This bibliography includes genomic studies attempting to reconstruct full genomes. PCR-based studies are not currently not listed.
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.
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.
Paper presenting the oldest Y. pestis genome with full genetic capacity to spread via fleas, in contrast to the other LNBA strains.
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.
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 genome of the First Pandemic from Aschheim, Germany, confirming earlier PCR-based evidence.
Second genome in higher coverage from the close-by site of Altenerding, Germany. Identical after correction of false SNPs in the Aschheim genome.
Paper presenting additional genomes of the First Pandemic from France, Germany, Spain and UK, with genetic diversity supporting single introduction and maintenance of plague.
First pathogen genome reconstructed from ancient DNA from the well-studied sites of London East-Smithfield and, as revealed later, London St. Mary Graces.
Paper on the same site, focussing on the virulence plasmid pPCP1.
Paper presenting genomes of the Great Plague of Marseille 1720-1722, indicative of local persistence of plague in Europe after the Black Death.
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.
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.
Four plague genomes of 15th-century Lithuania. One individual shows a coinfection with Treponema pallidum pertenue, causative agent of yaws.
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.
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.
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.
Paper presenting two genomes from Kyrgyzstan and Russia, associated with the First Pandemic.
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.
Response to the criticism of Keller et al. 2019.
last updated 2020-11-23 MK