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Reconstructing Pathogen Evolution Using Ancient Genomics

Swali, Pooja; (2024) Reconstructing Pathogen Evolution Using Ancient Genomics. Doctoral thesis (Ph.D), UCL (University College London).

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Ancient DNA has allowed us to investigate the dynamic interactions between hosts and the pathogens that infect them over time. By using a metagenomic approach on data from human remains, I successfully detect ancient pathogens through multiple time periods, and specifically focus on two human bacterial pathogens from Britain during this thesis, Yersinia pestis and Borrelia recurrentis I identify two lineages of Y. pestis, the earliest lineage, the ‘Late Neolithic Early Bronze Age’ lineage, is found in three individuals dating back ~4,000 years. Combined with published genomes from the same lineage, these results demonstrate genome decay resulting in the loss of genes over time. The precise transmission dynamics of this lineage remain uncertain, but the absence of population structure suggests a potential absence or unsustainable infections in reservoir populations. The presence of this lineage in Britain highlights its connection to the mainland during the migration of farmers from the Eurasian steppe. The lineage associated with the Justinianic plague, occurring from 1,200-1,400 years ago, was previously detected in Cambridgeshire. In this project, I identify an additional genome from Cambridgeshire, contextualised within the same time period. Additionally, I retrieve four B. recurrentis genomes: three from the Iron Age (~2,500-1,700 years ago) and one from the Medieval period (~500 years ago). B. recurrentis, the only species causing relapsing fever with a vector specialisation for human lice, exhibits the highest mortality rate compared to other relapsing fever species. Although the mechanism behind this vector switch is unknown, genome decay likely plays a significant role in its specialisation and pathogenicity. Overall, this thesis illuminates the complex evolutionary history of B. recurrentis and Y. pestis within Britain, with genes being lost over time and allows us to see how strains identified in Britain relate to those found on mainland Eurasia.

Type: Thesis (Doctoral)
Qualification: Ph.D
Title: Reconstructing Pathogen Evolution Using Ancient Genomics
Language: English
Additional information: Copyright © The Author 2024. Original content in this thesis is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) Licence (https://creativecommons.org/licenses/by-nc/4.0/). Any third-party copyright material present remains the property of its respective owner(s) and is licensed under its existing terms. Access may initially be restricted at the author’s request.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
URI: https://discovery.ucl.ac.uk/id/eprint/10185174
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