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HIV-1 infection currently cannot be cured because the virus persists asintegrated proviral DNA in long-lived cells despite years of suppressiveantiretroviral therapy (ART). To characterize establishment, turnover, andevolution of viral DNA reservoirs we deep-sequenced the p17gag region of theHIV-1 genome from samples obtained after 3-18 years of suppressive ART from 10patients. For each of these patients, whole genome deep-sequencing data ofHIV-1 RNA populations before onset of ART were available from 6-12 longitudinalplasma samples spanning 5-8 years of untreated infection. This enabled adetailed analysis of the dynamics and origin of proviral DNA during ART. Amedian of 14% (range 0-42%) of the p17gag DNA sequences were overtly defectivedue to G-to-A hypermutation. The remaining sequences were remarkably similar topreviously observed RNA sequences and showed no evidence of evolution over manyyears of suppressive ART. Most sequences from the DNA reservoirs were verysimilar to viruses actively replicating in plasma (RNA sequences) shortlybefore start of ART. The results do not support persistent HIV-1 replication asa mechanism to maintain the HIV-1 reservoir during suppressive therapy. Rather,the data indicate that viral DNA variants are turning over as long as patientsare untreated and that suppressive ART halts this turnover.

Establishment and stability of the latent HIV-1 DNA reservoir