Long-term effects of early antiretroviral initiation on HIV reservoir markers: a longitudinal analysis of the MERLIN clinical study

Marta Massanella, Rachel A Bender Ignacio, Javier R Lama, Amélie Pagliuzza, Sayan Dasgupta, Ricardo Alfaro, Jessica Rios, Carmela Ganoza, Delia Pinto-Santini, Trupti Gilada, Ann Duerr, Nicolas Chomont, Marta Massanella, Rachel A Bender Ignacio, Javier R Lama, Amélie Pagliuzza, Sayan Dasgupta, Ricardo Alfaro, Jessica Rios, Carmela Ganoza, Delia Pinto-Santini, Trupti Gilada, Ann Duerr, Nicolas Chomont

Abstract

Background: Early antiretroviral therapy (ART) initiation (ie, within 3 months of infection) limits establishment of the HIV reservoir. However, the effect of early ART initiation on the long-term dynamics of the pool of infected cells remains unclear.

Methods: In this longitudinal analysis, we included cisgender men who have sex with men (MSM) and transgender women (aged 18-54 years) at high risk for HIV infection, enrolled in the ongoing longitudinal MERLIN study in Peru between Oct 28, 2014, and Nov 8, 2018. Participants were eligible if they had been infected with HIV less than 90 days before enrolment, and if they had cryopreserved peripheral blood mononuclear cell (PBMC) samples. Participants were stratified into three groups on the basis of whether they initiated ART at 30 days or less (acute group), at 31-90 days (early group), or more than 24 weeks (deferred group) after the estimated date of detectable infection. PBMC samples were collected before ART initiation and longitudinally for up to 4 years on ART. The main outcomes were to establish the size of the HIV reservoir before ART initiation and to assess the effect of the timing of ART initiation on the decay of the HIV reservoir over 4 years follow-up. We quantified viral load, and isolated CD4 cells to quantify total HIV DNA, integrated HIV DNA and 2-long terminal repeat circles. Longitudinal analysis of active and inducible HIV reservoirs were measured by quantifying the frequency of CD4 cells producing multiply-spliced HIV RNA ex vivo and after in-vitro stimulation with a tat/rev induced limiting dilution assay (TILDA). A mixed-effects model from the time of ART initiation was used to measure longitudinal decays in viral loads and each HIV reservoir measure in each of the three groups.

Findings: We included 56 participants in this analysis, all of whom were MSM: 15 were in the acute group, 19 were in the early group, and 22 were in the deferred group. Participants in all three groups had similar levels of all HIV reservoir markers before ART initiation. All participants, including those in the acute group, had a pool of transcriptionally silent HIV-infected cells before ART initiation, as indicated by a substantial increase in TILDA measures upon stimulation. Longitudinal analysis over 4 years of ART revealed a biphasic decay of all HIV persistence markers, with a rapid initial decline followed by a slower decay in all participants. During the first-phase decay, the half-lives of both total and integrated HIV DNA and TILDA measures were significantly shorter in the acute group than in the early and deferred groups. During the second-phase decay, HIV reservoir markers continued to decline only in participants in the acute group.

Interpretation: Participants who initiated ART within 30 days or less of HIV infection showed a steeper and more sustained decay in HIV reservoir measures, suggesting long-term benefit of acute ART initiation on reservoir clearance.

Funding: The US National Institutes of Health and the Canadian Institutes for Health Research.

Conflict of interest statement

Declaration of interests We declare no competing interests.

