Biology subjects

Fray, E. J.

Publications and source records attributed to Fray, E. J..

5 recordsLinked to original sources

bioRxiv2025

Inhibitory potential of autologous neutralizing antibodies sets quantitative limits on the rebound-competent HIV-1 reservoir

HIV-1 cure requires preventing viral rebound after treatment interruption, but quantitative criteria defining the rebound-competent reservoir are lacking. We studied individuals undergoing observational treatment interruption without confounding interventions to identify virologic and immunologic determinants of rebound. In 9 of 13 participants, rebound viruses were genetically identical or similar to proviruses in circulating resting CD4+ T-cells. We found no evidence of recombination among rebound sequences. Instead, resistance to autologous neutralizing antibodies (aNAbs) was a critical determinant of viral rebound. Increased suppression of viral outgrowth by contemporaneous IgG isolated from plasma was correlated with longer time to rebound. Using inhibitory potential (IP), the log reduction in single-round infection at physiologic IgG concentrations, we defined quantitative limits governing rebound-competency with respect to contemporaneous aNAbs. Contemporaneous IgG antibodies inhibited different reservoir variants with a wide range of IP values (0.4-8.2 logs), whereas rebound viruses were minimally inhibited (0.5-2.8 logs), indicating that inhibition by even up to 2.8 logs (631-fold) cannot prevent rebound. Longitudinal analyses revealed that waning aNAb potency over time on ART allows previously neutralized variants to gain rebound potential, consistent with the finding that rebound can come from variants deposited in the reservoir at different pre-ART time points. Thus, rebound competency is a dynamic, immune-governed property defined by quantitative immunologic constraints, including those exerted by aNAbs. SIGNIFICANCE STATEMENTPreventing viral rebound after treatment interruption is the goal of HIV-1 cure research, but the latent proviruses responsible remain undefined. Although rebound is initiated in lymphoid tissues, we found rebound viruses are genetically similar to proviruses in circulating resting CD4+ T-cells. Rebound is not explained by recombination and is not solely from proviruses seeded at treatment initiation. Instead, rebound potential is governed by autologous neutralizing antibodies (aNAbs). We define a quantitative threshold of aNAb-mediated inhibition identifying reservoir variants with rebound potential. During treatment, waning aNAb levels allow previously neutralized variants to become rebound-competent. Thus rebound-competency is not a static property, but a dynamic immune-governed feature. Durable aNAb responses against all rebound-competent reservoir variants may be required for functional HIV-1 cure.

immunology↗

bioRxiv2025

Longitudinal transcriptomic analysis of SIV-infected rhesus macaques reveals peripheral immune dynamics throughout untreated SIV infection and long-term antiretroviral therapy

Developing a working knowledge of immune dynamics during prolonged infection and treatment has become critical for both advancing HIV cure strategies and understanding non-AIDS comorbidities, given rises in the age and average time spent on antiretroviral therapy (ART) among people living with HIV. However, at present, we do not fully appreciate the ways in which prolonged suppressive therapy influences immune function. Toward addressing this key knowledge gap comprehensively, we applied single-cell RNA-sequencing (scRNA-seq) to longitudinally profile peripheral blood mononuclear cells from SIV-infected non-human primates longitudinally. Our data reveal significant immune shifts during acute and chronic infection, as well as over five years of subsequent ART. We observe a decline in CD4+ T cells and an increase in aberrant B cells and CD16+ monocytes during untreated chronic infection, as well as widespread dampened transcriptional activity. Further, we uncover transcriptional signatures suggestive of unresolved immune dysregulation during long-term suppressive therapy - most prominently among myeloid cell populations. By examining concurrent measurements of intact proviral DNA, we link peripheral responses to reservoir size via IPDA. We furthermore identify ribosomal-associated pathways as key differentiators of infection stage, treatment status, and time on ART. Finally, we tested whether previously published transcriptional correlates of differential outcomes (e.g. viral rebound, vaccine efficacy) changed over time on ART. Overall, our findings capture dynamic immune remodeling from acute infection through long-term ART, highlighting complexities in achieving complete immune recovery that may influence future therapeutic strategies.

immunology↗

bioRxiv2025

Superinfection with intact HIV-1 results in conditional replication of defective proviruses and nonsuppressible viremia in people living with HIV-1

