Palaeogenomics of Plague

This bibliography includes genomic studies attempting to reconstruct full genomes. PCR-based studies are not currently not listed.

Prehistoric Plague:

Rasmussen, S. et al. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell 163, 571–582 (2015)

First paper presenting plague genomes from sites dating to the Late Neolithic to Bronze Age in Armenia, Estonia, Poland and Russia. Genomic differences to modern Y. pestis suggest that this early form of plague was not adapted to the spread via fleas.

Andrades Valtueña, A. et al. The Stone Age Plague and Its Persistence in Eurasia. Curr. Biol. 27, 3683–3691.e8 (2017)

Additional LNBA genomes clustering with the Rasmussen et al. genomes from Croatia, Estonia, Germany, Lithuania and Russia, linking spread of plague to Yamnaya-related human migrations.

Spyrou, M. A. et al. Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague. Nat. Commun. 9, 2234 (2018)

Paper presenting the oldest Y. pestis genome with full genetic capacity to spread via fleas, in contrast to the other LNBA strains.

Rascovan, N. et al. Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline. Cell 176, 295–305.e10 (2019)

Oldest and phylogenetically most basal Y. pestis genome published to date, challenging previous claims about the spread through human migration offering a new hypothesis of spread via Neolithic trade networks.

Yu, H. et al. Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia. Cell 181, 1232-1245.e20

Most eastern LNBA genome published so far from Lake Baikal. Remarkably, the individuals carrying plague have no Yamnaya-related ancestry, in contrast to the individuals in Andrades Valtueña et al. 2017.

First Pandemic:

Wagner, D. M. et al. Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis. Lancet Infect. Dis. 14, 319–326 (2014)

First genome of the First Pandemic from Aschheim, Germany, confirming earlier PCR-based evidence.

Feldman, M. et al. A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim. Mol. Biol. Evol. 33, 2911–2923 (2016)

Second genome in higher coverage from the close-by site of Altenerding, Germany. Identical after correction of false SNPs in the Aschheim genome.

Keller, M. et al. Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750). Proc. Natl. Acad. Sci. U. S. A. 116, 12363–12372 (2019)

Paper presenting additional genomes of the First Pandemic from France, Germany, Spain and UK, with genetic diversity supporting single introduction and maintenance of plague. 

Second Pandemic:

Bos, K. I. et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506–510 (2011)

First pathogen genome reconstructed from ancient DNA from the well-studied sites of London East-Smithfield and, as revealed later, London St. Mary Graces.

Schuenemann, V. J. et al. Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. Proc. Natl. Acad. Sci. U. S. A. 108, E746–52 (2011)

Paper on the same site, focussing on the virulence plasmid pPCP1.

Bos, K. I. et al. Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus. Elife 5, e12994 (2016)

Paper presenting genomes of the Great Plague of Marseille 1720-1722, indicative of local persistence of plague in Europe after the Black Death.

Spyrou, M. A. et al. Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics. Cell Host Microbe 19, 874–881 (2016)

Paper presenting more Second Pandemic genomes from Germany, Russia and Spain. The genome from Bolgar, Russia, is interpreted as evidence for the spread of the Black Death lineage back to Asia.

Namouchi, A. et al. Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period. Proc. Natl. Acad. Sci. U. S. A. 115, E11790–E11797 (2018)

Paper presenting more Second Pandemic genomes from France, Italy, the Netherlands and Norway. The data is interpreted as evidence for the repeated reintroduction of plague from the Lower Volga region.

Spyrou, M. A. et al. Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes. Nat. Commun. 10, 4470 (2019)

Additional Second Pandemic genomes from France, Germany, Russia, Switzerland and UK. Data is interpreted as evidence introduction of the Black Death via Russia and maintenance in Europe. 

Giffin, K. et al. A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Sci. Rep. 10, 9499 (2020)

Four plague genomes of 15th-century Lithuania. One individual shows a coinfection with Treponema pallidum pertenue, causative agent of yaws.

Susat, J. et al. Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic. Sci. Rep. 10, 14628 (2020)

Plague genomes from in Riga, Latvia, falling in two distinct positions in the phylogeny. The authors claim that the pPCP1 plasmid was duplicated in all post-Black Death strains, with one of them lacking the pla gene.

Morozova, I. et al. New ancient Eastern European Yersinia pestis genomes illuminate the dispersal of plague in Europe. Philos. Trans. R. Soc. Lond. B Biol. Sci. 375, 20190569 (2020)

Plague genomes from Gdańsk, Poland as well as Azov and Rostov-on-Don, Russia, dating to the 15th-18th century. Remarkably, the authors were able to detect Y. pestis DNA in rat bones.

Guellil, M. et al. A genomic and historical synthesis of plague in 18th century Eurasia. Proc. Natl. Acad. Sci. U. S. A. (2020) 

Plague genomes of four different sites in Italy, Sweden, and Chechnya (Russia) with a focus on the 18th century. The authors argue for repeated reintroductions of plague from the Caucasus region at least in the later phase of the Second Pandemic.


Damgaard, P. de B. et al. 137 ancient human genomes from across the Eurasian steppes. Nature 557, 369–374 (2018)

Paper presenting two genomes from Kyrgyzstan and Russia, associated with the First Pandemic.

Keller, M. et al. Ancient Yersinia pestis genomes provide no evidence for the origins or spread of the Justinianic Plague. bioRxiv 819698 (2019) 

Comment on Damgaard et al. 2019 challenging their claims, interpreting the Kyrgyz genome as early cousin of the First Pandemic lineage and the Russian genome as potential precursor of the Black Death.

Rasmussen, S. et al. Response to Keller et al on Justinianic Plague. (2019) 

Response to the criticism of Keller et al. 2019.


last updated 2020-11-23 MK

Interdisciplinary approaches to the 14th century crisis and the history of plague

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