Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article


Doctor of Philosophy


Microbiology and Immunology

Collaborative Specialization

Global Health Systems in Africa


Arts, Eric J.


Human immunodeficiency syndrome (HIV-1) has infected over 75 million people and over 35 million have succumbed to virus related illnesses. Despite access to a variety of antiretroviral therapy (ART) options, ART programs have been disproportionally spread in the world with low-and middle-income countries (LMICs) facing challenges to access the most potent ART options. With less potent ART remaining in use in LMICs, HIV-1 drug resistance (HIVDR) presents a growing challenge in LMICs. Since approval of the first-generation integrase strand transfer inhibitor (INSTIs), Raltegravir (RAL) in 2007, INSTIs remain the best choice as a backbone of ART. Access to second generation INSTIs, Dolutegravir (DTG) and bictegravir (BIC) in LMICs is based on need and not on a full evaluation of the effectiveness of these treatments in patients infected with non-B HIV-1 subtypes. To address this challenge of limited INSTIs associated HIVDR data in non-B HIV subtypes, we first screened for the presence of INSTIs associated drug resistance mutations (DRMs) in ART naïve and experienced patients in Uganda using Sanger and Illumina sequencing. In Uganda, 47% of patients failing on RAL carry resistance to RAL-and elvitegravir (EVG), and only 4% harbor resistant virus to DTG. A panel of recombinant viruses from patient-derived HIV-1 integrases carrying resistant mutations was created and tested for susceptibility to a panel of INSTIs: EVG, RAL, DTG, BIC, and CAB. The virus carrying N155H or Y143R/S was susceptible to DTG, BIC, and CAB but highly resistant to RAL and EVG (>50-fold change). Two patients, one with E138A/G140A/Q148R/G163R and one with E138K/G140A/S147G/Q148K, displayed the highest reported resistance to RAL, EVG (FC, >1000) and even DTG (FC, >100), BIC (FC, 60->100), and CAB (FC, 429->1000). All viruses had impaired replication fitness and <50% reduction in integration capacity. We further determined potential novel polymorphisms associated with INSTI resistance in HIV-1 subtype A and D using simple vector machine analysis. The identified I208L and I203M, did not show reduced susceptibility to RAL or DTG with 1.3-1.8-fold and 1-1.4-fold observed, respectively. Further investigation is required to determine how these novel mutations influence susceptibility to INSTIs in HIV-1 subtype A and D infected patients.

Summary for Lay Audience

Human immunodeficiency syndrome virus type 1 (HIV-1) is the causative agent for Acquired immunodeficiency syndrome (AIDS) which is characterized by rapid depletion of CD4+ T cells which eventually results in emergence of opportunistic infections. HIV-1 like other retroviruses, hijack host DNA machinery to be able to replicate and cause havoc in the infected individual. Because of high replication rate and numerous errors during replication, there are diverse strains of HIV-1 circulating in world population which are commonly referred to as subtypes, circulating recombinant forms, and unique recombinant forms. The non-B HIV-1 subtypes are predominantly in low- and middle-income countries (LMICs) and account for up to ~ 90% of HIV-1 infections. The antiretroviral therapy (ART) has tremendously improved the lives of individuals infected with HIV-1 and discovery of an even more potent class of ART, the integrase strand transfer inhibitors (INSTIs) has further improved HIV-1 treatment outcomes. Despite these advances, research of HIV-1 drug resistance associated with INSTIs has historically been done in HIV-1 subtype B virus which is predominant in high-income countries. With improved access to INSTIs by HIV-1 patients in LMICs, there is urgent need to assess susceptibility of HIV-1 non-B strains to INSTIs and also discover novel potential pathways to resistance in these strains. From a cohort of HIV-1 infected patients in Uganda, we show that prolonged virological failure on INSTI, raltegravir, leads to accumulation of drug resistance mutations which confer resistance to all currently available INSTIs. Novel mutations in the HIV-1 integrase gene which show no impact on INSTIs susceptibility by themselves, may act as secondary mutations to other drug resistance mutations outside HIV-1 integrase gene which merits further investigation.

Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.