Morgane Rolland

The two parallel antibody-mediated prevention (AMP) efficacy trials evaluated whether intravenous infusion of the anti-CD4 binding site broadly neutralizing antibody VRC01 prevents HIV-1 acquisition. Here, we analyzed HIV-1 acquisition in AMP through the week 104 final study visit. Against viruses considered highly sensitive to VRC01 [80% inhibitory concentration (IC ₈₀ ) < 1 microgram/milliliter], VRC01 prophylaxis maintained cumulative prevention efficacy of 66.3% (95% confidence interval: 32.4, 83.2%), suggesting that the antibody successfully blocked or cleared these infections. In the post–week 80 period (after the final dose at week 72), HIV diagnosis and resistance to VRC01 were more frequent and greater in the VRC01 groups versus placebo. For instance, more HIV diagnoses with viruses considered moderately sensitive or resistant to VRC01 (IC ₈₀ ≥ 5 microgram/milliliter) were made in the VRC01 groups compared with placebo groups (11 versus 1). Plausibly, as in vivo VRC01 concentration waned, suppressed viruses—often evolving greater resistance because of selective pressure—emerged as detectable infections. Our findings suggest that, whereas single antibodies can block sensitive strains, multiple antibodies are likely required to prevent both viral escape and breakthrough infections.

Broadly neutralizing antibodies (bnAbs) show promise in HIV prevention, yet viral escape remains a challenge. In the Antibody-Mediated Prevention (AMP) trials, the CD4 binding site (CD4bs) bnAb VRC01 blocked acquisition by VRC01-sensitive strains. However, its influence on viral evolution post acquisition is not fully understood. Here we analysed 11,730 HIV envelope sequences generated during the AMP trials from 47 participants, identifying VRC01-mediated de novo escape mutations in 8 of 26 VRC01-treated participants but none in 21 placebo participants. These mutations were found at very low frequencies (<1%) in globally circulating viruses, suggesting that they may confer fitness costs. Escape mutations, primarily located in the Loop-D and β23/V5 regions of Env, conferred cross-resistance to several CD4bs bnAbs; however, more potent CD4bs bnAbs such as N6 and 1–18 largely retained their activity. Our findings demonstrate that prophylactic VRC01 can select for viral escape after infection, underscoring the need for next-generation bnAbs with improved breadth and potency to enhance durability and efficacy of antibody-based HIV prevention.

Background: The Antibody Mediated Prevention trials (HVTN 703 and HVTN 704) demonstrated that infusions of the bnAb VRC01 prevented HIV-1 acquisition with viruses sensitive to VRC01 neutralization. We evaluated how VRC01 epitope distances differed across groups in the trials. Methods: We calculated VRC01 epitope distances (a 3D structure informed measure of how the VRC01 epitope in a sequence differs from that epitope in known VRC01 sensitive strains) to compare >35,000 Envelopes sampled from 172 participants with mostly subtype C viruses in HVTN 703 and subtype B in HVTN 704. Results: At the first visit with detectable HIV-1, we found fewer distinct VRC01 epitopes in the sequences from participants in the VRC01 high-dose group in HVTN 704 (p=0.054), suggesting that some epitope variants were blocked in these participants who harbored subtype B viruses. In both trials, VRC01 epitope distances were significantly larger in the VRC01 high-dose groups than in the placebo groups (p≤0.010). Moreover, sequences sampled in the first month after diagnosis showed that the rate of change in VRC01 epitope distances was significantly higher in the VRC01 groups than in the placebo in the HVTN 703 trial (p≤0.036). Conclusions: These findings show the impact of sieve acquisition (variants blocked among subtype B viruses) and post-acquisition (stronger impact of VRC01-mediated escape in subtype C) effects, highlighting a complex intersection between HIV-1 subtypes, escape pathways and antibody-mediated prevention. The differential pressure exerted by VRC01 on subtype B vs. C viruses emphasizes that escape pathways need to be considered when selecting bnAbs for clinical trials.

