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HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers
Radwa Sharaf, Guinevere Q. Lee, Xiaoming Sun, Behzad Etemad, Layla M. Aboukhater, Zixin Hu, Zabrina L. Brumme, Evgenia Aga, Ronald J. Bosch, Ying Wen, Golnaz Namazi, Ce Gao, Edward P. Acosta, Rajesh T. Gandhi, Jeffrey M. Jacobson, Daniel Skiest, David M. Margolis, Ronald Mitsuyasu, Paul Volberding, Elizabeth Connick, Daniel R. Kuritzkes, Michael M. Lederman, Xu G. Yu, Mathias Lichterfeld, Jonathan Z. Li
Radwa Sharaf, Guinevere Q. Lee, Xiaoming Sun, Behzad Etemad, Layla M. Aboukhater, Zixin Hu, Zabrina L. Brumme, Evgenia Aga, Ronald J. Bosch, Ying Wen, Golnaz Namazi, Ce Gao, Edward P. Acosta, Rajesh T. Gandhi, Jeffrey M. Jacobson, Daniel Skiest, David M. Margolis, Ronald Mitsuyasu, Paul Volberding, Elizabeth Connick, Daniel R. Kuritzkes, Michael M. Lederman, Xu G. Yu, Mathias Lichterfeld, Jonathan Z. Li
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Research Article AIDS/HIV Infectious disease

HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers

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Abstract

HIV posttreatment controllers (PTCs) represent a natural model of sustained HIV remission, but they are rare and little is known about their viral reservoir. We obtained 1,450 proviral sequences after near-full-length amplification for 10 PTCs and 16 posttreatment noncontrollers (NCs). Before treatment interruption, the median intact and total reservoir size in PTCs was 7-fold lower than in NCs, but the proportion of intact, defective, and total clonally expanded proviral genomes was not significantly different between the 2 groups. Quantification of total but not intact proviral genome copies predicted sustained HIV remission as 81% of NCs, but none of the PTCs had a total proviral genome greater than 4 copies per million peripheral blood mononuclear cells (PBMCs). The results highlight the restricted intact and defective HIV reservoir in PTCs and suggest that total proviral genome burden could act as the first biomarker for identifying PTCs. Total and defective but not intact proviral copy numbers correlated with levels of cell-associated HIV RNA, activated NK cell percentages, and both HIV-specific CD4+ and CD8+ responses. These results support the concept that defective HIV genomes can lead to viral antigen production and interact with both the innate and adaptive immune systems.

Authors

Radwa Sharaf, Guinevere Q. Lee, Xiaoming Sun, Behzad Etemad, Layla M. Aboukhater, Zixin Hu, Zabrina L. Brumme, Evgenia Aga, Ronald J. Bosch, Ying Wen, Golnaz Namazi, Ce Gao, Edward P. Acosta, Rajesh T. Gandhi, Jeffrey M. Jacobson, Daniel Skiest, David M. Margolis, Ronald Mitsuyasu, Paul Volberding, Elizabeth Connick, Daniel R. Kuritzkes, Michael M. Lederman, Xu G. Yu, Mathias Lichterfeld, Jonathan Z. Li

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Figure 3

Comparison of reservoir measures between PTCs and NCs.

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Comparison of reservoir measures between PTCs and NCs.
(A) Copy numbers ...
(A) Copy numbers and (B) percentages of intact proviral genomes within total reservoir are compared between both groups. (C) Copy numbers of total proviral genomes per million PBMCs are compared between groups. (D) Copy numbers and (E) percentages of defective proviral genomes are depicted for each group. (F) Copy numbers and (G) percentages of hypermutated proviral genomes are depicted for each group. The size of each data point corresponds to total number of sequences amplified per participant as indicated in the legend in A–G. (H) A comparison between PTCs and NCs in the hypermutation rate ratio, calculated as the ratio of the number of match sites out of potential sites to the number of control sites out of potential sites. (I) Pie charts reflecting the median relative contribution of each proviral species for all participants, normalized to 100%. Numbers in parentheses indicate absolute frequency of analyzed sequences in each group. (J–L) Longitudinal analysis of intact (J), total (K), and defective (L) proviral genome copy numbers from the pre- and post-ATI time points for 7 PTCs. Each PTC is shown in a different color. Significance was calculated using a Wilcoxon rank-sum test: *P < 0.05, **P < 0.01, ***P < 0.001. NCs are depicted in blue and PTCs in red. PTC, posttreatment controllers; NC, posttreatment noncontrollers; PSI, packaging signal; PSC, premature stop codon.

Copyright © 2026 American Society for Clinical Investigation
ISSN: 0021-9738 (print), 1558-8238 (online)

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