural sites were not spared from repeated outbreaks, as we could show for the site of Mäletjärve (Eastern Estonia). Moreover, we observe a prominent role of the Baltic region in a diversification event in the phylogeny of Y. pestis in the 15th or early 16th century which still lacks a precise date or clear association with historically reported outbreaks.
Coming upon a population weakened by years of war and famine, one of the most notorious outbreaks known as the Plague of the Great Northern War affected almost all urban centers in the Baltic region in between 1709 and 1713. Supposedly, it caused mortality rates outnumbering even those of the Black Death in the region (1349-1351). Complementing the published genome from Sweden, we were able to sequence two more genomes of this outbreak from Tallinn and its periphery, most likely dating to the siege of Tallinn in 1710.
In conclusion, our newly generated Y. pestis genomes and those recently published for the Baltic region opened a window to the history of plague in Northeastern Europe, so far only reconstructable from historical reports.

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

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