Utilizing the pediatric SIV macaque model of HIV, the data generated are informative for pediatric HIV remission by early interventions, based on our novel findings: 1) dynamic of tissue viral reservoirs and delayed onset of viral genome integration in neonates at the early time stage of SIV infection; 2) rapid suppression of viral replication and effective decay of nonintegrated viral DNA in infants by early ART combined with an integrase inhibitor at or near the timepoint of proviral reservoir seeding; and 3) complete eradication of reside reservoir and sustained virologic remission achieved by “long-term” intervention initiated prior to viral genome integration. The magnitude and persistence of proviral reservoirs, which are difficult to eradicate with current therapy, may determine the outcome of treatment interventions. If effective treatment is initiated prior to proviral reservoir seeding, sustained virologic remission or even a cure may be possible for pediatric HIV infection. In summary, ART-free viral remission may be achieved in a proportion of HIV-infected infants by rational early treatment regimens.
Given a unique immune system in developing neonatal infants, immune maturation, viral susceptibility, viral reservoir seeding in neonates exposed to HIV might differ from those in adults 24, 25. Compared to unstable nonintegrated viral DNAs which may yield productive viral particles in a limited range of early HIV/SIV infection 30, 31, 32, 33, 34, 35 even the presence of integrase inhibitors 34, 35. HIV genome integration is an essential hallmark for stable HIV replication and persistence, as integrated proviral DNA is the dominant template for persistent HIV replication 36, and difficult to eradicate by conventional cure strategies 37, 38, 39. Insight into the timing and onset of proviral reservoir seeding in infants exposed to HIV is critical for providing a clue in pediatric HIV therapy. Current scalable assays to measure replication-competent proviral reservoirs are difficult to reflect the bona fide functional provirus size and overall tissue distribution in the body 40, 41, 42, 43, 44, 45, 46, 47, 48. For example, a small proportion of proviruses might exist in the body during long-term treatment, not limited to peripheral blood and lymphoid tissue samples. Viral reservoirs examined by Quantitative Viral Outgrowth Assays (QVOA) or Tat/rev Induced Limiting Dilution Assays (TILDA) may not fully reactivated by stimulators, especially when the proviruses are located in the "gene desert" sites of chromosomes enriched in repressive chromatin marks 45, 49, 50, 51. Near full-length Individual proviral sequencing (FLIPS) and intact proviral DNA assay (IPDA) may also not accurately distinguish the functional proviral reservoir, as indicated by existence of intact proviral “quasispecies” and viral polymorphism 52, 53, difficulties to predict production of replication-competent virions in the process of viral life cycle of HIV/SIV, functionality of viral genomes by various depletions and mutations 47, 54, 55, 56, or potential functional revertant mutation from deficient viral genome 57, 58, thereby lack of absolute gold standard approach to assess the genuine size of proviral reservoirs in the body 59. Although qPCR may overestimate the viral reservoirs because of defective proviruses, total proviral DNA levels still reflects approximate size of intact viral genome, as intact viral genome accounts for ~11.7% in HIV+ patients and exists with higher fraction in SIV+ macaques on cART 60, 61. Here we combined a ddPCR-based total viral RNA assay with nested qPCR for proviral DNA quantification targeting multiple repetitive Alu DNA islands on macaque chromosomes, providing a rapid and sensitive approach to generate comparable data in the assessment of proviral reservoir seeding and size from various tissues. Our data show that cell-associated SIV DNA/RNA is essentially detected in systemic and lymphoid tissues as early as 1dpi in neonates once infected with SIV at birth, concomitant with detectable plasma viral load in ~50% neonates at 1dpi. These data suggest that detectable plasma viral load at very early SIV infection is irrelevant to contamination of virus inoculation due to rapid viral replication. Unexpectedly, viral genome integration confers distinct patterns, as indicated by integrated proviral DNA is not detected until day 3 of infection, and only detectable in one of five infant animals (axillary LN and tonsil only in same infant) at this time point, suggesting routine PBMC samples may not be adequate to assess the proviral reservoir seeding. In such a scenario, nonintegrated viral DNA is able to produce virus particles 31, 32, 33, which was also confirmed by our in vitro studies, lacking intregrated SIV DNA in presence of integrase inhibitor. All these findings suggest that early interventions at a key time checkpoint, combined with an INSTI prior to proviral reservoir seeding, can potentially block viral genome integration, thereby likely achieving sustained virologic remission and even a cure in infants exposed/infected with to HIV.
