Phylogenetic analysis of HIV-1 archived DNA in blood and gut-associated lymphoid tissue in two patients under antiretroviral therapy

AbstractOne of the approaches to cure human immunodeficiency virus (HIV) is the use of therapeutic vaccination. We have launched the Provir/Latitude 45 study to identify conserved CTL epitopes in archived HIV-1 DNA according to the HLA class I alleles in aviremic patients under antiretroviral therapy (ART). A HIV-1 polypeptidic therapeutic vaccine based on viral sequence data obtained from circulating blood was proposed; here, our aim was to compare the proviral DNA in blood and gut-associated lymphoid tissue (GALT). Peripheral blood mononuclear cells and gut biopsies were obtained from two HIV-1 infected patients under successful antiretroviral therapy. Total DNA was extracted including the proviral DNA. The HIV-1 reverse transcriptase was sequenced in both compartments using next generation sequencing followed by single genome sequencing; phylogenetic trees were established and compared. The proviral sequences of both compartments intra-patient exhibited a very low genetic divergence while it was possible to differentiate the sequences inter-patients; single genome sequencing analysis of two couples of samples confirmed that there was no compartmentalization of the sequences intra-patient. We conclude that, considering these two cases, the proviral DNA sequences in blood and GALT are similar and that the epitope analysis of HIV-1 provirus in blood should be considered as relevant to that observed in the GALT, a hard-to-reach major compartment, and can therefore be used for therapeutic vaccine approaches.

Download Full-text

Phylogenetic analysis of HIV-1 archived DNA in blood and gut-associated lymphoid tissue in patients receiving antiretroviral therapy: a study from Provir/Latitude45 project

10.1101/2020.05.05.078634 ◽

2020 ◽

Author(s):

Patricia Recordon-Pinson ◽

Camille Tumiotto ◽

Pantxika Bellecave ◽

Franck Salin ◽

Patricia Thebault ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Dna Sequences ◽

Lymphoid Tissue ◽

Phylogenetic Trees ◽

Therapeutic Vaccine ◽

Hla Alleles ◽

Ctl Epitopes ◽

Proviral Dna ◽

Significant Difference ◽

Hiv 1

AbstractOne of the approaches to cure HIV is the use of therapeutic vaccination. We have launched the Provir/Latitude 45 study to identify conserved CTL epitopes in archived HIV-1 DNA according to the HLA class I alleles in aviremic patients under antiretroviral therapy (ART). A HIV-1 polypeptidic therapeutic vaccine based on viral sequence data obtained from circulating blood was proposed; here, our aim was to compare the proviral DNA in blood and gut-associated lymphoid tissue (GALT) at two different levels : nucleotide sequences and potential CTL epitopes. The reverse transcriptase was sequenced in both compartments using next generation sequencing (NGS) in samples from nine individuals, two of which had also single genome sequencing (SGS) performed; phylogenetic trees were established and compared; CTL epitopes were also identified according to their potential affinity for the HLA alleles. The proviral sequences of both compartments intra-patient exhibited a very low genetic divergence while it was possible to differentiate the sequences inter-patients; SGS analysis of two couples of samples confirmed that there was not a compartmentalization of the sequences intra-patient.When we simulated the CTL epitopes which can be presented by the corresponding HLA alleles in both compartments, no significant difference was observed. We conclude that the proviral DNA sequences in blood and GALT are similar and that the epitope analysis in blood can be considered as relevant to that observed in the GALT, a hard-to-reach major compartment, and can therefore be used for therapeutic vaccine approaches.

