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Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis

Wagner, David M, Klunk, Jennifer, Harbeck, Michaela, Devault, Alison, Waglechner, Nicholas, Sahl, Jason W, Enk, Jacob, Birdsell, Dawn N, Kuch, Melanie, Lumibao, Candice, Poinar, Debi, Pearson, Talima, Fourment, Mathieu, Golding, Brian, Riehm, Julia M, Earn, David J D, DeWitte, Sharon, Rouillard, Jean-Marie, Grupe, Gisela, Wiechmann, Ingrid, Bliska, James B, Keim, Paul S, Scholz, Holger C, Holmes, Edward C, Poinar, Hendrik·2014·The Lancet Infectious Diseases
DOI 10.1016/s1473-3099(13)70323-2
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Abstract

Background Yersinia pestis has caused at least three human plague pandemics. The second (Black Death, 14-17th centuries) and third (19-20th centuries) have been genetically characterised, but there is only a limited understanding of the first pandemic, the Plague of Justinian (6-8th centuries). To address this gap, we sequenced and analysed draft genomes of Y pestis obtained from two individuals who died in the first pandemic. Methods Teeth were removed from two individuals (known as A120 and A76) from the early medieval Aschheim-Bajuwarenring cemetery (Aschheim, Bavaria, Germany). We isolated DNA from the teeth using a modified phenol-chloroform method. We screened DNA extracts for the presence of the Y pestis-specific pla gene on the pPCP1 plasmid using primers and standards from an established assay, enriched the DNA, and then sequenced it. We reconstructed draft genomes of the infectious Y pestis strains, compared them with a database of genomes from 131 Y pestis strains from the second and third pandemics, and constructed a maximum likelihood phylogenetic tree. Findings Radiocarbon dating of both individuals (A120 to 533 AD [plus or minus 98 years]; A76 to 504 AD [plus or minus 61 years]) places them in the timeframe of the first pandemic. Our phylogeny contains a novel branch (100% bootstrap at all relevant nodes) leading to the two Justinian samples. This branch has no known contemporary representatives, and thus is either extinct or unsampled in wild rodent reservoirs…

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Metadata

Authors
Wagner, D. M., Klunk, J., Harbeck, M., Devault, A., Waglechner, N., Sahl, J. W., Enk, J., Birdsell, D. N., Kuch, M., Lumibao, C., Poinar, D., Pearson, T., Fourment, M., Golding, B., Riehm, J. M., Earn, D. J. D., DeWitte, S., Rouillard, J.-M., Grupe, G., Wiechmann, I., Bliska, J. B., Keim, P. S., Scholz, H. C., Holmes, E. C., & Poinar, H.
Venue
The Lancet Infectious Diseases
Publisher
Elsevier BV
Published
2014-04
Volume
14
Issue
4
Pages
319-326
ISSN
1473-3099
DOI
10.1016/s1473-3099(13)70323-2
Cited by
404
References
5
Language
en
Licence
Funders
  • Michael G DeGroote Institute of Infectious Disease Research, Social Sciences and Humanities Research Council Canada, McMaster University, a Canada Research Chair to HP, the Cowden Endowment at Northern Arizona University, and the US Department of Homeland Security (2010-ST-108-000015; HSHQDC-10-C-00139)
  • Northeast Biodefense Center (U54-AI057158-Lipkin)

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The paper
Wagner, D. M., Klunk, J., Harbeck, M., Devault, A., Waglechner, N., Sahl, J. W., Enk, J., Birdsell, D. N., Kuch, M., Lumibao, C., Poinar, D., Pearson, T., Fourment, M., Golding, B., Riehm, J. M., Earn, D. J. D., DeWitte, S., Rouillard, J.-M., Grupe, G., . . . Poinar, H. (2014). Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis. The Lancet Infectious Diseases. https://doi.org/10.1016/s1473-3099(13)70323-2