Open Collections

Lapointe, Hope Ryan

University of British Columbia

Deoxyribonucleic acid (DNA) sequencing technologies allow novel research and public health opportunities to characterize and intervene in viral outbreaks across the globe. The overarching aim of this thesis is to utilize various sequencing technologies to characterize viral pathogens for different purposes. Here, three different sequencing approaches for monitoring the human pathogens Human Immunodeficiency Virus (HIV), Hepatitis C Virus (HCV), and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are discussed. HIV genotyping can be utilized to identify drug resistance-associated mutations and guide HIV treatment. However, access to such testing is currently insufficient in resource-limited settings to enable routine genotypic HIV drug resistance testing. Retrospective studies in the form of resistance surveys can be performed to assess population-level HIV drug resistance. Here, two large HIV resistance surveys were performed for Eswatini and Malawi to identify the proportion of individuals with pre-existing HIV drug resistance. These data were pivotal in these countries’ selection of HIV treatments for their populations. Sequencing also has the potential to identify the time of viral infection based the accumulation of mutations in the genome. A discussion is provided where this approach is used in the context of identifying causes of failure of tenofovir pre-exposure prophylaxis for preventing HIV infection. Conversely, phylogenetic analysis of sequence data, which reveals the relatedness between viral sequences, can inform outbreak monitoring. Another discussion on the practical and ethical considerations of utilizing HIV sequence data is provided. The second objective of this thesis is to develop and implement newer “next-generation” sequencing platforms to better characterize genetic patterns amongst other viruses. A genotype-independent sequencing assay for the Hepatitis C Virus (HCV) on the Illumina MiSeq is described and validated. This assay enables parallel identification of the HCV infection genotype, as well as detection of any resistance-associated mutations. Additionally, a nanopore sequencing assay was rapidly deployed during the onset of the COVID-19 pandemic to sequence the causative agent, SARS-CoV-2. A final study describes the development of a SARS-CoV-2 sequencing strategy in collaboration with the Artic Network. This thesis supports the ongoing use of sequencing to characterize viral pathogens for therapy optimization and molecular epidemiology.

Text

2023-08-28

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/85645

Experimental Medicine

University of British Columbia

UBCV

http://creativecommons.org/licenses/by-nc-nd/4.0/