Abstract
Background
Relatively few studies have investigated HIV-1 persistence in tissues, especially in healthy people-living-with-HIV-1 (PLWH) on a successful antiretroviral regimen containing second generation integrase inhibitors.
Methods
In the ANRS EP64 DOLUVOIR, we explore HIV-1 persistence in five accessible anatomical sites in 20 PLWH on an efficient first-line ART regimen containing dolutegravir with virological load <50 copies/mL: PBMCs, rectum, adipose tissue, lymph node and sperm. We quantify total HIV-DNA and cell-associated HIV-1 RNA in different compartments. We sequence HIV-1 DNA for searching drug resistance mutations (DRM) (in RT and INT) and for studying HIV diversity within tissues (ENV). Intact proviral DNA is estimated in PBMCs with an adapted IPDA assay.
Results
Broad ranges of total HIV-DNA and transcripts levels are detected in lymph nodes, PBMCs, adipose tissue and rectum with the highest levels being found in lymph nodes (2.77 log copies HIV-1-DNA/106 cells and 1.50 log copies of HIV-1 cell-associated-RNA/µg RNA). HIV-1 DNA is undetected in all sperm samples (n = 19) except for one (1.52 log copies HIV-1-DNA/106 cells). No difference is noted between the diversity in the four compartments. DRMs to the current regimen are found archived in compartments of six participants. Only two major DRMs to dolutegravir (G118R and R263K) are found archived in two participants. They are the results of APOBEC hypermutations.
Conclusions
Despite ongoing transcriptional activity, persistence of HIV-1 in deep tissues is not associated with the selection of DRMs to dolutegravir on intact proviruses. Our results suggest that the detectable transcriptional activity stems predominantly from defective proviral DNA.
Plain language summary
The main obstacle for the eradication of Human immunodeficiency Virus (HIV-1) is that the virus persists deep in the human body. In this present study, we explore this persistence by measuring the level of infection and expression of viral genes in five parts of the body: blood, rectum, lymph nodes, sperm and fat. We look in 20 People-living-with-HIV-1 on successful treatment with a combination of medicines including one called Dolutegravir. We demonstrate that the levels of infection are highest in lymph nodes. By testing HIV-1 DNA for drug resistance, we show that this persistence in the body does not lead to major resistance to Dolutegravir.
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Data availability
The quantification data that support the findings of this study and the source data presented in figures can be found in Supplementary Data 1. Sequenced fastq files are accessible on the European Nucleotide Archive with the following accession number: PRJEB104864 via https://www.ebi.ac.uk/ena/browser/view/PRJEB104864?show=reads.
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Acknowledgements
The study was funded and promoted by the ANRS-MIE. ViiV Healthcare acted as a cofounder. The funders had no role in the study design, data collection, data analysis, data interpretation or the writing of the manuscript.
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V.A.F., A.C., L.M. and A.B.T. conceptualized and designed the protocol. A.C. obtained funding. V.A.F. supervised virological analyses. G.M., A.C. and V.A.F. designed experiments. G.M., A.M. and E.G. carried out experiments. L.A. participated to data generation. V.A.F., G.M., A.M., K.D.S., A.Cha. and F.L. analyzed data. L.M. supervised data monitoring. S.O. and F.C. participated to the project administrative management. B.L., J.G., O.R. and J.P.V. included participants. G.M. and V.A.F. interpreted and analyzed results and wrote the original manuscript. All authors critically reviewed the manuscript and contributed to the final version.
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V.A.F. has received institutional grants from ViiV Healthcare and honoraria and travel grants from ViiV Healthcare and Gilead Sciences for participation in educational meetings and conferences. A.C. has received institutional grants from ViiV Healthcare and travel grants from Gilead Sciences. O.R. has received consulting fees and payment/honoraria for lectures from Gilead, MSD, Pfizer, and ViiV Healthcare. J.G. reports honoraria for consulting from Gilead Sciences, ViiV Healthcare, Bavarian Nordic and GSK. All other authors declare no competing interests.
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Mchantaf, G., Melard, A., Da Silva, K. et al. HIV persistence in tissues on dolutegravir-based therapy is not associated with resistance mutations to dolutegravir. Commun Med (2026). https://doi.org/10.1038/s43856-026-01405-z
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DOI: https://doi.org/10.1038/s43856-026-01405-z
