eprintid: 10045250 rev_number: 30 eprint_status: archive userid: 608 dir: disk0/10/04/52/50 datestamp: 2018-04-27 07:24:12 lastmod: 2022-04-01 06:10:14 status_changed: 2018-04-27 07:24:12 type: thesis metadata_visibility: show creators_name: Coltart, Cordelia Emma Maitland title: Exploring the integration of traditional and molecular epidemiological methods for infectious disease outbreaks ispublished: unpub divisions: UCL divisions: A01 divisions: B02 divisions: C09 divisions: D01 note: third party copyright material has been removed from ethesis. abstract: BACKGROUND: Understanding the transmission dynamics of infectious pathogens is critical to developing effective public health strategies. Traditionally, time consuming epidemiological methods were used, often limited by incomplete or inaccurate datasets. Novel phylogenetic techniques can determine transmission events, but have rarely been used in real-time outbreak settings to inform interventions and limit the impact of outbreaks. METHODS: I undertook a series of novel studies to explore the utility of combining phylogenetics with traditional epidemiological analysis to enhance the understanding of transmission dynamics. I investigated HIV in an endemic South African setting and Ebola in an acute outbreak in Sierra Leone. The strengths and limitations of this combined approach are explored, ethical issues investigated and recommendations made regarding the implications of this work for public health. RESULTS: Phylogenetics provides an exciting and synergistic tool to epidemiological analysis in outbreak investigation and control. These combined methods enable a more detailed understanding than is possible through either discipline alone. My key findings include: • Identification of infection source: Phylogenetics gives new insight into the role of external introductions (e.g. migrators) in driving and sustaining the high incidence of HIV. • Earlier identification of new emerging clusters: I identified a new cluster of HIV from around a mining community. This is one of the first examples of molecular methods detecting a previously unknown outbreak. • Identification of novel mechanisms of transmission: This work suggests that children may have been infected by playing in puddles contaminated with Ebola, a previously unrecognised route of transmission. CONCLUSION: The integration of these two methods facilitate sophisticated real-time techniques to maximise understanding of transmission dynamics, allowing faster and more effectively targeted interventions. Moving forwards, sequence data should be incorporated into standard outbreak investigation. This is critical at a time when infectious disease outbreaks have led to the some of the most significant global health threats of the recent past. date: 2018-03-28 date_type: published oa_status: green full_text_type: other thesis_class: doctoral_embargoed thesis_award: Ph.D language: eng thesis_view: UCL_Thesis primo: open primo_central: open_green verified: verified_manual elements_id: 1541836 lyricists_name: Coltart, Cordelia lyricists_id: CEMCO63 actors_name: Coltart, Cordelia actors_id: CEMCO63 actors_role: owner full_text_status: public pages: 354 event_title: UCL institution: UCL (University College London) department: Institute for Global Health thesis_type: Doctoral citation: Coltart, Cordelia Emma Maitland; (2018) Exploring the integration of traditional and molecular epidemiological methods for infectious disease outbreaks. Doctoral thesis (Ph.D), UCL (University College London). Green open access document_url: https://discovery-pp.ucl.ac.uk/id/eprint/10045250/13/PhD%20thesis%20CColtart%20redacted%20version.pdf