Fig 1.

HIVε-seq pipeline. Illustration of HIV ε-seq workflow to detect intact HIV proviral genomes. DNA is extracted from either PBMCs or CD4⁺ T cells, and nearly full-length PCR is performed on the extracted DNA. The reads are aligned to the HXB2 reference HIV sequence. Intact reads are inferred through the bioinformatic removal of reads containing large deletions/inversions, premature stop codons, or regulatory region defects.