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Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes.

ABSTRACT: The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14^th and 18^th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541-750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.

SUBMITTER: Spyrou MA

PROVIDER: S-EPMC6775055 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes.

Spyrou Maria A MA Keller Marcel M Tukhbatova Rezeda I RI Scheib Christiana L CL Nelson Elizabeth A EA Andrades Valtueña Aida A Neumann Gunnar U GU Walker Don D Alterauge Amelie A Carty Niamh N Cessford Craig C Fetz Hermann H Gourvennec Michaël M Hartle Robert R Henderson Michael M von Heyking Kristin K Inskip Sarah A SA Kacki Sacha S Key Felix M FM Knox Elizabeth L EL Later Christian C Maheshwari-Aplin Prishita P Peters Joris J Robb John E JE Schreiber Jürgen J Kivisild Toomas T Castex Dominique D Lösch Sandra S Harbeck Michaela M Herbig Alexander A Bos Kirsten I KI Krause Johannes J

Nature communications 20191002 1

The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14<sup>th</sup> and 18<sup>th</sup> centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death ...[more]

PMID: 31578321

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Project description:BackgroundYersinia pestis appears to be maintained in multiple, geographically separate, and phylogenetically distinct subpopulations within the highlands of Madagascar. However, the dynamics of these locally differentiated subpopulations through time are mostly unknown. To address that gap and further inform our understanding of plague epidemiology, we investigated the phylogeography of Y. pestis in Madagascar over an 18 year period.Methodology/principal findingsWe generated whole genome sequences for 31 strains and discovered new SNPs that we used in conjunction with previously identified SNPs and variable-number tandem repeats (VNTRs) to genotype 773 Malagasy Y. pestis samples from 1995 to 2012. We mapped the locations where samples were obtained on a fine geographic scale to examine phylogeographic patterns through time. We identified 18 geographically separate and phylogenetically distinct subpopulations that display spatial and temporal stability, persisting in the same locations over a period of almost two decades. We found that geographic areas with higher levels of topographical relief are associated with greater levels of phylogenetic diversity and that sampling frequency can vary considerably among subpopulations and from year to year. We also found evidence of various Y. pestis dispersal events, including over long distances, but no evidence that any dispersal events resulted in successful establishment of a transferred genotype in a new location during the examined time period.Conclusions/significanceOur analysis suggests that persistent endemic cycles of Y. pestis transmission within local areas are responsible for the long term maintenance of plague in Madagascar, rather than repeated episodes of wide scale epidemic spread. Landscape likely plays a role in maintaining Y. pestis subpopulations in Madagascar, with increased topographical relief associated with increased levels of localized differentiation. Local ecological factors likely affect the dynamics of individual subpopulations and the associated likelihood of observing human plague cases in a given year in a particular location.

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Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes.

Publications

Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes.

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