Antiretroviral therapy (ART) effectively suppresses HIV-1 replication. However, HIV-1 rebounds when ART is interrupted due to the persistence of HIV-1 proviruses in CD4+ T cells during suppressive ART. We performed an extensive genetic characterisation of HIV-1 to investigate the cellular and viral mechanisms contributing to this viral rebound. First, we used the full-length individual proviral sequencing (FLIPS) assay to investigate the HIV-1 proviruses that persist in memory CD4+ T cells sorted into 4 cell subsets based on the expression of the immune checkpoint markers programmed cell death protein-1 (PD-1) and/or cytotoxic T-lymphocyte-associated protein-4 (CTLA-4). We found that during long-term ART, memory CD4+ T cells that express PD-1, rather than those that express CTLA-4, have characteristics, such as increased cellular proliferation, that allow the persistence of HIV-1 proviruses. However, we identified considerable participant-specific variation in the enrichment of HIV-1 proviruses within CD4+ T cells expressing PD-1 and/or CTLA-4. Next, we presented a novel assay for genetically characterising near-full-length HIV-1 RNA genomes from the plasma of viremic individuals living with HIV-1, called the plasma-derived HIV-1 RNA using long-range sequencing (PRLS) assay. We used this assay to demonstrate that a considerable proportion of HIV-1 virions during untreated HIV-1 infection contain genetically-defective genomes. Then, we employed the PRLS assay to genetically characterise HIV-1 RNA genomes from rebound viral variants in 5 individuals undergoing 3 analytical treatment interruptions (ATIs). We found an association between the emergence of genetically distinct viral variants during an ATI and a delayed time to viral rebound. These findings increase our knowledge of the mechanisms behind HIV-1 rebound when ART is interrupted, and contributes to the identification of possible therapeutic strategies to prevent this viral rebound in the absence of ART.