Distinct HIV-1 Proviral Integration Region Landscapes Across Acute Naïve, Chronic Naïve, and Successfully Treated Patient Cohorts

HIV-1 proviral integration into the human genome dictates viral and host gene expression, as well as HIV reservoir persistence. This study analyzed insertion site (IS) landscapes in three groups of people with HIV (PWH): acute (AHI) naïve (n = 8), chronic (CHI) naïve (n = 12), and CHI on long-term antiretroviral therapy (cART, n = 12). Host DNA was digested with restriction enzymes, ligated to a linker, and amplified by a PCR targeting both the linker and the HIV LTR. Amplicons were sequenced on the Ion Torrent S5 system. A bioinformatics pipeline was designed to detect ISs on the basis of a set of pre-defined parameters. Of all the 388 different ISs obtained, 58.5% were in gene regions. The highest number of ISs was observed in the CHI naïve group, followed by CHI on cART and AHI, showing a statistically significant difference in the distributions. IS patterns varied among groups, eg., chr8:102,815,760 was absent in the AHI group but was found in 92% of the CHI naïve group, reaching 100% in CHI on cART subjects. Although proving causality remains complex, these findings add new data to the literature on this topic, suggesting that active/passive mechanisms for specific IS enrichment may operate during HIV infection and antiretroviral therapy.