Applying phylogenetic lineage-level diversification rate to infer epidemiological risk factors and spatiotemporal distribution of HIV transmission in British Columbia
department or school: Medicine, Faculty of
department or school: Population and Public Health (SPPH), School of
data provider: DSpace
degree campus: UBCV
creator: McLaughlin, Angela
issued: 2019-04-16T22:11:45Z
issued: 2019
related degree: Master of Science - MSc
degree grantor: University of British Columbia
description: Background Despite the widespread availability of antiretroviral therapy, sub-populations are burdened by disproportionately high HIV transmission within both developed and un-developed countries. By identifying groups and areas where people are at a higher risk of HIV transmission, we can better target interventions to those communities. Phylogenetic analysis of HIV genetic sequences generated from resistance testing for people living with HIV can augment traditional epidemiological methods to quantify transmission. Each virus’ branching rate in the phylogenetic tree, referred to as its lineage-level diversification rate, is an estimate of its transmission rate. Methods The viral diversification rate was calculated for 36,271 partial pol HIV sequences representing 9,310 participants in the British Columbia Drug Treatment Program between May 1996 and March 2018. First, the relationships between patient-level diversification rate with age, viral load, health authority, risk behavior, ethnicity, and clinical background were explored using a generalized linear model. Subsequently, patient data was aggregated according to their census tract of residence in order to build a community-level zero-inflated negative binomial model to predict new HIV cases. Results At the patient level, high HIV diversification rate was positively associated with being younger, reporting injection drug use, having co-infection with hepatitis C virus, having a high most recent viral load, and residing within the Northern BC Health Authority, while having ever had AIDS and identifying as black were both significantly associated with lower diversification rates. At the census tract level, the sum of patients’ annual change in diversification rate improved the specificity, accuracy, and correlation of observed and predicted values of a model to predict new HIV cases relative to a model including only epidemiological and clinical patient data. Conclusions Analyzing the distribution of phylogenetic…
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/69723
note: APPLYING PHYLOGENETIC LINEAGE-LEVEL DIVERSIFICATION RATE TO INFER EPIDEMIOLOGICAL RISK FACTORS AND SPATIOTEMPORAL DISTRIBUTION OF HIV TRANSMISSION IN BRITISH COLUMBIA by Angela McLaughlin B.Sc. Microbiology and Immunology, The University of British Columbia, 2014 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Population and Public Health) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) April 2019 © Angela McLaughlin, 2019 ii The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, a thesis/dissertation entitled: APPLYING PHYLOGENETIC LINEAGE-LEVEL DIVERSIFICATION RATE TO INFER EPIDEMIOLOGICAL RISK FACTORS AND SPATIOTEMPORAL DISTRIBUTION OF HIV TRANSMISSION IN BRITISH COLUMBIA submitted by Angela McLaughlin in partial fulfillment of the requirements for the degree of Master of Science in Population and Public Health Examining Committee: Jeffrey Joy Co-supervisor Jean Shoveller Co-supervisor Rodney Knight Supervisory Committee Member Jennifer Gardy Additional Examiner Additional Supervisory Committee Members: Richard Harrigan Supervisory Committee Member iii Abstract Background Despite the widespread availability of antiretroviral therapy, sub-populations are burdened by disproportionately high HIV transmission within both developed and un-developed countries. By identifying groups and areas where people are at a higher risk of HIV transmission, we can better target interventions to those communities. Phylogenetic analysis of HIV genetic sequences generated from resistance testing for people living with HIV can augment traditional epidemiological methods to quantify transmission. Each virus’ branching rate in the phylogenetic tree, referred to as its lineage-level diversification rate, is an estimate of its transmission rate. Methods The viral diversification rate was calculated for 36,27…
has type: Thesis/Dissertation
date issued: 2019-05
is shown at: 10.14288/1.0378250
language: eng
degree discipline: Population and Public Health
provider: Vancouver : University of British Columbia Library
publisher: University of British Columbia
rights: Attribution-NonCommercial-NoDerivatives 4.0 International
rights URI: http://creativecommons.org/licenses/by-nc-nd/4.0/
scholar level: Graduate
type: Text
identifier URI: http://hdl.handle.net/2429/69723