Defective HIV-1 proviral abundance and their immune effects in children and adolescents living with perinatal HIV-1

During suppressive antiretroviral therapy (ART), HIV-1 persists in long-lived resting memory CD4+ T cells of children and young adults with perinatal HIV-1 as both intact and defective proviral genomes. The intact, replication-competent proviruses contribute to the latent reservoir and are a lifelong barrier to cure. In perinatal HIV-1, the reservoir is established early and shaped by unique immunologic factors. A growing body of evidence suggests that while defective proviruses cannot contribute to rebound in the absence of ART, these proviruses are transcriptionally and translationally active, potentially leading to adverse immune effects. However, the frequency, composition, and potential immunologic effects of defective proviruses across pediatric age groups remain poorly understood. In this proposal, we aim to characterize the defective proviral reservoir in children and young adults living with perinatal HIV-1 by determining the abundance and sequences of proviruses that are maintained for years despite ART and assessing their ability to produce viral mRNA and proteins. This project leverages well-characterized, bio-banked peripheral blood mononuclear cell (PBMC) and plasma specimens from pediatric HIV-1 cohorts to systematically characterize the landscape of defective proviruses in perinatal infection from infancy through adolescence. Our hypothesis is that in longstanding treated perinatal HIV-1, defective proviruses are transcriptionally and translationally active and drive persistent residual HIV-1 viremia during ART, promoting immune activation and exhaustion despite replication incompetence. Defective proviruses may also serve to produce decoy viral proteins that elicit autologous neutralizing antibodies, thereby reducing the efficacy of autologous neutralization of the latent reservoir. We propose three specific aims. In Aim 1, we will quantify and characterize intact and defective proviruses across pediatric age groups using near full-length single genome sequencing. In Aim 2, we will assess the transcriptional activity of defective proviruses following ex vivo stimulation in co-culture for HIV-1 mRNA analyses and their correlation with immunologic and clinical measures, including markers of immune activation and exhaustion. We will then compare it to sequences from low level plasma viremia to determine whether defectives are the source. In Aim 3, we will perform the quantitative viral outgrowth assay (QVOA) with the ultrasensitive p24 Simoa assay to identify if high- and low-level p24 producing wells are harboring intact or defective proviruses. We will then determine whether env-pseudotyped virus derived from intact or defective proviral sequences can be neutralized with autologous plasma IgG. By integrating molecular virology and immunology profiling in a pediatric context, this study will generate novel insights into the role of defective proviruses in HIV-1 persistence in children. Our findings will inform the design of age-specific cure strategies and contribute to the broader goal of ART-free remission in children with perinatal HIV-1 towards a life free of co-morbidities. Project Number: 1R01AI198053-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of Allergy and Infectious Diseases (NIAID) | Principal Investigator: Deborah Persaud | Institution: JOHNS HOPKINS UNIVERSITY, BALTIMORE, MD | Award Amount: $779,616 | Activity Code: R01 | Study Section: HIV Immunopathogenesis and Vaccine Development Study Section[HIVD] View on NIH RePORTER: https://reporter.nih.gov/project-details/1R01AI19805301