Figures

Figure 1:. Virological markers of HIV persistence…
Figure 1:. Virological markers of HIV persistence before ART initiation.
Plasma viral load (A), frequency of CD4 cells harbouring total HIV DNA (B), integrated HIV DNA (C), and 2-LTR circles (D), and frequency of CD4 cells producing msRNA spontaneously (TILDA ex vivo) or after 12 h stimulation (E) in participants stratified by whether they received ART within 30 days or less (acute group; n=9), at 31–90 days (early group; n=14), or more than 24 weeks (deferred group; n=19) after the EDDI. (F) Correlation matrix between the virological markers of HIV persistence. In A–E, samples with undetectable levels of virological markers (ie, less than the lower limit of the detection of the assay, which can vary according to the number of cells analysed), were considered as 0 for statistical analyses and are indicated as open circles. In A–D, p values were derived from the Kruskal-Wallis test, and in E, p values were derived from the Wilcoxon test for paired samples. In F, r values from Spearman correlation test are indicated in the bottom left part of the matrix and are reflected by the colour of the ellipses in the top right (blue indicates a positive correlation and red indicates a negative correlation); the shape of the ellipsis reflects the level of significance (ie, a narrower ellipsis reflects a lower p value), which are also included in the upper part of the matrix. Only significant correlations are shown in F. ART=antiretroviral therapy. TILDA=tat/rev induced limiting dilution assay. msRNA=multiply-spliced RNA. 2-LTR=2-long terminal repeat. EDDI=estimated date of detectable infection.
Figure 2:. Longitudinal analysis of viral load…
Figure 2:. Longitudinal analysis of viral load and HIV DNA decay during up to 4 years on ART
Longitudinal analysis of plasma viral loads (A, B), total HIV DNA (C, D), integrated HIV DNA (E, F), and 2-LTR circles (G, H) in enriched CD4 cells from participants stratified by whether they received ART within 30 days or less (acute group; n=15), at 31–90 days (early group; n=19), or more than 24 weeks (deferred group; n=22) after the estimated date of detectable infection. Samples collected immediately before ART initiation (0 weeks) were included. Participants were followed for up to 4 years on ART. For all decay slopes (A, C, E, and G), a two-phase segmentation model of viral load and HIV DNA was applied; for each group and each virological marker, the optimal change point was selected by use of the minimisation of the Akaike information criterion. Each dot represents a timepoint analysed for a given participant, and samples from the same individual are connected. The best fitted model for each virological marker is presented in red. The p values of slope 2 reflect a significant decay of a given marker. The t1/2 values of slopes 1 and 2 are indicated. In B, D, F, and H, comparisons of slopes 1 and 2 for each group and virological marker calculated from the models are shown; error bars indicate the SEs. ART=antiretroviral therapy. t1/2=half-life. 2-LTR=2-long terminal repeat.
Figure 3:. Longitudinal analysis of active (TILDA…
Figure 3:. Longitudinal analysis of active (TILDA ex vivo) and inducible (TILDA after stimulation) HIV reservoirs during up to 4 years on ART.
Longitudinal analysis of TILDA ex vivo (A, B) and after stimulation (C, D) measures in enriched CD4 cells from participants stratified by whether they received ART within 30 days or less (acute group; n=15), at 31–90 days (early group; n=19), or more than 24 weeks (deferred group; n=22) after the estimated date of detectable infection. Samples collected immediately before ART initiation (0 weeks) were included. Participants were followed for up to 4 years on ART. We applied a linear function for TILDA ex-vivo measures. We applied a two-phase segmentation model of TILDA after stimulation measures; for each group, the optimal change point was selected by use of the minimisation of the Akaike information criterion. For all decay slopes (A and C), each dot represents a timepoint analysed for a given participant, and samples from the same individual are connected; the best fitted model for each virological marker is represented in red. The t1/2 values of slopes 1 and 2 are indicated. Comparisons of slope 1 in B, and slopes 1 and 2 in D for each group and virological marker calculated from the models are shown; error bars indicate SEs. TILDA=tat/rev induced limiting dilution assay. ART=antiretroviral therapy. msRNA=multiply-spliced mRNA. t1/2=half-life.

