In-depth characterization of HIV-1 reservoirs reveals links to viral rebound during treatment interruption

The HIV-1 reservoir is composed of cells harboring latent proviruses that are capable of refuelling viremia upon antiretroviral treatment interruption. This reservoir is in part maintained by clonal expansion of infected cells. However, the contribution of large, infected cell clones to rebound remains underexplored. Here, we performed an in-depth study on four chronically treated HIV-1 infected individuals that underwent an analytical treatment interruption (ATI). A combination of single-genome sequencing, integration site analysis, near-full length proviral sequencing and multiple displacement amplification was used to identify infected cell clones and link these to plasma viruses before and during an ATI. A total of six proviruses could be linked to plasma sequences recovered during ATI. Interestingly, only two of six proviruses were genome intact, one of which is integrated in the ZNF141 gene. To our knowledge, this is the first instance of an intact provirus with its matched IS being matched to plasma virus during an ATI. These findings demonstrate that with in-depth reservoir characterization, clones of infected cells harboring genome-intact proviruses can be linked to rebound viremia, confirming the previously proposed notion that infected clonal cell populations play an important role in the long-term maintenance of the replication-competent HIV-1 reservoir.