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Kayondo JK, Ndembi N, Parry CM, Cane PA, Hué S, Goodall R, Dunn DT, Kaleebu P, Pillay D, Mbisa JL. Intrapatient Evolutionary Dynamics of Human Immunodeficiency Virus Type 1 in Individuals Undergoing Alternative Treatment Strategies with Reverse Transcriptase Inhibitors. AIDS Res Hum Retroviruses 2015; 31:749-56. [PMID: 25953118 PMCID: PMC4505773 DOI: 10.1089/aid.2015.0035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Structured treatment interruption (STI) has been trialed as an alternative to lifelong antiretroviral therapy (ART). We retrospectively performed single genome sequencing of the HIV-1 pol region from three patients representing different scenarios. They were either failing on continuous therapy (CT-F), failing STI (STI-F), or suppressing on STI (STI-S). Over 460 genomes were generated from three to five different time points over a 2-year period. We found multiple-linked-resistant mutations in both treatment failures. However, the CT-F patient showed a stepwise accumulation of diverse, linked mutations whereas the STI-F patient had lineage turnover between treatment periods with recirculation of wild-type and resistant variants from reservoirs. The STI-F patient showed a 7-fold increase in the third codon position substitution rate relative to the first and second positions compared to a 2-fold increase for CT-F and increased purifying selection in the pol gene (62 vs. 22 sites, respectively). An understanding of intrapatient viral dynamics could guide the future direction of treatment interruption strategies.
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Affiliation(s)
- Jonathan K. Kayondo
- Uganda Virus Research Institute (UVRI), Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Nicaise Ndembi
- Medical Research Council (MRC)/UVRI, Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Chris M. Parry
- Medical Research Council (MRC)/UVRI, Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Patricia A. Cane
- Virus Reference Department, Public Health England, London, United Kingdom
| | - Stephane Hué
- Department of Infection and Immunity, University College London, London, United Kingdom
| | - Ruth Goodall
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | - David T. Dunn
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | - Pontiano Kaleebu
- Uganda Virus Research Institute (UVRI), Uganda Research Unit on AIDS, Entebbe, Uganda
- Medical Research Council (MRC)/UVRI, Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Deenan Pillay
- Department of Infection and Immunity, University College London, London, United Kingdom
| | - Jean L. Mbisa
- Virus Reference Department, Public Health England, London, United Kingdom
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