Antiretroviral therapy (ART) can reduce plasma HIV-1 levels below the limit of detection of clinical assays. However, incomplete suppression of virus can lead to rapid emergence of significant drug resistance mutations (DRM) that render certain drugs ineffective. The integration of drug resistant viruses into the host DNA and persistence in CD4+ cells in a latent state poses a major obstacle to effective treatment strategies and challenges new universal treatment paradigms for the eradication of HIV infection. The latent cellular reservoir functions as a historical archive of viral genotypes that have previously circulated in the host including provirus harboring DRM. However, little is known about the duration, persistence, and decay of DRM in the proviral reservoir over time. To address these questions, we identified subjects with known dates of virologic failure of Efavirenz-based regimens with emergence of drug resistant viremia (with the K103N mutation). These subjects were previously enrolled in ACTG trials but were subsequently treated with an effective second-line, boosted protease inhibitor-based regimen. CD4 count and viral load were measured and cryopreserved PBMC were collected every 6 months for up to 10 years. Following a failed first-line regimen, we hypothesize that consensus resistance mutations rapidly decay to levels below detection (<20%) in proviral DNA but persist in the latent reservoir with gradual decay over months to years. To test this hypothesis, our proposed study will 1) examine the frequency of DRM in proviral DNA following virologic failure and the detection of DRM in plasma RNA and 2) define the factors that affect fixation, retention, and decay over time and 3) use ultra-deep sequencing to quantify DRM over time in proviral DNA and establish the linkage between reverse transcriptase mutations. The information generated will have important implications for developing future treatment options for ART strategies to reduce clinical failure and mitigate the transmission of drug resistance. !
Drug resistance mutations are archived in latent cellular reservoirs, however, little is known about the durability of archived mutations and if they are maintained for the life of the host or if they decay such that drugs might be recycled after a period of suppression. From serial samples obtained for up to 10 years after suppression, we will use innovative sequencing methods to analyze the emergence, fixation, retention, and decay of drug resistance mutations in the proviral CD4 reservoir. !