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Mol Biol Evol. 2016 Nov;33(11):2911-2923. doi: 10.1093/molbev/msw170. Epub 2016 Aug 30.

A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim.

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Max Planck Institute for the Science of Human History, Jena, Germany.
Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany.
Bundeswehr Institute of Microbiology, Munich, Germany.
German Center for Infection Research (DZIF), Munich, Germany.
Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilian University Munich, Germany.
Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University of Munich, Germany.
Department of History, Harvard University, Initiative for the Science of the Human Past.


The Justinianic Plague, which started in the sixth century and lasted to the mid eighth century, is thought to be the first of three historically documented plague pandemics causing massive casualties. Historical accounts and molecular data suggest the bacterium Yersinia pestis as its etiological agent. Here we present a new high-coverage (17.9-fold) Y. pestis genome obtained from a sixth-century skeleton recovered from a southern German burial site close to Munich. The reconstructed genome enabled the detection of 30 unique substitutions as well as structural differences that have not been previously described. We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestis genome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth century in rural southern Germany.


Yersinia pestis; ancient DNA; justinianic plague; reconstruction; whole genome

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