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

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 initi...

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Bibliographic Details
Published in:	Nature communications Vol. 10; no. 1; pp. 4470 - 13
Main Authors:	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
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 02-10-2019 Nature Publishing Group Nature Portfolio
Subjects:	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 Europe, Eastern Europe
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 PMCID: PMC6775055
ISSN:	2041-1723 2041-1723
DOI:	10.1038/s41467-019-12154-0