Clonally expanded HIV-1 proviruses with 5′-leader defects can give rise to nonsuppressible residual viremia
Jennifer A. White, … , Janet D. Siliciano, Francesco R. Simonetti
Jennifer A. White, … , Janet D. Siliciano, Francesco R. Simonetti
Published January 5, 2023
Citation Information: J Clin Invest. 2023;133(6):e165245. https://doi.org/10.1172/JCI165245.
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Clonally expanded HIV-1 proviruses with 5′-leader defects can give rise to nonsuppressible residual viremia

Abstract

Background Antiretroviral therapy (ART) halts HIV-1 replication, decreasing viremia to below the detection limit of clinical assays. However, some individuals experience persistent nonsuppressible viremia (NSV) originating from CD4+ T cell clones carrying infectious proviruses. Defective proviruses represent over 90% of all proviruses persisting during ART and can express viral genes, but whether they can cause NSV and complicate ART management is unknown.Methods We undertook an in-depth characterization of proviruses causing NSV in 4 study participants with optimal adherence and no drug resistance. We investigated the impact of the observed defects on 5′-leader RNA properties, virus infectivity, and gene expression. Integration-site specific assays were used to track these proviruses over time and among cell subsets.Results Clones carrying proviruses with 5′-leader defects can cause persistent NSV up to approximately 103 copies/mL. These proviruses had small, often identical deletions or point mutations involving the major splicing donor (MSD) site and showed partially reduced RNA dimerization and nucleocapsid binding. Nevertheless, they were inducible and produced noninfectious virions containing viral RNA, but lacking envelope.Conclusion These findings show that proviruses with 5′-leader defects in CD4+ T cell clones can give rise to NSV, affecting clinical care. Sequencing of the 5′-leader can help in understanding failure to completely suppress viremia.Funding Office of the NIH Director and National Institute of Dental and Craniofacial Research, NIH; Howard Hughes Medical Institute; Johns Hopkins University Center for AIDS Research; National Institute for Allergy and Infectious Diseases (NIAID), NIH, to the PAVE, BEAT-HIV, and DARE Martin Delaney collaboratories.

Authors

Jennifer A. White, Fengting Wu, Saif Yasin, Milica Moskovljevic, Joseph Varriale, Filippo Dragoni, Angelica Camilo-Contreras, Jiayi Duan, Mei Y. Zheng, Ndeh F. Tadzong, Heer B. Patel, Jeanelle Mae C. Quiambao, Kyle Rhodehouse, Hao Zhang, Jun Lai, Subul A. Beg, Michael Delannoy, Christin Kilcrease, Christopher J. Hoffmann, Sébastien Poulin, Frédéric Chano, Cécile Tremblay, Jerald Cherian, Patricia Barditch-Crovo, Natasha Chida, Richard D. Moore, Michael F. Summers, Robert F. Siliciano, Janet D. Siliciano, Francesco R. Simonetti

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Figure 2

Paired full-genome sequencing and integration site analysis of 5′-L–defective proviruses causing NSV.

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Paired full-genome sequencing and integration site analysis of 5′-L–defe...
(A) Mapped sequences of proviruses contributing to plasma HIV-1 RNA in each participant. Proviruses of interest are color-coded throughout the figure. Light-shaded areas indicate small 5′-L deletions. Stars indicate point mutations affecting the MSD site. (B) Percentage contributions to NSV of defective proviruses of interest. (C) 5′-L defects aligned to the HXB2 reference. DIS, dimerization initiation signal; PSI, packaging signal; AUG, Gag start codon. Dashes indicate length polymorphisms. Gray lines highlight GAG repeats at deletion junctions causing misplaced jumping of reverse transcriptase (dashed gray arrows). (D) Chromosomal and gene locations of proviruses causing viremia. Sets of arrows indicate direction of proviral and host gene transcription. Schematic gene tracks are shown in black, with vertical bars representing exons.