The Human Immunodeficiency Virus (HIV), infects and depletes CD4+ T-cells from our immune system and could lead to AIDS. Current therapies halt HIV replication but cannot completely cure infected patients due to the early formation of the HIV-1 reservoir in which the virus hides in a latent state. If therapy is interrupted, a relapse of infection can occur in a few weeks from this reservoir. The need for a definitive cure is urgent and could cure the 38 million people living with HIV worldwide. The goal of this project is to develop an HIV-1 DNA based (‘helix’) sorting strategy to enrich for the HIV-1 reservoir from a background of non-infected cells (‘haystack’). This approach combines in-situ whole genome amplification with fluorescence in-situ hybridization targeting the HIV-1 genome followed by Fluorescence-Activated Cell Sorting to sort HIV-1 infected cells. The assay will be developed to allow for simultaneous downstream analysis of HIV-1 proviral sequences and integration sites of the sorted single-cells. Our assay can be used in HIV cure research, where different layers of information are obtained in one single assay instead of using current separate, laborious and expensive assays. To conclude, we propose a novel, innovative strategy capable of enriching genome-intact proviruses that can be used in HIV-1 cure studies to measure the size of the reservoir and provide qualitative information of the proviral landscape.