Abstract
The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data.1,2 A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th–18th century CE.3 Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.4,5 To better understand the historical epidemiology and evolutionary history of plague in this region, we performed in-depth (n = 298) longitudinal screening (800 years) for the plague bacterium Yersinia pestis (Y. pestis) across 13 archaeological sites in Denmark from 1000 to 1800 CE. Our genomic and phylogenetic data captured the emergence, continuity, and evolution of Y. pestis in this region over a period of 300 years (14th–17th century CE), for which the plague-positivity rate was 8.3% (3.3%–14.3% by site). Our phylogenetic analysis revealed that the Danish Y. pestis sequences were interspersed with those from other European countries, rather than forming a single cluster, indicative of the generation, spread, and replacement of bacterial variants through communities rather than their long-term local persistence. These results provide an epidemiological link between Y. pestis and the unknown pestilence that afflicted medieval and early modern Europe. They also demonstrate how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology and help pave the way for the next generation of historical disease research.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Current Biology |
| Vol/bind | 33 |
| Udgave nummer | 6 |
| Sider (fra-til) | 1147-1152.e5 |
| ISSN | 0960-9822 |
| DOI | |
| Status | Udgivet - 27. mar. 2023 |
Bibliografisk note
Funding Information:This work was supported by the Social Sciences and Humanities Research Council of Canada to H.N.P. and J.A.G. (#20008499 and grant No. 430-2017-01193 ) and the MacDATA Institute ( McMaster University, Canada ). This research was enabled in part by support provided by Compute Ontario ( https://www.computeontario.ca/ ) and Compute Canada ( https://www.computecanada.ca ). E.C.H. is supported by an Australian Research Council Australian Laureate Fellowship ( FL170100022 ). S.D. and L.F. are supported by the Australian Research Council ( FT220100629 ). We thank Julianna Stangroom, Michael Klowak, Dr. Emil Karpinski, Dr. Matthew Emery, and Dr. Stephanie Marciniak for their assistance in laboratory procedures. We also thank Dr. Ana Duggan for her insight regarding Bayesian methods for phylogenetic analysis. We thank members of the Sherman Centre for Digital Scholarship, including Dr. Andrea Zeffiro, Dr. John Fink, Dr. Matthew Davis, and Dr. Amanda Montague, for their assistance in developing the underlying genomic database. We thank all past and present members of the McMaster Ancient DNA Centre and the Golding Lab at McMaster University.
Funding Information:
This work was supported by the Social Sciences and Humanities Research Council of Canada to H.N.P. and J.A.G. (#20008499 and grant No. 430-2017-01193) and the MacDATA Institute (McMaster University, Canada). This research was enabled in part by support provided by Compute Ontario (https://www.computeontario.ca/) and Compute Canada (https://www.computecanada.ca). E.C.H. is supported by an Australian Research Council Australian Laureate Fellowship (FL170100022). S.D. and L.F. are supported by the Australian Research Council (FT220100629). We thank Julianna Stangroom, Michael Klowak, Dr. Emil Karpinski, Dr. Matthew Emery, and Dr. Stephanie Marciniak for their assistance in laboratory procedures. We also thank Dr. Ana Duggan for her insight regarding Bayesian methods for phylogenetic analysis. We thank members of the Sherman Centre for Digital Scholarship, including Dr. Andrea Zeffiro, Dr. John Fink, Dr. Matthew Davis, and Dr. Amanda Montague, for their assistance in developing the underlying genomic database. We thank all past and present members of the McMaster Ancient DNA Centre and the Golding Lab at McMaster University. K.E. R.K.S. J.K. E.C.H. and H.N.P. designed the study. J.A.G. identified and collected the Danish samples and contributed to the archaeological dating. J.L.B. and S.N.D. provided access to archaeological sites and materials, and J.L.B. reviewed the archaeological dating. V.G. performed radiocarbon dating. K.E. R.K.S. and J.K. performed laboratory analysis. A.G.C. and N.V. provided historical sources and interpretation. S.D. and L.F. critiqued and revised the computational methods and discussion. G.B.G. provided access to computational resources and data storage. H.N.P. E.C.H. and G.B.G. supervised the study. K.E. wrote the manuscript with contributions from all authors. J.K. declares financial interest in Daicel Arbor Biosciences, which provided the myBaits probes for targeted capture. One or more of the authors of this paper self-identifies as an underrepresented ethnic minority in their field of research or within their geographical location. One or more of the authors of this paper self-identifies as a gender minority in their field of research.