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

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

doi:10.1038/s41467-019-12154-0

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.

Highlights

The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries Archaeological site dates (AD)
Sample screening for signatures of Y. pestis DNA
Two approaches were used for the assessment of Y. pestis DNA in tooth specimens (n = 206) from ten archaeological sites spanning the 14th–17th centuries AD in Europe (Fig. 1, Supplementary Figs. 1–10 and Supplementary Note 1)

Summary

Introduction

The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. 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. After the BD, plague was a common scourge in Europe as evidenced by the thousands of recorded epidemics it supposedly caused between 1353 and the late 18th century[2,11]. Whether these were caused by multiple introductions of the disease from an.

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Conclusion