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UBC Theses and Dissertations

Phylodynamic quantification of pathogen transmission dynamics Miller, Rachel


As the transmission dynamics of HIV change in response to public health action and other external factors, rapid, scalable and unbiased methods of transmission monitoring become increasingly crucial to gaining and maintaining epidemic control. Analyses of transmission dynamics can direct allocation of public health resources expediently, monitor public health program effectiveness, and identify both existing and developing gaps in prevention. Investigation of lineage-level diversification rate, a phylogenetic approximation of transmission, as a measure for prioritization of transmission clusters for public health intervention was conducted. Both empirical and simulated data were used to compare lineage-level diversification rate-based measures to commonly used non-phylogenetic prioritization measures in ability to statistically separate high and low priority populations, strength of relationship with future growth and number of downstream transmissions produced by prioritized clusters. Further analyses employ phylogenetic methods in the detection of cluster-level transmission changes associated with reductions in access to HIV services related to SARS-CoV-2 restrictions in British Columbia. Cluster growth, branching events and change in lineage-level diversification rates quantify transmission across three sixty-day periods representing “pre-lockdown”, “lockdown” and “post-lockdown”. Results reveal that lineage-level diversification rate-based measures frequently outperform non-phylogenetic measures in prioritizing transmission clusters with the greatest growth potential, while remaining more robust to the effects of missing data. Change in lineage-level diversification rates, in combination with branching events and cluster growth, also indicate increased transmission in clusters associated with people who inject drugs (PWID) relative to clusters associated with men who have sex with men (MSM) during the period of time following SARS-CoV-2 restriction implementation. Overall, lineage-level diversification rates provide a quantitative and consistent approach to transmission cluster prioritization free of need for external data and aid in the formation of a multi-faceted phylogenetic approach to detecting broader trends in transmission. Phylogenetic methods offer valuable insights crucial to epidemic control in the modern epidemiological landscape of HIV.

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