Download Full-text

Evolution of HIV-1 genotype in plasma RNA and peripheral blood mononuclear cells proviral DNA after interruption and resumption of antiretroviral therapy

Antiviral Therapy ◽

10.3851/imp2037 ◽

2012 ◽

Vol 17 (3) ◽

pp. 597

Author(s):

Arkaitz Imaz ◽

◽

Montserrat Olmo ◽

Maria Peñaranda ◽

Félix Gutiérrez ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Peripheral Blood Mononuclear Cells ◽

Peripheral Blood ◽

Mononuclear Cells ◽

Peripheral Blood Mononuclear ◽

Proviral Dna ◽

Blood Mononuclear Cells ◽

Plasma Rna ◽

Hiv 1

Download Full-text

Early ART-initiation Reduces HIV-1 Proviral DNA Levels in Children from the CHER Trial

10.21203/rs.3.rs-389348/v1 ◽

2021 ◽

Author(s):

Helen Payne ◽

Man Chan ◽

Sarah Watters ◽

Kennedy Otwombe ◽

Yuan Hsiao ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Mononuclear Cells ◽

Peripheral Blood Mononuclear ◽

Factors Associated ◽

Proviral Dna ◽

Art Initiation ◽

Latent Hiv ◽

Dna Reduction ◽

Living With Hiv ◽

Hiv 1

Abstract BACKGROUND: Reduction of the reservoir of latent HIV-infected cells might increase the possibility of long-term remission in individuals living with HIV. We investigated factors associated with HIV-1 proviral DNA levels in children receiving different antiretroviral therapy (ART) strategies in the Children with HIV Early Antiretroviral Therapy (CHER) trial. METHODS: Infants with HIV <12 weeks old with CD4% ≥25% were randomized in the CHER trial to early limited ART for 40 or 96 weeks (ART-40W, ART-96W), or deferred ART (ART-Def). For ART-Def infants or following ART interruption in ART-40W/ART-96W, ART was started/re-started for clinical progression or CD4% <25%. In 229 participants, HIV-1 proviral DNA was quantified by PCR from stored peripheral blood mononuclear cells from children who had received ≥24 weeks ART and two consecutive undetectable HIV-1 RNA 12-24 weeks apart. HIV-1 proviral DNA was compared between ART-Def and ART-96W at week 96, and in all arms at week 248. Factors associated with HIV-1 proviral DNA levels were evaluated using linear regression.FINDINGS: Longer duration of ART was significantly associated with lower HIV-1 proviral DNA at both 96 (p=0.0003) and 248 weeks (p=0.0011). Higher total CD8 count at ART initiation was associated with lower HIV-1 proviral DNA at both 96 (p=0.0225) and 248 weeks (p=0.0398). Week 248 HIV-1 proviral DNA was significantly higher in those with positive HIV-1 serology at week 84 than those with negative serology (p=0.0042).INTEPRETATION: Longer ART duration is key to HIV-1 proviral DNA reduction. Further understanding is needed of the effects of “immune-attenuation” through early HIV-1 exposure.FUNDING: Wellcome Trust, National Institutes of Health, Medical Research Council.

Download Full-text

Evolution of HIV-1 genotype in plasma RNA and peripheral blood mononuclear cells proviral DNA after interruption and resumption of antiretroviral therapy

Antiviral Therapy ◽

10.3851/imp2025 ◽

2011 ◽

Vol 17 (3) ◽

pp. 577-583 ◽

Cited By ~ 2

Author(s):

Arkaitz Imaz ◽

◽

Montserrat Olmo ◽

Maria Peñaranda ◽

Félix Gutiérrez ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Peripheral Blood Mononuclear Cells ◽

Peripheral Blood ◽

Mononuclear Cells ◽

Peripheral Blood Mononuclear ◽

Proviral Dna ◽

Blood Mononuclear Cells ◽

Plasma Rna ◽

Hiv 1

Download Full-text

Early ART-initiation and longer ART duration reduces HIV-1 proviral DNA levels in children from the CHER trial

AIDS Research and Therapy ◽

10.1186/s12981-021-00389-1 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Helen Payne ◽

Man K. Chan ◽

Sarah A. Watters ◽

Kennedy Otwombe ◽

Nei-Yuan Hsiao ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Mononuclear Cells ◽

