Figure 1. The HIV-1 proviral landscape is different between Tn and memory CD4⁺ T cell subsets isolated from ART-suppressed individuals.

Near-full-length HIV-1 proviral sequences were obtained by FLIPS from Tn and memory CD4⁺ T cell subsets of participants on suppressive ART. Genetically intact HIV-1 proviral sequences were identified and the intact infection frequency was calculated using a mixed logistic model for each cell subset: (A) including all intact sequences and (B) counting identical intact proviral sequences only once for each cell subset. Data represent average genetically intact proviruses per 10⁶ cells ± 95% CIs. P values were calculated with a likelihood ratio test. (C) Proviral sequences were classified as full length (>8800 bp) or deleted (<8800 bp) and further categorized according to their predominant characteristic. In each cell subset, the percentage of each type of provirus was calculated: (D) intact; (E) full-length; (F) cis-acting defect; (G) hypermutated; (H) 5′ deleted; (I) 3′ deleted; and (J) 75% deleted. Genetically identical sequences were counted only once for each subset. Data represent the adjusted overall percentage ± 95% CI. P values were calculated with a likelihood ratio test. Tn, naive; Tcm, central memory; Ttm, transitional memory; Tem, effector memory. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001.