Yersinia pestis and the Plague of Justinian 541-543 AD: A genomic analysis

David M Wagner, Jennifer Klunk, Michaela Harbeck, Alison Devault, Nicholas Waglechner, Jason W. Sahl, Jacob Enk, Dawn N. Birdsell, Melanie Kuch, Candice Lumibao, Debi Poinar, Talima R Pearson, Mathieu Fourment, Brian Golding, Julia M. Riehm, David J D Earn, Sharon DeWitte, Jean Marie Rouillard, Gisela Grupe, Ingrid WiechmannJames B. Bliska, Paul S Keim, Holger C. Scholz, Edward C. Holmes, Hendrik Poinar

Research output: Contribution to journalArticle

163 Citations (Scopus)

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. The Justinian branch is interleaved between two extant groups, 0.ANT1 and 0.ANT2, and is distant from strains associated with the second and third pandemics. Interpretation: We conclude that the Y pestis lineages that caused the Plague of Justinian and the Black Death 800 years later were independent emergences from rodents into human beings. These results show that rodent species worldwide represent important reservoirs for the repeated emergence of diverse lineages of Y pestis into human populations. Funding: McMaster University, Northern Arizona University, Social Sciences and Humanities Research Council of Canada, Canada Research Chairs Program, US Department of Homeland Security, US National Institutes of Health, Australian National Health and Medical Research Council.

Original languageEnglish (US)
Pages (from-to)319-326
Number of pages8
JournalThe Lancet Infectious Diseases
Volume14
Issue number4
DOIs
StatePublished - 2014

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Yersinia pestis
Plague
Pandemics
Rodentia
Genome
Canada
Radiometric Dating
DNA
Tooth
Cemeteries
Social Sciences
National Institutes of Health (U.S.)
Phylogeny
Chloroform
Phenol
Research
Germany
Biomedical Research
Plasmids
Databases

ASJC Scopus subject areas

  • Infectious Diseases

Cite this

Wagner, D. M., Klunk, J., Harbeck, M., Devault, A., Waglechner, N., Sahl, J. W., ... Poinar, H. (2014). Yersinia pestis and the Plague of Justinian 541-543 AD: A genomic analysis. The Lancet Infectious Diseases, 14(4), 319-326. https://doi.org/10.1016/S1473-3099(13)70323-2

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 R; 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.

In: The Lancet Infectious Diseases, Vol. 14, No. 4, 2014, p. 319-326.

Research output: Contribution to journalArticle

Wagner, DM, Klunk, J, Harbeck, M, Devault, A, Waglechner, N, Sahl, JW, Enk, J, Birdsell, DN, Kuch, M, Lumibao, C, Poinar, D, Pearson, TR, Fourment, M, Golding, B, Riehm, JM, Earn, DJD, DeWitte, S, Rouillard, JM, Grupe, G, Wiechmann, I, Bliska, JB, Keim, PS, Scholz, HC, Holmes, EC & Poinar, H 2014, 'Yersinia pestis and the Plague of Justinian 541-543 AD: A genomic analysis', The Lancet Infectious Diseases, vol. 14, no. 4, pp. 319-326. https://doi.org/10.1016/S1473-3099(13)70323-2
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 R ; 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. / Yersinia pestis and the Plague of Justinian 541-543 AD : A genomic analysis. In: The Lancet Infectious Diseases. 2014 ; Vol. 14, No. 4. pp. 319-326.
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AU - Waglechner, Nicholas

AU - Sahl, Jason W.

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