All children exposed to HIV before, during, and after birth should receive early antiretroviral (ARV) drugs to reduce the risk of HIV acquisition, morbidity, and mortality 12, 16, 25, 62, 63. Although nucleoside reverse transcriptase inhibitors (NRTIs) block viral RNA conversion into double strand viral DNA in the viral life cycle, current early ART regimen with a combination of dual-NRTI (AZT+3TC) plus protease inhibitors (LPV/r) may not effectively prevent new or continual viral integration in infants infected with HIV. Existence of nonintegrated viral DNA predisposes the high risk to the viral genome integration in absence of INSTI application. In such situation, the regimen combined with integrase inhibitors necessitate to prevent potential proviral reservoir seeding for early pediatric HIV therapy. Of integrase inhibitors, DTG, a very well-tolerated, highly effective, and affordable INSTI drug in low- and middle-income countries 64, achieves more rapid and complete viral suppression compared to raltegravir 65. Although one study in Botswana shows that DTG used in the early first trimester of pregnancy may be associated with the incidence of neural tube defects (NTDs) in newborns 66, whereas additional data from this cohort also indicate the risk may only be slightly greater over any non-DTG ART 67. Worldwide pharmacovigilance data do not provide strong support concerning the relationship between NTDs and DTG 68, 69 and irrelevant to HIV-infected infants. DTG could be combined with two NRTIs (TFV and FTC) in an early intervention in pediatric HIV infection.
Early ART in infants may restrict viral reservoirs and reduce HIV proviral DNA 12, 13, 16, 62, 63, 70, 71, 72, 73, 74. However, there is no reported case to eventually achieve an ART-free sustained virologic remission or cure in the HIV+ infants treated by early ART (immediate treatment to several years of age) in the Pediatric AIDS Clinical Trials and cases, including Mississippi and Canadian babies, South African Children with HIV Early Antiretroviral Therapy (CHER) trial, IMPAACT, Pediatric Early HAART and Strategic Treatment Interruption Study (PEHSS), Botswana and European Pregnancy and Pediatric HIV Cohort Collaboration (EPPICC) study. Unfortunately, the eventual viral rebound is observed during the follow-up of analytical treatment interruption 13, 14, 15, 18, 25, 71, 75, 76, 77, 78. Notably, the status of viral genome integration is not fully examined in various tissues of these infants owing to limited sample collection at the initiation of ART. Also, conventional regimen administered to infants generally lacks integrase inhibitors combination, likely resulting in viral DNA integration in infants during pediatric HIV therapy. Building on patterns of proviral reservoir seeding in infants exposed to SIV at birth, intervention initiated at day 3, but not one day or two days delayed when viral genome integration essentially occurs in tissues, can rapidly and efficiently suppress viral replication to undetectable levels. These unexpected results are very interesting, yet which are consistent with onset of proviral reservoir seeding in general in newborn macaques exposed to SIV, suggesting the timing of early intervention initiation is a critical factor for blockade of viral integration and ultimate ART-free virologic remission in pediatric HIV infection. Although our data regarding early proviral reservoir seeding may not rule out the possibility that viral genome integration may occur in other unexamined tissues at 1-3dpi, however, early proviral reservoirs seeding in majority of systemic and lymphoid tissues essentially reflect their emergence, existence and distribution in neonates upon intravenously exposed to SIV, as directly supported by further investigation that nine months of treatment intervention initiated at day 3dpi indeed achieved pediatric viral remission in 4 of 5 infants. Pediatric early intervention but not prevention could be considered, as both plasma viral load and cell-associated viral RNA/DNA were detectable at the timepoint of cART initiation, yet ultimate viral rebound was not observed after CD8+ cell depletion in vivo when these early intervention is initiated at 3dpi for 9 months. Together, these findings might be associated with successful blockade of viral integration and viral reservoir eradication by rational early interventions, since a small viral reservoirs in anatomic tissues are high risk of viral rebound after ATI 16, 79, 80, 81, 82.
