Journal Article

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

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

2019

Overview

The second plague pandemic, caused by Yersinia pestis , devastated Europe and the nearby regions between the 14 th and 18 th 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. The second plague pandemic, caused by Yersinia pestis , started in the 14th century and recurred in Europe until the 18th century. Here, the authors reconstruct ancient Y. pestis genomes from human remains spanning this period, shedding light into the phylogeography and population structure of the European strains.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 45 / 45/23 / 49 / 49/22 / 631/181/2474 / 631/208/325/2482 / 631/326/421 / Archaeological sites / Archaeology - methods / Archaeology and Prehistory / Bubonic plague / DNA, Bacterial - chemistry / DNA, Bacterial - classification / DNA, Bacterial - genetics / Europe, Eastern - epidemiology / Evolution / Fossils / Genetic diversity / Genome, Bacterial - genetics / Genomes / High-Throughput Nucleotide Sequencing - methods / Historic sites / History / Humanities and Social Sciences / Humans / multidisciplinary / Pandemics / Pathogens / Phylogeny / Phylogeography / Plague - epidemiology / Plague - microbiology / Polymorphism, Single Nucleotide / Science / Science (multidisciplinary) / Time Factors / Virulence / Virulence - genetics / Yersinia pestis / Yersinia pestis - genetics / Yersinia pestis - pathogenicity