Publication

Title: Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes

Authors: Maria A. Spyrou, Marcel Keller, Rezeda I. Tukhbatova, Christiana L. Scheib, Elizabeth A. Nelson, Aida Andrades Valtueña, Gunnar U. Neumann, Don Walker, Amelie Alterauge, Niamh Carty, Craig Cessford, Hermann Fetz, Michaël Gourvennec, Robert Hartle, Michael Henderson, Kristin von Heyking, Sarah A. Inskip, Sacha Kacki, Felix M. Key, Elizabeth L. Knox, Christian Later, Prishita Maheshwari-Aplin, Joris Peters, John E. Robb, Jürgen Schreiber, Toomas Kivisild, Dominique Castex, Sandra Lösch, Michaela Harbeck, Alexander Herbig, Kirsten I. Bos and Johannes Krause

Publication: Nature Communications, DOI: 10.1038/s41467-019-12154-0

Contact

Maria A. Spyrou
Maria A. Spyrou
Phone: +49 3641 686-666
Room: 225
Prof. Dr. Johannes Krause
Prof. Dr. Johannes Krause
Director

Phone: +49 3641 686-600
Room: 209
Dr. Kirsten Bos
Dr. Kirsten Bos
Phone: +49 3641 686-678

Media contact

Anne Gibson
+49 3641 686-950
Petra Mader

+49 3641 686-960
presse@shh.mpg.de

Ancient genomes provide insight into the genetic history of the second plague pandemic

Analysis of 34 ancient plague genomes from the Black Death and succeeding plague epidemics in Europe between the 14th and 17th centuries, reveals how the bacterium diversified after a single introduction.

October 02, 2019

An international team of researchers has analyzed remains from ten archaeological sites in England, France, Germany, Russia, and Switzerland to gain insight into the different stages of the second plague pandemic (14th-18th centuries) and the genetic diversity of Yersinia pestis during and after the Black Death. In a study published in Nature Communications, the researchers reconstructed 34 Y. pestis genomes, tracing the genetic history of the bacterium, which revealed key insights into the initiation and progression of the second plague pandemic in Europe.

Map showing the locations of newly sequenced (circles) and previously published (triangles) plague genomes, colored by their temporal order. Zoom Image

Map showing the locations of newly sequenced (circles) and previously published (triangles) plague genomes, colored by their temporal order.

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The second plague pandemic, which began with the Black Death in the mid-14th century and continued with devastating outbreaks in Europe and the vicinity until the 18th century, decimated the continent, causing the death of up to 60% of the population. But where did this strain of Yersinia pestis, the plague causing bacterium, come from? And how did it evolve and expand once it arrived?

A likely point of entry for Y. pestis during the second pandemic

Despite the ubiquity of the Black Death in historical texts and the popular imagination, the entry point of the Y. pestis bacterium at this time and the route it traveled through Europe remain unclear, due to a lack of data from early outbreaks and a general scarcity of published ancient Y. pestis genomes. In the current study, researchers reconstructed plague genomes from the teeth of 34 individuals, including two from Laishevo, in the Volga region of Russia, and found a single strain that is ancestral to all second pandemic strains. In addition, the researchers observe an absence of genomic diversity from samples during the Black Death. “These findings indicate a single entry of Y. pestis into Europe through the east”, explains first author Maria Spyrou of the Max Planck Institute for the Science of Human History. “However, it is possible that additional interpretations may be revealed with future discoveries of un-sampled diversity in western Eurasia”, she notes.

Mass grave dating to the Black Death period, identified in the “16 rue des Trente Six Ponts” archaeological site in Toulouse, France. Zoom Image

Mass grave dating to the Black Death period, identified in the “16 rue des Trente Six Ponts” archaeological site in Toulouse, France.

Persistence of Y. pestis within Europe

Although the researchers found that the European-wide Black Death was likely caused by a single strain, analysis of genomes from later in the pandemic shows the emergence of a lineage displaying a higher genetic diversity. “In the later phase of the second pandemic, we see the development of multiple branches within Europe, which suggests that plague was maintained in different local foci”, says Marcel Keller, co-first author of the Max Planck Institute for the Science of Human History. “No modern descendants of this lineage have been found to date, possibly indicating the extinction of these reservoirs.”

The researchers also identified a deletion including two virulence-related genes from genomes within this second lineage. Interestingly, genomes from the late stages of the first plague pandemic have shown a deletion in the same region. “Given that this deletion occurred in lineages from the first and second pandemic, both now extinct, determining how these genes impact maintenance in human and flea hosts would be an important area for future study”, comments Kirsten Bos, research group leader of the Max Planck Institute for the Science of Human History.

Maria Spyrou in the clean lab of the Max Planck Institute for the Science of Human History in Jena. Zoom Image

Maria Spyrou in the clean lab of the Max Planck Institute for the Science of Human History in Jena.

The current study provides new perspectives into the initiation and progression of the second plague pandemic and adds significantly to the database of published ancient Y. pestis genomes. “We have shown that extensive analysis of ancient Y. pestis genomes can provide unique insights into the microevolution of a pathogen over a period of several hundred years”, says senior author Johannes Krause, Director of the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History. In the future, integrating this data into disease modelling efforts, in conjunction with data from other areas such as climate science, epidemiology and history, will be important for better understanding the second plague pandemic.

 
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