Fig 1.
Flow diagram of QVOA wells yielding NIPG.
“N” represents the number of QVOA culture wells; “n” represents the number of PCR reactions performed at limiting dilution and therefore, the number of NIPG recovered at a clonal level. QVOA: quantitative viral outgrowth assay, NIPG: non-induced proviral genomes, PCR: polymerase chain reaction.
Table 1.
Characteristics of the study population.
Fig 2.
(A) Distribution of NIPG within each study participant. Purple: hypermutation; Green: Gag deletion; Red: intact near-full length, replication-deficient due to nonsense mutations or INDELs; Blue: undefined non-Gag deletion; Orange: defined non-Gag deletion; empty circle: not evaluable. (B) Distribution of NIPG across study participants after Gag and near-full length sequencing. NIPG: non-induced proviral genomes.
Fig 3.
Deletions in NIPG with defined junctions.
Letters and numbers correspond to participant identifiers listed in Table 1. A) Sequences are aligned to HXB2. Sequenced positions appear as a black polygon. Gray thin lines indicate deleted regions of genomes. B) Regions with relatively high coverage were extracted for phylogenetic analysis. Location shown is according to HXB2 numbering. Colors correspond to nucleotides on the left. Sequences designated with a red dot were not used in subsequent analysis due to missing sequence segments. C) Phylogenetic analysis of sequences rooted using HXB2 and aligned to positions 3350–4327 and 9105–9597.
Fig 4.
HIV DNA concentrations from cultured resting CD4+ T cell QVOA wells with and without NIPG.
“N” represents the number of QVOA culture wells.
Table 2.
HIV-specific antibody responses of plasma samples.