References

    1. Finzi D, Blankson J, Siliciano JD, et al. Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat Med 1999; 5: 512–17.
    1. Siliciano JD, Kajdas J, Finzi D, et al. Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells. Nat Med 2003; 9: 727–28.
    1. Wong JK, Hezareh M, Günthard HF, et al. Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. Science 1997; 278: 1291–95.
    1. Finzi D, Hermankova M, Pierson T, et al. Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science 1997; 278: 1295–300.
    1. Chun TW, Engel D, Berrey MM, Shea T, Corey L, Fauci AS. Early establishment of a pool of latently infected, resting CD4(+) T cells during primary HIV-1 infection. Proc Natl Acad Sci USA 1998; 95: 8869–73.
    1. Little SJ, McLean AR, Spina CA, Richman DD, Havlir DV. Viral dynamics of acute HIV-1 infection. J Exp Med 1999; 190: 841–50.
    1. Fiebig EW, Wright DJ, Rawal BD, et al. Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS 2003; 17: 1871–79.
    1. Robb ML, Eller LA, Kibuuka H, et al. Prospective study of acute HIV-1 infection in adults in east Africa and Thailand. N Engl J Med 2016; 374: 2120–30.
    1. Crowell TA, Phanuphak N, Pinyakorn S, et al. Virologic failure is uncommon after treatment initiation during acute HIV infection. AIDS 2016; 30: 1943–50.
    1. Strain MC, Little SJ, Daar ES, et al. Effect of treatment, during primary infection, on establishment and clearance of cellular reservoirs of HIV-1. J Infect Dis 2005; 191: 1410–18.
    1. Ananworanich J, Chomont N, Eller LA, et al. HIV DNA set point is rapidly established in acute HIV infection and dramatically reduced by early ART. EBioMedicine 2016; 11: 68–72.
    1. Archin NM, Vaidya NK, Kuruc JD, et al. Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection. Proc Natl Acad Sci USA 2012; 109: 9523–28.
    1. Hocqueloux L, Avettand-Fénoêl V, Jacquot S, et al. Long-term antiretroviral therapy initiated during primary HIV-1 infection is key to achieving both low HIV reservoirs and normal T cell counts. J Antimicrob Chemother 2013; 68: 1169–78.
    1. Buzon MJ, Martin-Gayo E, Pereyra F, et al. Long-term antiretroviral treatment initiated at primary HIV-1 infection affects the size, composition, and decay kinetics of the reservoir of HIV-1-infected CD4 T cells. J Virol 2014; 88: 10056–65.
    1. Laanani M, Ghosn J, Essat A, et al. Impact of the timing of initiation of antiretroviral therapy during primary HIV-1 infection on the decay of cell-associated HIV-DNA. Clin Infect Dis 2015; 60: 1715–21.
    1. Hey-Cunningham WJ, Murray JM, Natarajan V, et al. Early antiretroviral therapy with raltegravir generates sustained reductions in HIV reservoirs but not lower T-cell activation levels. AIDS 2015; 29: 911–19.
    1. Koelsch KK, Boesecke C, McBride K, et al. Impact of treatment with raltegravir during primary or chronic HIV infection on RNA decay characteristics and the HIV viral reservoir. AIDS 2011; 25: 2069–78.
    1. Ananworanich J, Schuetz A, Vandergeeten C, et al. Impact of multi-targeted antiretroviral treatment on gut T cell depletion and HIV reservoir seeding during acute HIV infection. PLoS One 2012; 7: e33948.
    1. Leyre L, Kroon E, Vandergeeten C, et al. Abundant HIV-infected cells in blood and tissues are rapidly cleared upon ART initiation during acute HIV infection. Sci Transl Med 2020; 12: eaav3491.
    1. Colby DJ, Trautmann L, Pinyakorn S, et al. Rapid HIV RNA rebound after antiretroviral treatment interruption in persons durably suppressed in Fiebig I acute HIV infection. Nat Med 2018; 24: 923–26.
    1. Henrich TJ, Hatano H, Bacon O, et al. HIV-1 persistence following extremely early initiation of antiretroviral therapy (ART) during acute HIV-1 infection: an observational study. PLoS Med 2017; 14: e1002417.
    1. Whitney JB, Hill AL, Sanisetty S, et al. Rapid seeding of the viral reservoir prior to SIV viraemia in rhesus monkeys. Nature 2014; 512: 74–77.
    1. Okoye AA, Hansen SG, Vaidya M, et al. Early antiretroviral therapy limits SIV reservoir establishment to delay or prevent post-treatment viral rebound. Nat Med 2018; 14: 55.
    1. Cheret A, Nembot G, Mélard A, et al. Intensive five-drug antiretroviral therapy regimen versus standard triple-drug therapy during primary HIV-1 infection (OPTIPRIM-ANRS 147): a randomised, open-label, phase 3 trial. Lancet Infect Dis 2015; 15: 387–96.
    1. Puertas MC, Massanella M, Llibre JM, et al. Intensification of a raltegravir-based regimen with maraviroc in early HIV-1 infection. 2014; 28: 325–34.
    1. Yerly S, Perneger TV, Vora S, Hirschel B, Perrin L. Decay of cell-associated HIV-1 DNA correlates with residual replication in patients treated during acute HIV-1 infection. AIDS 2000; 14: 2805–12.
    1. Jones RB, Mueller S, O’Connor R, et al. A subset of latency-reversing agents expose HIV-infected resting CD4+ T-cells to recognition by cytotoxic T-lymphocytes. PLoS Pathog 2016; 12: e1005545.
