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

McMaster Ancient DNA researchers and collaborators identified Yersinia pestis as the causative agent behind the Plague of Justinian. Notably, the the Justinian strain is unique from strains in later pandemics and has either gone extinct or remains unsampled in wild rodent reservoirs.

Feb 05, 2014

Authors: 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 Pearson, Mathieu Fourment, Brian Golding, Julia M Riehm, David J D Earn, Sharon DeWitte, Jean-Marie Rouillard, Gisela Grupe, Ingrid Wiechmann, James B Bliska, Paul S Keim, Holger C Scholz, Edward C Holmes, Hendrik Poinar

The Lancet Infectious Diseases, Vol. 14, No. 4, pp. 319-326. January 2014. DOI:10.1016/S1473-3099(13)70323-2



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.


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.


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.


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.

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