A draft genome of Yersinia pestis from victims of the Black Death

By Sara Sheehan, Kirsten I. Bos, V. Schuenemann, G. B. Golding, Hernán A. Burbano, Nicholas Waglechner, B. Coombes, Joseph B. McPhee, S. DeWitte, M. Meyer and 7 more. Nature, 2011

676 citations recorded by the source corpus.

Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348–1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347–1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections.

Subfields: Genetics, Molecular Biology, Public Health, Environmental and Occupational Health

View Paper: https://www.semanticscholar.org/paper/19f69132eadb6830ff89a3b7e9b559d00f3b0688

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Citations in the corpus

Plague and Lethal Epidemics in the Pre-Industrial World (2017, background): “Alfani and Murphy318 and others were indeed caused by the Yersinia pestis Bos et al. 2011).”
Next generation sequencing technology: Advances and applications. (2014, background): “colony collapse disorder killing honeybees [38] but also to identify the cause of diseases that killed thousands of humans in the past, inclusive the black death [39].”
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX (2014, methodology): “In addition, target-enrichment approaches have revealed a plethora of complete ancient mitochondrial genome sequences 27–35 , the sequence of the Neandertal exome 36 , a complete chromosome of an ~50,000-year-old human from China 31 and the complete genome sequence of microbial pathogens responsible”
From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era (2017, neutral): “…(Bos et al. 2014), Mycobacterium leprae responsible for the leprosy (Schuene-mann et al. 2013), Yersinia pestis responsible for the plague (Bos et al. 2011; Schuenemann et al. 2011; Devault, McLoughlin, et al. 2014; Gilbert 2014; Wagner et al. 2014), and Vibrio cholerae responsible for…”
Molecular phylogenetics: principles and practice (2012, background): “Currently, the data are mostly from humans and their close relatives, but genomes from other species are being sequenced as well, such as mastodons and mam-moths 123 and the bacterium Yersinia pestis from Black Death victims 124 .”