To identify strategies for augmenting vaccine immunogenicity, we compared a pox-protein prime-boost regimen comprising recombinant modified vaccinia virus Ankara and multimeric HIV-1 Env gp145, adjuvanted with Army Liposomal Formulation (ALF) either adsorbed to aluminum salt (ALFA) or formulated with the QS-21 saponin (ALFQ), in rhesus macaques. ALFQ promoted greater magnitude and more durable humoral and cellular immune responses than ALFA, which exhibits similar immunogenicity to aluminum-based adjuvants. Peak Env-specific CD4 ⁺ T cell responses assessed by intracellular cytokine staining were 10-fold greater with ALFQ, and CD8 ⁺ T cell responses were unexpectedly robust, averaging greater than 1%. ALFQ induced higher levels of several immunostimulatory cytokines in plasma, which correlated with adaptive immune responses. However, vaccination did not protect against heterologous intrarectal challenge with transmitted/founder SHIV-CH505. We provide evidence that CH505 Env may maintain a relatively closed conformation, rendering it less susceptible to targeting by Fc-mediated antibody functions. Overall, ALFQ is a promising adjuvant to improve antibody and T cell response magnitude. IMPORTANCE: An effective and durable vaccine preventing HIV-1 acquisition is urgently needed to end the HIV-1 pandemic. To date, of the nine vaccine efficacy trials conducted in humans, only the RV144 vaccine trial demonstrated efficacy in reducing infections, although immune responses waned rapidly. We evaluated a modified HIV-1 vaccine regimen incorporating next-generation adjuvants to improve immune responses and vaccine efficacy in a gold standard, pre-clinical primate model. Adjuvanted protein boosting markedly increased antibody, T cell, and pro-inflammatory response magnitude. These data, combined with the adjuvant’s strong safety and immunogenicity track record in clinical trials, indicate that novel adjuvants represent a promising strategy for improving immune responses to protein immunogens. Future vaccine regimens against HIV-1 and other pathogens for which eliciting robust immunity has been difficult may benefit from incorporating these or related next-generation adjuvants.

Understanding the selective forces acting upon HIV early in infection is crucial to design prevention strategies. By leveraging deep sequencing and the short diagnostic intervals of the FRESH and RV217 cohorts between the last-negative and first-positive RNA tests (median 4 days), we captured a precise and early snapshot of acute HIV infection. The frequency of multiple transmitted viruses of 37% in these as well as placebo recipients from the AMP trials (NCT02716675 and NCT02568215) was higher than previously published, with the true frequency likely to be higher. The relative abundance of lineages fluctuated substantially over time in two-thirds of the multilineage infections, generating uncertainty in identifying the specific viruses that were transmitted and founding the infection. At the population level, viral populations exhibited limited diversity and selection on the Gag and Env proteins at the earliest times examined, with sites inferred to be undergoing negative selection most evident. These data may help explain vaccination failures and provide new targets for prevention.

In the antibody mediated prevention (AMP) trials, the broadly neutralizing antibody (bNAb) VRC01 demonstrated protective efficacy against susceptible HIV strains. To understand how VRC01 shaped breakthrough infections, deep sequencing was performed on 172 participants (>100,000 gag-Δpol and rev-env-Δnef sequences), at diagnosis and over time, in the placebo and treatment arms of the African (HVTN703/HPTN081; NCT02568215) and Americas/Europe (HVTN704/HPTN085; NCT02716675) cohorts. A high frequency of multilineage infections was detected (38%), including co-infection with both VRC01 sensitive and resistant viruses. This high frequency is largely accounted for by low-abundance lineages. Although VRC01 does not significantly affect the genetic transmission bottleneck compared to placebo, higher VRC01 doses trend towards greater VRC01 neutralization differences among co-infecting lineages. Two-thirds of multilineage infections showed evidence of recombination at the diagnostic timepoint. In the treatment group there is evidence of recombinant viruses preferentially inheriting resistance-associated mutations. This study provides critical insights into viral genetic and antigenic diversity that needs to be targeted to achieve protection, and highlights the role of recombination in facilitating escape.

HIV serologic responses measured by clinical screening assays may be blunted when antiretroviral treatment (ART) suppresses HIV replication from the initial infection stages, with further decay following long-term treatment. Sensitivity may vary according to the timing of ART initiation after HIV acquisition, antigens (Ags) utilized to detect anti-HIV antibodies (Abs), and HIV subtype. We obtained samples from long-term ART-suppressed persons with HIV (PWH) who started ART at acute/early or during chronic infection, from blood donors with undetectable HIV RNA and nonreactive serology, and from blood donors with positive RNA and reactive serology (presumably untreated infections) spanning multiple HIV subtypes to compare patterns of serologic reactivity using two Ag/Ab screening assays (Alinity and VITROS). We found that earlier ART initiation was associated with progressively lower signal-to-cutoff ratios (S/CO) in both assays. Serologic reactivity in clinical samples from participants initiating ART at Fiebig 2 was somewhat lower for CRF01_AE (67%) than other HIV subtypes (91%) on the Alinity platform. In the late-ART initiation group, reactivity was high for both assays despite long-term treatment, with higher S/CO values in samples from blood donors with presumably untreated infection. We observed no strong evidence of S/CO waning >96 weeks after ART initiation in the early-ART initiation group. Our findings suggest potential limitations for HIV infection ascertainment in clinical samples from long-term treated PWH who started ART at early infection stages using currently approved serologic tests. IMPORTANCE: This manuscript increases our understanding of how the timing of initiation of HIV treatment affects our ability to detect the infection using commercial blood tests that measure HIV antigens or antibodies. Being able to detect HIV is important for clinical diagnostics and blood screening, and HIV is not as easily detected in persons who begin therapy shortly after infection using serological tests. In contrast to prior work, we show that current clinical HIV tests have stable reactivity over time in persons on long-term HIV treatment.

