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Cited by 182Yersinia bacterium, plague, ectoparasites researchForensic and Genetic ResearchGenetic diversity and population structure

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

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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·2019·Nature Communications
DOI 10.1038/s41467-019-12154-0PMC PMC6775055
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Abstract

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.

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  • Analyses of the victims of both the Plague of Justinian and the Black Death have shown that Y. pestis was indeed the cause of both pandemics, and further genomic analysis has provided insight into the course of these pandemics over time, including parallel changes in the pathogen itself.

    “For example, analyses of the victims of both the Plague of Justinian and the Black Death have shown that Y. pestis was indeed the cause of both pandemics 65,303 , and further genomic analysis has provided insight into the course of these pandemics over time, including parallel changes in the pathogen itself [304][305][306] .”

    From Ancient DNA analysis (2021) · cites this paper as [303]

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  • Ancient DNA analysis

    Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411

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Metadata

Authors
Spyrou, M. A., Keller, M., Tukhbatova, R. I., Scheib, C. L., Nelson, E. A., Andrades Valtueña, A., Neumann, G. U., Walker, D., Alterauge, A., Carty, N., Cessford, C., Fetz, H., Gourvennec, M., Hartle, R., Henderson, M., von Heyking, K., Inskip, S. A., Kacki, S., Key, F. M., Knox, E. L., Later, C., Maheshwari-Aplin, P., Peters, J., Robb, J. E., Schreiber, J., Kivisild, T., Castex, D., Lösch, S., Harbeck, M., Herbig, A., Bos, K. I., & Krause, J.
Affiliations
  • Max Planck Institute of Geoanthropology (DE)
  • University of Tartu (EE)
  • Museum of London Archaeology (GB)
  • University of Bern (CH)
  • University of Cambridge (GB)
  • Staatsarchiv Nidwalden (CH)
  • Bavarian Natural History Collections (DE)
  • Centre National de la Recherche Scientifique (FR)
  • Massachusetts Institute of Technology (US)
Corresponding author
  • Spyrou, Maria A.
  • Bos, Kirsten I.
  • Krause, Johannes
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2019-10-02
Volume
10
Issue
1
Pages
4470-4470
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-019-12154-0
PMC
PMC6775055
OpenAlex
W2978619983
Cited by
182
References
8
Citations by year
2026: 17 · 2025: 17 · 2024: 31 · 2023: 26 · 2022: 31 · 2021: 30 · 2020: 24 · 2019: 6
FWCI
17.68
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Durham Research Online (Durham University) (acceptedVersion, other-oa)
  • White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
  • Durham Research Online (Durham University) (submittedVersion, cc-by)
  • Lirias (KU Leuven) (submittedVersion, other-oa)
  • HAL (submittedVersion)
  • HAL (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • Bern Open Repository and Information System (University of Bern) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Open access LMU (Ludwid Maxmilian's Universitat Munchen) (submittedVersion, cc-by)
  • MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • Apollo (cc-by)
Funders
  • University of Bern
  • Wellcome Trust (200368/Z/15/Z)
  • European Commission (2014‐2020, 2020 ‘, 2014-2020.4.01.16-0030)
  • Eesti Teadusagentuur (PRG243, 2014-2020)
  • Queen's University
  • Max-Planck-Gesellschaft
  • European Regional Development Fund (2014-2020’, 2014-2020.4.01.16-0030)
Topics
  • Health Sciences › Medicine › Infectious Diseases › Yersinia bacterium, plague, ectoparasites research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
Yersinia pestis, Black Death, second plague pandemic, phylogeography, ancient genomes, human remains, genetic diversity, virulence gene deletion, disease reservoirs, bacterial evolution
MeSH terms
Archaeology, DNA, Bacterial, Europe, Eastern, Fossils, Humans, Phylogeny, Plague, Time Factors, Virulence, Yersinia pestis, Genome, Bacterial, Polymorphism, Single Nucleotide, Pandemics, Phylogeography, High-Throughput Nucleotide Sequencing

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