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Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.

Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CM, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Pontén T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E - Cell (2015)

Bottom Line: How and when it originated remains contentious.We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague.Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark.

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Phylogenetic Reconstructions(A) Maximum Likelihood reconstruction of the phylogeny of Y. pseudotuberculosis (blue) and Y. pestis (red). The tree is rooted using Y. similis (not shown). The full tree including three additional Y. pseudotuberculosis strains (O:15 serovar) can be seen in Figure S4. Major branching nodes within Y. pseudotuberculosis with > 95% bootstrap support are indicated with an asterisk and branch lengths are given as substitutions per site.(B) Maximum Likelihood reconstruction of the phylogeny in (A) showing only the Y. pestis clade. The clades are collapsed by population according to branches and serovars, as given in (Achtman et al., 1999, Achtman et al., 2004, Cui et al., 2013). See Figure S4 for an uncollapsed tree and Table S2 for details on populations. Nodes with more than 95% bootstrap support are indicated with an asterisk and branch lengths are given as substitutions per site.(C) BEAST2 maximum clade credibility tree showing median divergence dates. Branch lengths are given as years before the present (see Divergence estimations in Experimental Procedures). Only the Y. pseudotuberculosis (blue), the ancient Y. pestis samples (magenta) and the most basal branch 0 strains (black) are shown. For a full tree including all Y. pestis see Figure S5. See also Figure S3, S4, and S5 and Table S5.
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fig4: Phylogenetic Reconstructions(A) Maximum Likelihood reconstruction of the phylogeny of Y. pseudotuberculosis (blue) and Y. pestis (red). The tree is rooted using Y. similis (not shown). The full tree including three additional Y. pseudotuberculosis strains (O:15 serovar) can be seen in Figure S4. Major branching nodes within Y. pseudotuberculosis with > 95% bootstrap support are indicated with an asterisk and branch lengths are given as substitutions per site.(B) Maximum Likelihood reconstruction of the phylogeny in (A) showing only the Y. pestis clade. The clades are collapsed by population according to branches and serovars, as given in (Achtman et al., 1999, Achtman et al., 2004, Cui et al., 2013). See Figure S4 for an uncollapsed tree and Table S2 for details on populations. Nodes with more than 95% bootstrap support are indicated with an asterisk and branch lengths are given as substitutions per site.(C) BEAST2 maximum clade credibility tree showing median divergence dates. Branch lengths are given as years before the present (see Divergence estimations in Experimental Procedures). Only the Y. pseudotuberculosis (blue), the ancient Y. pestis samples (magenta) and the most basal branch 0 strains (black) are shown. For a full tree including all Y. pestis see Figure S5. See also Figure S3, S4, and S5 and Table S5.

Mentions: Besides applying standard precautions for working with ancient DNA (Willerslev and Cooper, 2005), the authenticity of our findings are supported by the following observations: (1) The Y. pestis sequences were identified in significant amounts in shotgun data from eight of 101 samples, showing that this finding is not due to a ubiquitous contaminant in our lab or in the reagents. Indeed, further analysis showed that one of these eight was most likely not Y. pestis. We also sequenced all negative DNA extraction controls and found no signs of Y. pestis DNA in these (Table S3). (2) Consistent with an ancient origin, the Y. pestis reads were highly fragmented, with average read lengths of 43–65 bp (Table S3) and also displayed clear signs of C-T deamination damage at the 5′ termini typical of ancient DNA (Figure 3, Figure S1). Because the plasmids are central for discriminating between Y. pestis and Y. pseudotuberculosis, we tested separately for DNA damage patterns for the chromosome and for each of the plasmids. For the seven samples, we observe similar patterns of DNA damage for chromosome and plasmid sequences (Figure 3, Figure S1). (3) We observe correlated DNA degradation patterns when comparing DNA degradation in the Y. pestis sequences and the human sequences from the host individual. Given that DNA decay can be described as a rate process (Allentoft et al., 2012), this suggests that the DNA molecules of the pathogen and the human host have a similar age (Figure 3, Figure S1, Table S3 and Supplemental Experimental Procedures). (4) Because of the high sequence similarity between Y. pestis and Y. pseudotuberculosis, we mapped all reads both to the Y. pestis CO92 and to the Y. pseudotuberculosis IP32953 reference genomes (Chain et al., 2004). Consistent with being Y. pestis, the seven investigated samples displayed more reads matching perfectly (edit distance = 0) toward Y. pestis (Figure 3, Figure S2). One sample (RISE392) was most likely not Y. pestis based on this criterion. (5) A naive Bayesian classifier trained on known genomes predicts the seven samples to be Y. pestis with 100% posterior probability, while RISE392 is predicted to have 0% probability of being Y. pestis (Figure S2, Table S3). (6) If the DNA was from other organisms than Y. pestis, we would expect the reads to be more frequently associated with either highly conserved or low-complexity regions. However, we find the reads to be distributed across the entire genome (Figure S2), and comparison of actual coverage versus the coverage that would be expected from read length distributions and mappability of the reference sequences are also in agreement for the seven samples (Figure 3). (7) In a maximum likelihood phylogeny, the recovered Y. pestis genomic sequences of RISE505 and RISE509 are clearly within the Y. pestis clade and basal to all contemporary Y. pestis strains (Figure 4) (see below).


Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.

Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CM, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Pontén T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E - Cell (2015)

Phylogenetic Reconstructions(A) Maximum Likelihood reconstruction of the phylogeny of Y. pseudotuberculosis (blue) and Y. pestis (red). The tree is rooted using Y. similis (not shown). The full tree including three additional Y. pseudotuberculosis strains (O:15 serovar) can be seen in Figure S4. Major branching nodes within Y. pseudotuberculosis with > 95% bootstrap support are indicated with an asterisk and branch lengths are given as substitutions per site.(B) Maximum Likelihood reconstruction of the phylogeny in (A) showing only the Y. pestis clade. The clades are collapsed by population according to branches and serovars, as given in (Achtman et al., 1999, Achtman et al., 2004, Cui et al., 2013). See Figure S4 for an uncollapsed tree and Table S2 for details on populations. Nodes with more than 95% bootstrap support are indicated with an asterisk and branch lengths are given as substitutions per site.(C) BEAST2 maximum clade credibility tree showing median divergence dates. Branch lengths are given as years before the present (see Divergence estimations in Experimental Procedures). Only the Y. pseudotuberculosis (blue), the ancient Y. pestis samples (magenta) and the most basal branch 0 strains (black) are shown. For a full tree including all Y. pestis see Figure S5. See also Figure S3, S4, and S5 and Table S5.
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Related In: Results  -  Collection

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fig4: Phylogenetic Reconstructions(A) Maximum Likelihood reconstruction of the phylogeny of Y. pseudotuberculosis (blue) and Y. pestis (red). The tree is rooted using Y. similis (not shown). The full tree including three additional Y. pseudotuberculosis strains (O:15 serovar) can be seen in Figure S4. Major branching nodes within Y. pseudotuberculosis with > 95% bootstrap support are indicated with an asterisk and branch lengths are given as substitutions per site.(B) Maximum Likelihood reconstruction of the phylogeny in (A) showing only the Y. pestis clade. The clades are collapsed by population according to branches and serovars, as given in (Achtman et al., 1999, Achtman et al., 2004, Cui et al., 2013). See Figure S4 for an uncollapsed tree and Table S2 for details on populations. Nodes with more than 95% bootstrap support are indicated with an asterisk and branch lengths are given as substitutions per site.(C) BEAST2 maximum clade credibility tree showing median divergence dates. Branch lengths are given as years before the present (see Divergence estimations in Experimental Procedures). Only the Y. pseudotuberculosis (blue), the ancient Y. pestis samples (magenta) and the most basal branch 0 strains (black) are shown. For a full tree including all Y. pestis see Figure S5. See also Figure S3, S4, and S5 and Table S5.
Mentions: Besides applying standard precautions for working with ancient DNA (Willerslev and Cooper, 2005), the authenticity of our findings are supported by the following observations: (1) The Y. pestis sequences were identified in significant amounts in shotgun data from eight of 101 samples, showing that this finding is not due to a ubiquitous contaminant in our lab or in the reagents. Indeed, further analysis showed that one of these eight was most likely not Y. pestis. We also sequenced all negative DNA extraction controls and found no signs of Y. pestis DNA in these (Table S3). (2) Consistent with an ancient origin, the Y. pestis reads were highly fragmented, with average read lengths of 43–65 bp (Table S3) and also displayed clear signs of C-T deamination damage at the 5′ termini typical of ancient DNA (Figure 3, Figure S1). Because the plasmids are central for discriminating between Y. pestis and Y. pseudotuberculosis, we tested separately for DNA damage patterns for the chromosome and for each of the plasmids. For the seven samples, we observe similar patterns of DNA damage for chromosome and plasmid sequences (Figure 3, Figure S1). (3) We observe correlated DNA degradation patterns when comparing DNA degradation in the Y. pestis sequences and the human sequences from the host individual. Given that DNA decay can be described as a rate process (Allentoft et al., 2012), this suggests that the DNA molecules of the pathogen and the human host have a similar age (Figure 3, Figure S1, Table S3 and Supplemental Experimental Procedures). (4) Because of the high sequence similarity between Y. pestis and Y. pseudotuberculosis, we mapped all reads both to the Y. pestis CO92 and to the Y. pseudotuberculosis IP32953 reference genomes (Chain et al., 2004). Consistent with being Y. pestis, the seven investigated samples displayed more reads matching perfectly (edit distance = 0) toward Y. pestis (Figure 3, Figure S2). One sample (RISE392) was most likely not Y. pestis based on this criterion. (5) A naive Bayesian classifier trained on known genomes predicts the seven samples to be Y. pestis with 100% posterior probability, while RISE392 is predicted to have 0% probability of being Y. pestis (Figure S2, Table S3). (6) If the DNA was from other organisms than Y. pestis, we would expect the reads to be more frequently associated with either highly conserved or low-complexity regions. However, we find the reads to be distributed across the entire genome (Figure S2), and comparison of actual coverage versus the coverage that would be expected from read length distributions and mappability of the reference sequences are also in agreement for the seven samples (Figure 3). (7) In a maximum likelihood phylogeny, the recovered Y. pestis genomic sequences of RISE505 and RISE509 are clearly within the Y. pestis clade and basal to all contemporary Y. pestis strains (Figure 4) (see below).

Bottom Line: How and when it originated remains contentious.We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague.Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark.

Show MeSH
Related in: MedlinePlus