Accurate timing estimates of when participants acquire HIV in HIV prevention trials are necessary for determining antibody levels at acquisition. The Antibody-Mediated Prevention (AMP) Studies showed that a passively administered broadly neutralizing antibody can prevent the acquisition of HIV from a neutralization-sensitive virus. We developed a pipeline for estimating the date of detectable HIV acquisition (DDA) in AMP Study participants using diagnostic and viral sequence data. Using a Bayesian strategy that combines three streams of data (REN [rev/vpu/env/Δnef] sequence, GP [gag/Δpol] sequence, and diagnostic) where their 95% credible intervals overlap based on pre-specified criteria and decision rules. We evaluated the performance of our AMP pipeline using PacBio viral sequence data from 41 participants across two prospective acute HIV acquisition cohort studies, FRESH and RV217, with twice-weekly sampling. These cohort studies enrolled young women in South Africa and men and women in Kenya and Thailand, respectively, with a high likelihood of HIV acquisition. In evaluating performance, “true DDA” was the center of bounds between last-negative and first-positive RNA diagnostic tests (median time 4 days, range 2–7 days); bias was the mean difference between estimated and true DDA. Using diagnostic data alone yielded timing estimates with a bias of 2.4 days and root mean square error (RMSE) of 7.9 days. These results were improved using sequence + diagnostic data (bias 1.5 days, RMSE 6.9 days), as well as by restricting sequence-based estimation to samples from ≤5 weeks post-DDA (bias 0.2 days, RMSE 7.8 days). IMPORTANCE: In HIV prevention trials, accurate timing estimates of when individual participants acquire HIV can be used to estimate antibody levels at the time of acquisition, which is useful for projecting antibody levels needed for prevention. The results we report here suggest that if sequence-based estimation of acquisition timing is used in future clinical trials of combination broadly neutralizing antibody (bnAb) regimens or multispecific bnAbs for HIV prevention, a sampling frequency of at least monthly is needed. Moreover, in the samples analyzed here, we observed less bias in sequence-based timing estimation for samples taken <5 weeks post-DDA. This observation is consistent with the timing of immune-driven selective pressures that may negatively impact the power to detect acquisition sieve effects.

Introduction: Cases of spontaneous control of HIV‐1 can help define strategies to induce remission. Since the identification of viral control in the absence of treatment typically occurs after a prolonged period post‐HIV‐1 diagnosis, our knowledge of the early events after HIV‐1 acquisition that led to viral control is limited. Methods: The RV217 prospective cohort enrolled 2276 participants in East Africa (Kenya, Uganda, Tanzania) and Thailand between 2009 and 2015. We analysed HIV‐1 sequences and clinical data from 102 individuals who were diagnosed with acute HIV‐1 infection and had a negative HIV‐1 RNA test in the week before. We focused on 69 participants with longitudinal follow‐up and identified viraemic controllers who maintained viral loads n = 6), or A1 recombinant strains ( n = 4), with one living with subtype D; 10 were from Kenya, one from Uganda. Controllers had significantly slower CD4+ T cell decline ( p = 0.028) and higher Natural Killer (NK) cell counts ( p = 0.047) than non‐controllers, but none carried human leukocyte antigen (HLA) alleles previously reported to be associated with viral control. Peak viraemia was recorded at an average of 541 million copies/ml with no difference between controllers and non‐controllers ( p = 0.97). Viral loads became lower in controllers (3459 copies/ml) than in non‐controllers (23,157 copies/ml) as early as nadir viraemia ( p = 0.009), with a more significant difference observed at set point (1069 vs. 24,084 copies/ml, respectively; p <0.0001). Conclusions: Our findings confirm the role of HIV‐1 subtype A1 in mediating viral control. The fact that controllers showed high viral loads in acute infection indicates that these viruses were not intrinsically impaired for replication, underlining the intersection between host immunity and favourable genotypes in the subsequent control of HIV‐1. These data suggest that conducting HIV‐1 remission studies in East Africa could provide favourable conditions to achieve durable post‐treatment control of viraemia.

The Janssen Ebola virus (EBOV) vaccine consists of the adenovirus type 26 vector encoding the EBOV glycoprotein (GP) (Ad26.ZEBOV) and the modified vaccinia Ankara (MVA) vector encoding GP from EBOV, Sudan virus, and Marburg virus and nucleoprotein from Tai Forest virus (MVA-BN-Filo) administered 8 weeks later. We conducted a systems immunology analysis of antibody-mediated and cellular immune responses induced after two immunizations with either vaccine used first. The response to vaccination was EBOV GP specific and defined by high antibody binding, Fc effector, and neutralizing responses with CD4 T cell responses also contributing. The vaccine-induced antibody profile did not distinguish people living with or without HIV-1. Samples from 48 survivors and 121 contacts from the 2007 Ugandan Bundibugyo virus epidemic also showed minimal cross-reactivity to other filovirus proteins after infection and exposure. The lack of cross-reactivity suggests that different multivalent vaccine candidates are required to provide broad protection across filoviruses.