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

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

Abstract

The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541–750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.

Citation

Spyrou, M. A., Keller, M., Tukhbatova, R. I., Scheib, C. L., Nelson, E. A., Andrades Valtueña, A., …Krause, J. (2019). Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes. Nature Communications, 10(1), Article 4470. https://doi.org/10.1038/s41467-019-12154-0

• Journal Article Type: Article
• Acceptance Date: Aug 15, 2019
• Online Publication Date: Oct 2, 2019
• Publication Date: Oct 2, 2019
• Deposit Date: Oct 15, 2019
• Publicly Available Date: Oct 15, 2019
• Journal: Nature Communications
• Publisher: Nature Research
• Peer Reviewed: Peer Reviewed
• Volume: 10
• Issue: 1
• Article Number: 4470
• DOI: https://doi.org/10.1038/s41467-019-12154-0