During replication of some RNA viruses, defective particles can spontaneously arise and interfere with wild-type (WT) virus replication. Recently, engineered versions of these defective interfering particles (DIPs) have been proposed as an HIV-1 therapeutic. However, DIPs have yet to be reported in people with HIV-1 (PWH). Here, we find DIPs in PWH who have a rare, polyclonal form of non-suppressible viremia (NSV). While antiretroviral therapy (ART) rapidly reduces viremia to undetectable levels, some individuals experience sustained viremia due to virus production from cell clones harboring intact or defective proviruses. We characterized the source of NSV in two PWH who never reached undetectable viral load despite ART adherence. Remarkably, in each participant, we found a diverse set of defective viral genomes all sharing the same fatal deletions. We found that this paradoxical accumulation of mutations by viruses with fatal defects was driven by superinfection with intact viruses, resulting in mobilization of defective genomes and accumulation of additional mutations during untreated infection. We show that these defective proviruses interfere with WT virus replication, conditionally replicate, and, in one case, have an R0 > 1, enabling in vivo spread. Despite this, clinical outcomes show no evidence of a beneficial effect of these DIPs.

microbiology↗

bioRxiv2023

Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4+ T cells

HIV can persist in a latent form as integrated DNA (provirus) in resting CD4+ T cells of infected individuals and as such is unaffected by antiretroviral therapy (ART). Despite being a major obstacle for eradication efforts, the genetic variation and timing of formation of this latent reservoir remains poorly understood. Previous studies on when virus is deposited in the latent reservoir have come to contradictory conclusions. To reexamine the genetic variation of HIV in CD4+ T cells during ART, we determined the divergence in envelope sequences collected from 10 SIV infected rhesus macaques. We found that the macaques displayed a biphasic decline of the viral divergence over time, where the first phase lasted for an average of 11.6 weeks (range 4-28 weeks). Motivated by recent observations that the HIV-infected CD4+ T cell population is composed of short- and long-lived subsets, we developed a model to study the divergence dynamics. We found that SIV in short-lived cells was on average more diverged, while long-lived cells harbored less diverged virus. This suggests that the long-lived cells harbor virus deposited starting earlier in infection and continuing throughout infection, while short-lived cells predominantly harbor more recent virus. As these cell populations decayed, the overall proviral divergence decline matched that observed in the empirical data. This model explains previous seemingly contradictory results on the timing of virus deposition into the latent reservoir, and should provide guidance for future eradication efforts. Significance statementHIV can persist in a latent reservoir unaffected by antiretroviral drugs. The genetic variation of this latent virus population is a major obstacle for eradication efforts, but also a clue to when HIV variants are deposited in the reservoirs. Unfortunately, previous studies assessing when the virus was deposited in latent reservoirs have come to contradictory conclusions. Here, we propose SIV proviral DNA exists in both short- and long-lived CD4+ T cells, and that these two cell subsets harbor different genetically diverged virus populations. Our model explains the contradictory findings and shows that when CD4+ T cells decay under effective drug treatment, which prevents virus replication, the resulting virus divergence decreases and recapitulates observed data. This knowledge should help in improving future eradication efforts.

microbiology↗

bioRxiv2023

Assessing the effect of antibody responses on viral rebound dynamics in postnatally SHIV-infected infant Rhesus macaques

AO_SCPLOWBSTRACTC_SCPLOWWhile the benefits of early antiretroviral therapy (ART) initiation in perinatally infected infants are well documented, early ART initiation is not always possible in postnatal pediatric HIV infections, which account for the majority of pediatric HIV cases worldwide. The timing of onset of ART initiation is likely to affect the size of the latent viral reservoir established, as well as the development of adaptive immune responses, such as the generation of neutralizing antibody responses against the virus. How these parameters impact the ability of infants to control viremia and the time to viral rebound after ART interruption is unclear. To gain insight into the dynamics, we utilized mathematical models to investigate the effect of time of ART initiation via latent reservoir size and autologous virus neutralizing antibody responses in delaying viral rebound when treatment is interrupted. We used an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model that mimics breast milk HIV transmission in human infants. Infant Rhesus macaques (RMs) were orally challenged with SHIV.C.CH505 375H dCT and either given ART at 4-7 days post-infection (early ART condition), at 2 weeks post-infection (intermediate ART condition), or at 8 weeks post-infection (late ART condition). These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We develop a stochastic mathematical model to investigate the joint effect of latent reservoir size, the autologous neutralizing antibody potency, and CD4+ T cell levels on the time to viral rebound and control of post-rebound viral loads. We find that the latent reservoir size is an important determinant in explaining time to viral rebound by affecting the growth rate of the virus. The presence of neutralizing antibodies also can delay rebound, but we find this effect for high potency antibody responses only.

immunology↗