Distinct clones of Yersinia pestis caused the black death

Abstract

From AD 1347 to AD 1353, the Black Death killed tens of millions of people in Europe, leaving misery and devastation in its wake, with successive epidemics ravaging the continent until the 18(th) century. The etiology of this disease has remained highly controversial, ranging from claims based on genetics and the historical descriptions of symptoms that it was caused by Yersinia pestis to conclusions that it must have been caused by other pathogens. It has also been disputed whether plague had the same etiology in northern and southern Europe. Here we identified DNA and protein signatures specific for Y. pestis in human skeletons from mass graves in northern, central and southern Europe that were associated archaeologically with the Black Death and subsequent resurgences. We confirm that Y. pestis caused the Black Death and later epidemics on the entire European continent over the course of four centuries. Furthermore, on the basis of 17 single nucleotide polymorphisms plus the absence of a deletion in glpD gene, our aDNA results identified two previously unknown but related clades of Y. pestis associated with distinct medieval mass graves. These findings suggest that plague was imported to Europe on two or more occasions, each following a distinct route. These two clades are ancestral to modern isolates of Y. pestis biovars Orientalis and Medievalis. Our results clarify the etiology of the Black Death and provide a paradigm for a detailed historical reconstruction of the infection routes followed by this disease.

Figure 1. Geographical position of the five archaeological sites investigated.

Green dots indicate the sites. Also indicated are two likely independent infection routes (black and red dotted arrows) for the spread of the Black Death (1347–1353) after Benedictow .

Figure 2. Schematic phylogenetic tree of Y. pestis derived from Achtman et al. with the position of the ancient strains.

The SNPs used to define the position of the ancient strains in the tree are indicated along each branch. The genotype from Hereford and Saint- Laurent-de-la-Cabrerisse is located at the node between branches 0, 1 and 2 because it had derived SNPs for branch 0, but only ancestral SNPs for branches 1 and 2. The genotype from Bergen op Zoom had one additional derived SNP (s12) on branch 1, but SNPs s11, s13 and s14 on branch 1 were ancestral.

Figure 3. Analysis of aDNA from human remains with 18 markers (glpD, napA and 16 SNPs [11]) that define the three main branches of the Y. pestis evolutionary tree.

The upper part shows the Y. pestis codons that were either similar to the Y. pseudotuberculosis ancestor strain (in blue) or exhibited a SNP (in green). These codons were used here to describe the various branches and sub-branches of the Y. pestis microevolutionary tree, as defined in . The lower part of the figure shows the codons obtained at each specific position in the aDNA from individuals originating from three different archeological sites (Bergen op Zoom [Ber], Hereford [Her], and Saint-Laurent-de-la-Cabrerisse [SLC]). Samples which failed to give an amplification product are indicated in grey. Yellow indicates sequencing results that did not unambiguously resolve a SNP. n.t.: not tested. *: Probably CGT, which could give rise to TGT by deamination.