New ancient Eastern European Yersinia pestis genomes illuminate the dispersal of plague in Europe

Abstract

Yersinia pestis , the causative agent of plague, has been prevalent among humans for at least 5000 years, being accountable for several devastating epidemics in history, including the Black Death. Analyses of the genetic diversity of ancient strains of Y. pestis have shed light on the mechanisms of evolution and the spread of plague in Europe. However, many questions regarding the origins of the pathogen and its long persistence in Europe are still unresolved, especially during the late medieval time period. To address this, we present four newly assembled Y. pestis genomes from Eastern Europe (Poland and Southern Russia), dating from the fifteenth to eighteenth century AD. The analysis of polymorphisms in these genomes and their phylogenetic relationships with other ancient and modern Y. pestis strains may suggest several independent introductions of plague into Eastern Europe or its persistence in different reservoirs. Furthermore, with the reconstruction of a partial Y. pestis genome from rat skeletal remains found in a Polish ossuary, we were able to identify a potential animal reservoir in late medieval Europe. Overall, our results add new information concerning Y. pestis transmission and its evolutionary history in Eastern Europe. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

Assessing the origins of the European Plagues following the Black Death: a synthesis of genomic, historical and ecological information

“…For the purpose of understanding the evolution of the plague bacteria, more than 100 ancient Y. pestis genomes have been published to date. The last 17 were recently reported during a short period by four distinct research groups (7-9, 12). Using most of the ancient genomes (criteria for exclusion are described in methods) along with 499 modern ones, we present here the most updated phylogeny (Fig.…”

“…The original hypothesis (Hypothesis 1) claims that such a plague reservoir existed in Western Europe (14), perhaps in the Alps (15). However, a newer hypothesis (Hypothesis 2) claims that the plague reservoir was in Asia, possibly close to Eastern Europe (6, 7, 9, 11, 13).…”

“…Thus, Hypothesis 1 needs to account for a back- and-forth spread, which reintroduced plague on two occasions to the Ottoman Empire and back again to Western Europe. Notably, none of the strains from the 18 th century appear to have originated in Western Europe according to historical sources (7, 9).…”

“…Researchers agree that the Second Plague Pandemic was caused by Yersinia pestis (1-9), which arrived in Europe from Caffa transported by Genoese galleys on the Black Sea at the beginning of the Black Death (10). However, there is no consensus among researchers as to the origins of plague epidemics in Europe following the Black Death and ravaging Europe until the 19 th century, as attested by historical documents (11).…”

“…The two main theories are that one or more plague reservoirs remained in Western Europe during the entire Second Plague Pandemic (referred to in the following as Hypothesis 1) (3, 4, 8, 12), or the bacteria repeatedly invaded Europe from non-Western European reservoir(s) during the same period (referred to in the following as Hypothesis 2) (6, 7, 9, 11, 13). Here, we assess these two hypotheses using a broad spectrum of evidence including historical and archeological, genetic and evolutionary, as well as ecological information.…”