Using deep sequencing with a primer ID to resolve the structure of viral populations and reveal pre-existing drug resistance mutations in the HIV and HCV protease genes Public Deposited

Downloadable Content

Download PDF
Last Modified
  • March 22, 2019
  • Jabara, Cassandra Baheeya
    • Affiliation: College of Arts and Sciences, Department of Biology
  • Human Immunodeficiency Virus (HIV) and Hepatitis C Virus (HCV) are among the most deadly chronic viral diseases affecting the human population. The rich genetic diversity produced within a host includes adaptive resistance alleles that may enable viral escape from drug selective pressures. An in-depth characterization of the intrahost population and the genetic path it takes to escape drug selection may reveal how to prevent the evolution of resistance. Resolving the fine-scale genetic structure of a viral population requires deep sampling of the genetic variation within a viral population. I developed a novel technique, Primer ID, which reproducibly (Chapter 4) captures viral diversity while correcting for PCR biases and error inherent in deep sequencing protocols (Chapter 2). Deep sequencing with a Primer ID was applied to the targeted re-sequencing of protease for two different viral genomes, HIV (Chapter 2-3) and HCV (Chapter 4). The allelic distribution of genetic variation of HIV and HCV was skewed towards low-frequency polymorphisms, some of which were resistance-associated variants (Chapters 2-4). I observed that pre-existing resistance mutations could be directly selected during a drug treatment (Chapter 2). However, the path to resistance was often complex and confounded by variance in the steady-state frequency of resistance alleles, sampling depth, and the effective population size (Chapter 3). Once a population of HIV escaped a drug, it was observed that resistance-associated variants were added de novo in a step-wise manner, not brought together by recombination of pre-existing haplotypes. HCV-HIV co-infection decreased overall population diversity (Chapter 4). This difference did not correlate with a change in the overall frequency of pre-existing resistance mutations, but specific resistance alleles were enriched in either mono- or co-infected populations. Further application of deep sequencing with a Primer ID will result in a greater understanding of the population dynamics of both HIV and HCV and determine if the standing genetic variation can be used to predict if a patient will fail therapy and how a viral population responds to selective pressures. Together, improvements in predictive power will result in an enhancement of therapeutic success rate and sustained virologic response.
Date of publication
Resource type
Rights statement
  • In Copyright
  • Jones, Corbin
  • Doctor of Philosophy
Graduation year
  • 2012

This work has no parents.