Peripheral Blood Mononuclear ◽

Factors Associated ◽

Proviral Dna ◽

Art Initiation ◽

Latent Hiv ◽

Dna Reduction ◽

Living With Hiv ◽

Hiv 1

Abstract Background Reduction of the reservoir of latent HIV-infected cells might increase the possibility of long-term remission in individuals living with HIV. We investigated factors associated with HIV-1 proviral DNA levels in children receiving different antiretroviral therapy (ART) strategies in the children with HIV early antiretroviral therapy (CHER) trial. Methods Infants with HIV < 12 weeks old with CD4% ≥ 25% were randomized in the CHER trial to early limited ART for 40 or 96 weeks (ART-40 W, ART-96 W), or deferred ART (ART-Def). For ART-Def infants or following ART interruption in ART-40 W/ART-96 W, ART was started/re-started for clinical progression or CD4% < 25%. In 229 participants, HIV-1 proviral DNA was quantified by PCR from stored peripheral blood mononuclear cells from children who had received ≥ 24 weeks ART and two consecutive undetectable HIV-1 RNA 12–24 weeks apart. HIV-1 proviral DNA was compared between ART-Def and ART-96 W at week 96, and in all arms at week 248. Factors associated with HIV-1 proviral DNA levels were evaluated using linear regression. Findings Longer duration of ART was significantly associated with lower HIV-1 proviral DNA at both 96 (p = 0.0003) and 248 weeks (p = 0.0011). Higher total CD8 count at ART initiation was associated with lower HIV-1 proviral DNA at both 96 (p = 0.0225) and 248 weeks (p = 0.0398). Week 248 HIV-1 proviral DNA was significantly higher in those with positive HIV-1 serology at week 84 than those with negative serology (p = 0.0042). Intepretation Longer ART duration is key to HIV-1 proviral DNA reduction. Further understanding is needed of the effects of “immune-attenuation” through early HIV-1 exposure. Funding Wellcome Trust, National Institutes of Health, Medical Research Council.

Download Full-text

Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1609057113 ◽

2016 ◽

Vol 113 (31) ◽

pp. 8783-8788 ◽

Cited By ~ 145

Author(s):

Hiromi Imamichi ◽

Robin L. Dewar ◽

Joseph W. Adelsberger ◽

Catherine A. Rehm ◽

Una O’Doherty ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Mononuclear Cells ◽

Amplicon Sequencing ◽

Combination Antiretroviral Therapy ◽

Peripheral Blood Mononuclear ◽

Protein Coding ◽

Hiv Rna ◽

Single Genome ◽

Hiv 1 ◽

Rna Levels

Despite years of plasma HIV-RNA levels <40 copies per milliliter during combination antiretroviral therapy (cART), the majority of HIV-infected patients exhibit persistent seropositivity to HIV-1 and evidence of immune activation. These patients also show persistence of proviruses of HIV-1 in circulating peripheral blood mononuclear cells. Many of these proviruses have been characterized as defective and thus thought to contribute little to HIV-1 pathogenesis. By combining 5′LTR-to-3′LTR single-genome amplification and direct amplicon sequencing, we have identified the presence of “defective” proviruses capable of transcribing novel unspliced HIV-RNA (usHIV-RNA) species in patients at all stages of HIV-1 infection. Although these novel usHIV-RNA transcripts had exon structures that were different from those of the known spliced HIV-RNA variants, they maintained translationally competent ORFs, involving elements ofgag,pol,env,rev, andnefto encode a series of novel HIV-1 chimeric proteins. These novel usHIV-RNAs were detected in five of five patients, including four of four patients with prolonged viral suppression of HIV-RNA levels <40 copies per milliliter for more than 6 y. Our findings suggest that the persistent defective proviruses of HIV-1 are not “silent,” but rather may contribute to HIV-1 pathogenesis by stimulating host-defense pathways that target foreign nucleic acids and proteins.

