Simian-Human Immunodeficiency Virus SHIV.C.CH505 Persistence in ART-Suppressed Infant Macaques Is Characterized by Elevated SHIV RNA in the Gut and a High Abundance of Intact SHIV DNA in Naive CD4 ⁺ T Cells

Abstract

Mother-to-child transmission of HIV-1 continues to cause new pediatric cases of infection through breastfeeding, a setting where it is not always possible to initiate early antiretroviral therapy (ART). Without novel interventions that do not rely on daily ART, HIV-1 infected children face lifelong medications to control infection. A detailed analysis of virus persistence following breastmilk transmission of HIV-1 and ART has not been performed. Here, we used infant rhesus macaques orally-infected with simian/human immunodeficiency virus (SHIV.C.CH505) to identify cellular and anatomical sites of virus persistence under ART. Viral DNA was detected at similar levels in blood and tissue CD4+ T cells after a year on ART, with virus in blood and lymphoid organs confirmed to be replication-competent. Viral RNA:DNA ratios were elevated in rectal CD4+ T cells compared to other sites (P≤0.0001), suggesting the gastrointestinal tract is an active site of virus transcription during ART-mediated suppression of viremia. SHIV.C.CH505 DNA was detected in multiple CD4+ T cell subsets, including cells with a naïve phenotype (CD45RA+CCR7+CD95-). While the frequency of naïve cells harboring intact provirus was lower than in memory cells, the high abundance of naïve cells in the infant CD4+ T cell pool made them a substantial source of persistent viral DNA (approximately 50% of total CD4+ T cell reservoir), with an estimated 1:2 ratio of intact provirus to total viral DNA. This viral reservoir profile broadens our understanding of virus persistence in a relevant infant macaque model and provides insight into targets for cure-directed approaches in the pediatric population. IMPORTANCE Uncovering the sanctuaries of the long-lived HIV-1 reservoir is crucial to develop cure strategies. Pediatric immunity is distinct from that of adults, which could alter where the reservoir is established in infancy. Thus, it is important to utilize pediatric models to inform cure-directed approaches for HIV-1-infected children. We used an infant rhesus macaque model of HIV-1 infection via breastfeeding to identify key sites of viral persistence under antiretroviral therapy (ART). The gastrointestinal tract was found to be a site for low-level viral transcription during ART. We also show naïve CD4+ T cells harbored intact provirus and were a major contributor to blood and lymphoid reservoir size. This is particularly striking as memory CD4+ T cells are generally regarded as the main source of latent HIV/SIV infection of adult humans and rhesus macaques. Our findings highlight unique features of reservoir composition in pediatric infection that should be considered for eradication efforts.

New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention, and Cure

“…Nearly all natural routes of HIV-1 acquisition result from transmission across mucosal surfaces, the exceptions being intrauterine and intravenous infections. Previously, we showed that SHIVs BG505, CH505, and D.191859 can be transmitted efficiently across rectal, vaginal, and oral mucosae ( 17 , 35 ), resulting in productive clinical infection with virus replication kinetics and plasma virus titers indistinguishable from human infections by HIV-1 ( 69 , 70 ). Penile acquisition is another important route of HIV-1 transmission in humans ( 78 ), and Fig.…”

“…Simian-human immunodeficiency virus (SHIV) infection of Indian rhesus macaques (RMs) is an important outbred animal model for studying HIV-1 transmission, prevention, immunopathogenesis and cure (1)(2)(3). Such research is especially timely, given recent progress with active and passive immunization (4)(5)(6)(7)(8)(9)(10)(11) and novel approaches to HIV-1 cure (https://www.niaid.nih.gov/diseases-conditions/hiv-cure-research) (12)(13)(14)(15)(16)(17)(18), all of which can benefit from rigorous testing and iterative refinement in animal models. Given the multifaceted roles of HIV-1 envelope (Env) in cell tropism and virus entry, and as a target for neutralizing and non-neutralizing antibodies, the particular features of HIV-1 Envs that are selected for SHIV construction and analysis are of paramount importance.…”

Rapid progression is associated with lymphoid follicle dysfunction in SIV-infected infant rhesus macaques

“…Thus, reduced Tfh in RP infants, and associated reductions in active germinal centers, may also be attributed to spatially altered CXCL13 expression impaired homing of T cells into B cell follicles. Specific infection of Tfh cells by HIV and SIV has been observed in both adult and infant macaques [ 53 – 56 ], yet rather than direct infection driving Tfh loss, infected Tfh cells are reported to serve as sanctuaries for viral persistence [ 53 ]. While RNAscope identified similar levels of cell free virus within B cell follicle light zones between RP and TyP infants ( Fig 9 ), the majority of SIV-infected cells, as well as the brightest areas of MX1 staining, were observed on the border of the B cell follicle, which can be populated by Tfh as well as other CD4 T cells.…”

Rapid progression is associated with lymphoid follicle dysfunction in SIV-infected infant rhesus macaques

“…While there is evidence for both expansion as well as early depletion of Tfh cells during SIV infection (53, 54), it is poorly understood whether loss of Tfh cells, and their precursors, may be attributed to direct killing from SIV or to aberrant inflammatory signaling driving apoptosis (46,54). Selective infection of Tfh cells by HIV and SIV has been observed in both adult and infant macaques (55)(56)(57)(58), yet rather than direct infection driving Tfh loss, infected Tfh cells are reported to serve as sanctuaries for viral persistence (55). Interestingly, adult macaques exhibiting a more rapid disease progression have trended toward lower proviral DNA levels in Tfh compared to those with more typical disease severity (54).…”