HIV-1-driven aberrant host gene expression may contribute to HIV-1 persistence

Using HIV-1 RNASortSeq, we identified HIV-1-infected cells containing inducible HIV-1 for RNAseq from resting CD4+ T cells treated with PMA/ionomycin for 16 hours from eight antiretroviral therapy treated, virally suppressed, HIV-1-infected individuals. Using custom bioinformatic pipeline, we identified HIV-1 genomic RNA, host RNA and HIV-1-host chimeric RNA junctions. We used custom bioinformatic pipelines to identify HIV-1 RNA sequences and HIV-1-host chimeric RNA sequences to examine HIV-1-host RNA interactions.