    1. Peluso MJ, Bacchetti P, Ritter KD, et al. Differential decay of intact and defective proviral DNA in HIV-1-infected individuals on suppressive antiretroviral therapy. JCI Insight 2020; 5: e132997.
    1. Procopio FA, Fromentin R, Kulpa DA, et al. A novel assay to measure the magnitude of the inducible viral reservoir in HIV-infected individuals. EBioMedicine 2015; 2: 872–81.
    1. Lama JR, Brezak A, Dobbins JG, et al. Design strategy of the Sabes study: diagnosis and treatment of early HIV infection among men who have sex with men and transgender women in Lima, Peru, 2013–2017. Am J Epidemiol 2018; 187: 1577–85.
    1. Lama JR, Ignacio RAB, Alfaro R, et al. Clinical and immunologic outcomes after immediate or deferred antiretroviral therapy initiation during primary human immunodeficiency virus infection: the Sabes randomized clinical study. Clin Infect Dis 2020; 373: 795–99.
    1. WHO. Guideline on when to start antiretroviral therapy and on pre-exposure prophylaxis for HIV. Geneva: World Health Organization, 2015.
    1. Grebe E, Facente SN, Bingham J, et al. Interpreting HIV diagnostic histories into infection time estimates: analytical framework and online tool. BMC Infect Dis 2019; 19: 894–10.
    1. Vandergeeten C, Fromentin R, Merlini E, et al. Cross-clade ultrasensitive PCR-based assays to measure HIV persistence in large-cohort studies. J Virol 2014; 88: 12385–96.
    1. Abdi H, Williams LJ. Tukey’s honestly significant difference (HSD) test. In Salkind N, ed. Encyclopedia of Research Design. Thousand Oaks, CA: Sage, 2010: 1–5.
    1. European Centre for Disease Prevention and Control. HIV testing. Monitoring implementation of the Dublin Declaration on Partnership to fight HIV/AIDS in Europe and Central Asia: 2017 progress report. Stockholm: European Centre for Disease Prevention and Control, 2017.
    1. Gianella S, Wyl von V, Fischer M, et al. Effect of early antiretroviral therapy during primary HIV-1 infection on cell-associated HIV-1 DNA and plasma HIV-1 RNA. Antivir Ther 2011; 16: 535–45.
    1. Lee GQ, Reddy K, Einkauf KB, et al. HIV-1 DNA sequence diversity and evolution during acute subtype C infection. Nat Comms 2019; 10: 2737–11.
    1. Bayón-Gil Á, Puertas MC, Urrea V, et al. HIV-1 DNA decay dynamics in early treated individuals: practical considerations for clinical trial design. J Antimicrob Chemother 2020; 75: 2258–63.
    1. Goedert JJ, O’Brien TR, Hatzakis A, Kostrikis LG, Multicenter Hemophilia Cohort Study. T cell receptor excision circles and HIV-1 2-LTR episomal DNA to predict AIDS in patients not receiving effective therapy. AIDS 2001; 15: 2245–50.
    1. Panther LA, Coombs RW, Zeh JE, Collier AC, Corey L. Unintegrated circular HIV-1 DNA in the peripheral mononuclear cells of HIV-1-infected subjects: association with high levels of plasma HIV-1 RNA, rapid decline in CD4 count, and clinical progression to AIDS. J Acquir Immune Defic Syndr Hum Retrovirol 1998; 17: 303–13.
    1. Teo IA, Morlese J, Choi JW, Shaunak S. Reliable and reproducible LightCycler qPCR for HIV-1 DNA 2-LTR circles. J Immunol Methods 2002; 270: 109–18.
    1. Strain MC, Günthard HF, Havlir DV, et al. Heterogeneous clearance rates of long-lived lymphocytes infected with HIV: intrinsic stability predicts lifelong persistence. Proc Natl Acad Sci U S A 2003; 100: 4819–24.
    1. Takata H, Buranapraditkun S, Kessing C, et al. Delayed differentiation of potent effector CD8(+) T cells reducing viremia and reservoir seeding in acute HIV infection. Sci Transl Med 2017; 9: eaag1809.
    1. Deng K, Pertea M, Rongvaux A, et al. Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations. Nature 2015; 517: 381–85.
    1. Warren JA, Zhou S, Xu Y, et al. The HIV-1 latent reservoir is largely sensitive to circulating T cells. eLife 2020; 9: 3556.
    1. Zhou Y, Zhang H, Siliciano JD, Siliciano RF. Kinetics of human immunodeficiency virus type 1 decay following entry into resting CD4+ T cells. J Virol 2005; 79: 2199–210.
    1. Valle-Casuso JC, Angin M, Volant S, et al. Cellular metabolism is a major determinant of HIV-1 reservoir seeding in CD4+ T Cells and offers an opportunity to tackle infection. Cell Metab 2019; 29: 611–15.
    1. Gantner P, Pagliuzza A, Pardons M, et al. Single-cell TCR sequencing reveals phenotypically diverse clonally expanded cells harboring inducible HIV proviruses during ART. Nat Comms 2020; 11: 4089.
    1. Blankson JN, Finzi D, Pierson TC, et al. Biphasic decay of latently infected CD4+ T cells in acute human immunodeficiency virus type 1 infection. J Infect Dis 2000; 182: 1636–42.
    1. Mendoza P, Jackson JR, Oliveira TY, et al. Antigen-responsive CD4+ T cell clones contribute to the HIV-1 latent reservoir. J Exp Med 2020; 217: 6441–13.
    1. Scully EP, Gandhi M, Johnston R, et al. Sex-based differences in human immunodeficiency virus type 1 reservoir activity and residual immune activation. J Infect Dis 2018; 219: 1084–94.

Source: PubMed

Sponsorer og samarbejdspartnere

Medicinske tilstande

Narkotikainterventioner

3
Abonner