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, 115 (50), E11790-E11797

Integrative Approach Using Yersinia pestis Genomes to Revisit the Historical Landscape of Plague During the Medieval Period


Integrative Approach Using Yersinia pestis Genomes to Revisit the Historical Landscape of Plague During the Medieval Period

Amine Namouchi et al. Proc Natl Acad Sci U S A.

Erratum in


Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of Y. pestis by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our Y. pestis genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement.

Keywords: Medieval; Second Pandemic; Yersinia pestis; ancient DNA; plague.

Conflict of interest statement

The authors declare no conflict of interest.


Fig. 1.
Fig. 1.
Geographic locations of previously and presently described ancient genomes. Map of previously and presently described ancient genomes. The red circles represent the locations of previously described ancient genomes. Yellow circles represent ancient genomes described in this study. For the newly described ancient genomes, the indicated years are discussed in Results and Discussion. Numbers in parentheses indicate number of ancient genomes included from each site.
Fig. 2.
Fig. 2.
Overview of the coverage of ancient Y. pestis genomes. Each ring corresponds to one ancient genome. The color intensity is proportional to the coverage across the chromosomal genome and plasmids. The coverage rate, as well as the GC content, was measured throughout the genome using a window size of 200 bp. The bars indicate the fraction of the genome with a depth of coverage of 3×. This figure was generated using anvio (69).
Fig. 3.
Fig. 3.
Reconstruction of the phylogenetic tree and evolutionary history of Y. pestis. (A) Maximum likelihood (ML) phylogenetic tree for Y. pestis. Consisting of 126 modern Y. pestis strains and 15 ancient genomes, the tree was built using IQ-Tree (version 1.5.5) (14), which implements ModelFinder (15) to find the right substitution model before ML tree search. A total number of 2,826 polymorphic sites were used to construct the ML tree, which was visualized and edited using FigTree (version 1.2.1). Strains belonging to branch 1, branch 2, and branch 3 were collapsed for clarity. The numbers at each node indicate the bootstrap values at 1,000 replicates, SH-alrt support values at 1,000 replicates, and local bootstrap support values, respectively. The nodes indicated by black circles correspond to 100/100/100 of the support values in the same order as previously described. The asterisk marks the polytomy known as the “Big Bang.” (B) Schematic representation of the evolutionary history of Y. pestis genomes dated to the Second Plague Pandemic. Each circle represents one sample. The numbers on each branch correspond to the number of sequentially accumulated SNPs (SI Appendix).
Fig. 4.
Fig. 4.
Schematic representation of the connection between the fur trade routes and the spread of plague during the early stage of the Second Plague Pandemic (14th century). This simplified map shows cities strategically situated along the fur trade routes (indicated as a white line). The city of Novgorod (Russia) has played a central role in fur export to cities like Hamburg and Lübeck. The regions highlighted in orange represent known modern plague reservoirs. The darker orange delimits the region in which we believe secondary plague reservoirs were established before the Black Death. The red dots represent the locations of all known ancient Y. pestis genomes. Black lines, Silk Road; dark-blue lines, maritime trade routes.

Comment in

  • Reply to Barbieri et al.: Out of the Land of Darkness: Plague on the fur trade routes.
    Bramanti B, Namouchi A, Schmid BV, Dean KR, Stenseth NC. Bramanti B, et al. Proc Natl Acad Sci U S A. 2019 Apr 16;116(16):7622-7623. doi: 10.1073/pnas.1902274116. Epub 2019 Apr 4. Proc Natl Acad Sci U S A. 2019. PMID: 30948635 Free PMC article. No abstract available.
  • Plague, camels, and lice.
    Barbieri R, Drancourt M, Raoult D. Barbieri R, et al. Proc Natl Acad Sci U S A. 2019 Apr 16;116(16):7620-7621. doi: 10.1073/pnas.1901145116. Epub 2019 Apr 4. Proc Natl Acad Sci U S A. 2019. PMID: 30948636 Free PMC article. No abstract available.

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