Ancient Pathogens Through Human History: A Paleogenomic Perspective

Marciniak, Stephanie; Poinar, Hendrik N.

doi:10.1007/13836_2018_52

Cited by 9 publications

(8 citation statements)

References 110 publications

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“…Ancient DNA (aDNA) studies can provide a new understanding of the emergence and evolution of diseases via the reconstruction of ancient pathogen genomes [ 12 , 13 ]. However, whereas several historical and ancient bacterial genomes are currently available, particularly for the causative agent of plague Yersinia pestis (e.g.…”

Section: Introductionmentioning

confidence: 99%

Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

Ferrari

Neukamm

Baalsrud

et al. 2020

Phil. Trans. R. Soc. B

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Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

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Section: Introductionmentioning

confidence: 99%

Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

Ferrari

Neukamm

Baalsrud

et al. 2020

Phil. Trans. R. Soc. B

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“…With the advent of high-throughput sequencing came the move from the simple identification of pathogens at a certain place and time to genome-level reconstruction and characterization, enabling a shift to hypothesis-driven research carried out within evolutionary frameworks [62][63][64][65]. The methodological tweaks to DNA extractions and novel library preparations designed to target short, damaged and sometimes single-stranded DNA have enhanced access to the target component of ancient extracts (Box 3) [66,67].…”

Section: Acquiring Ancient Pathogen Genomes and Microbiomesmentioning

confidence: 99%

The Recovery, Interpretation and Use of Ancient Pathogen Genomes

Duchêne

Carmichael

et al. 2020

Current Biology

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The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest-premodern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae)-and for three equally important endemic human disease agents-Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20 th century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens.

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“…It is also critical to emphasize that our understanding of JP-era Y. pestis is incomplete. Most reconstructed First and Second Pandemic genomes are draft genomes; they have been, as future reconstructed genomes will also be, enriched via the use of baits (small RNA molecules), designed on the basis of existing genomic diversity of Y. pestis from publicly available databases (60). Truly “novel” sequence, in late antique Y. pestis genomes, which might have enabled transmission and thus wide dissemination for instance, will not, under the current methods, be detected, unless enough Y. pestis DNA preserves in an individual from which the genome can be de novo reconstructed.…”

Section: Plague Dna Epidemiology and Ecologymentioning

confidence: 99%

“…Diseases such as malaria could have also resulted in atypical morbidity patterns (73, 74). Importantly, the pathogenic remnants of some of these diseases (notably RNA viruses) are difficult to detect today (60).…”

Section: Archaeological Contributions Reveal Continuity Rather Than Cmentioning

confidence: 99%

The Justinianic Plague: An inconsequential pandemic?

Mordechai

Eisenberg

Newfield

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Existing mortality estimates assert that the Justinianic Plague (circa 541 to 750 CE) caused tens of millions of deaths throughout the Mediterranean world and Europe, helping to end antiquity and start the Middle Ages. In this article, we argue that this paradigm does not fit the evidence. We examine a series of independent quantitative and qualitative datasets that are directly or indirectly linked to demographic and economic trends during this two-century period: Written sources, legislation, coinage, papyri, inscriptions, pollen, ancient DNA, and mortuary archaeology. Individually or together, they fail to support the maximalist paradigm: None has a clear independent link to plague outbreaks and none supports maximalist reconstructions of late antique plague. Instead of large-scale, disruptive mortality, when contextualized and examined together, the datasets suggest continuity across the plague period. Although demographic, economic, and political changes continued between the 6th and 8th centuries, the evidence does not support the now commonplace claim that the Justinianic Plague was a primary causal factor of them.

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Ancient Pathogens Through Human History: A Paleogenomic Perspective

Cited by 9 publications

References 110 publications

Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

The Recovery, Interpretation and Use of Ancient Pathogen Genomes

The Justinianic Plague: An inconsequential pandemic?

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