Download Full-text

the Study to Evaluate the Safety of UB-421 in Combination With Antiretroviral Therapy (ART) and the Efficacy in Reduction of HIV Viral Load and Proviral DNA as Compared to ART Alone in ART-experienced Viremic HIV-1 Patients

Case Medical Research ◽

10.31525/ct1-nct04041362 ◽

2019 ◽

Author(s):

Keyword(s):

Viral Load ◽

Antiretroviral Therapy ◽

Hiv Viral Load ◽

Proviral Dna ◽

Hiv 1

Download Full-text

108. Selective Decay of Intact HIV-1 Proviral DNA on Antiretroviral Therapy

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.418 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S183-S183

Author(s):

Rajesh Gandhi ◽

Joshua Cyktor ◽

Ronald Bosch ◽

Hanna Mar ◽

Gregory Laird ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Panel Member ◽

Plasma Viremia ◽

Research Support ◽

Review Panel ◽

Proviral Dna ◽

Hiv 1 ◽

Over Time ◽

Residual Plasma Viremia ◽

Research Grant

Abstract Background HIV-1 proviruses persist in people on antiretroviral therapy (ART) but most are defective and do not constitute a replication-competent reservoir. The decay of infected cells carrying intact compared with defective HIV-1 proviruses has not been well-defined in people on ART. Methods We separately quantified intact and defective proviruses (using an intact proviral DNA assay), residual plasma viremia, and markers of inflammation and activation in people on long-term ART. Longitudinal measurements were done at three timepoints: timepoint 1 was a median of 7.1 years on ART; timepoint 2 was a median of 3.7 years later; timepoint 3 was a median of 5.5 years after timepoint 1 and a median 12 years after starting ART (Figure 1). Figure 1: Study timepoints Results Among 40 participants tested longitudinally from a median of 7.1 years to 12 years after ART initiation, intact provirus levels declined significantly over time (median half-life 7.1 years; 95% confidence interval [CI], 3.9, 18), whereas defective provirus levels did not decrease. The median half-life of total HIV-1 DNA was 41.6 years (95% CI, 13.6, 75). When we evaluated the change in proviral DNA per year, intact proviral DNA declined significantly more (p< 0.001) than defective proviral DNA (the latter did not change) (Figure 2). The proportion of all proviruses that were intact diminished over time on ART, from about 10% at the first on-ART timepoint to about 5% at the last timepoint (Figure 3). At timepoint 1, intact provirus levels on ART correlated with total HIV-1 DNA and residual plasma viremia, but there was no evidence for associations between intact provirus levels and inflammation or immune activation. Figure 2: Percent change in HIV-1 proviral DNA per year Figure 3: Total HIV-1 proviruses (grey bars) and the percentage of intact proviruses (red lines, displaying median, Q1, Q3) by timepoint. Conclusion Cells containing intact, replication-competent proviruses are selectively lost during suppressive ART. Defining the mechanisms involved should inform strategies to accelerate HIV-1 reservoir depletion. Disclosures Rajesh Gandhi, MD, Merck (Advisor or Review Panel member) Gregory Laird, PhD, Accelevir Diagnostics (Shareholder, Other Financial or Material Support, Employee) Albine Martin, PhD, Accelevir Diagnostics (Shareholder, Other Financial or Material Support, Employee) Bernard Macatangay, MD, Gilead (Grant/Research Support) Joseph J. Eron, MD, Gilead Sciences (Consultant, Research Grant or Support)Janssen (Consultant, Research Grant or Support)Merck (Consultant)ViiV Healthcare (Consultant, Research Grant or Support) Janet Siliciano, PhD, Gilead (Advisor or Review Panel member)US Military HIV Research Program (Advisor or Review Panel member) John Mellors, MD, Abound Bio (Shareholder)Accelevir Diagnostics (Consultant)Co-Crystal Pharmaceuticals (Shareholder)Gilead (Consultant, Grant/Research Support)Merck (Consultant)

Download Full-text