It might be difficult to mediate viral reservoir clearance by prolonged early cART even beginning 4-9 d post SIV infection, as viral reservoirs including proviruses are essentially established in adult macaques as early as 3dpi 7, 8 and tissue viral reservoirs are still detectable at 28 day old of infants on continuous cART initiated at 4 or 5dpi. In SIV-infected macaques on 16-months therapy, there is still significantly higher frequency of intact SIV proviral genomes compared to ART-treated HIV-infected humans 61. In fact, intact HIV genomes decline more rapidly within first seven years yet then more slowly afterwards, and the half-life of the reservoirs is ~4.0 years until year seven and ~18.7 years thereafter 4, 5, 83. Also, residue HIV reservoirs still exist when cART is initiated during primary HIV infection 84. To date, only a rare HIV-infected individuals remain healthy without treatment, in which long-term treatment pressure drives proviruses to accumulate in human inactive gene regions of host chromosomes, likely stymieing new virus production 85, 86. All these studies suggest that viral genome integration highly correlates with outcomes of viral remission. It is reported that broadly neutralizing antibody (bnAb) therapy given at 30 h or cART regimen at 48 h in one-month-old macaques after oral exposure to low pathogenic SHIVSF162P3 87, 88 could clear tissue viral reservoirs 89, 90, in which all animals show aviremic outcomes over time treatment, inconsistent with our results that plasma viral load is essentially detectable in neonates at 24-48 h post intravenous SIV inoculation. It is also unknown whether viral genome integration occur in these infants and how bnAb treatment beginning at 1 day SHIV exposure could block virus replication, integration and production in SHIV-infected cells and completely eradicate productive/latent reservoirs established in immune developing infant, since rapid cell-associated viral RNA and nonintegrated viral DNA definitely emerge as early as 2 h in vitro infection (SIV RNA, ~1.5⋅105 copies/106 cells, nonintegrated SIV DNA, ~2.8⋅103 copies/106 cells) and 24-48 h in tissues of animals exposed to virus. Our data show that cART initiated as early as 3dpi for 1-month cannot eliminate cell-associated SIV RNA in various tissues examined, it is not understood how 21-day cART regimen beginning at 48 h could result in cell-associated viral RNA/DNA eradication and no viral rebound in infants after treatment is discontinued, especially when an amount of viral reservoirs probably exist in tissues in the body. However, our results may explain the efficacy of this early cART at 48 h p.i., as proviral reservoirs basically have not been established at this time point. To this end, multiple factors, including proviral reservoir seeding, timing of prolonged intervention, route of perinatal infection as well as pathogenic HIV/SIV/SHIV strains, are likely determine ultimate outcome in infants on early treatment.
The distinct proviral reservoir seeding and discrepant outcomes of early intervention in infants likely evolves immune maturation, ontogeny, susceptibility, host genetics, or other maternal factors 25. It remains unclear why infant animals show delayed proviral reservoir seeding, albeit identical SIV inoculum. Also, there are still tremendous fundamental gaps in the pediatric HIV infection and efficacy by early treatment, e.g., some infants infected with HIV/SIV show rapid AIDS development but not for others. HIV remission is proposed to be associated with multiple factors including initial viral suppression rate and rapidity with early ART 91. The latter is confirmed by this study that timing and regimen of early ART initiation likely determines the suppression of viral replication, decay of viral reservoirs and clinical outcomes. However, it seems a challenge to evaluate the status of proviral reservoir establishment from various tissues (besides blood sample). Conceivably, proviral reservoirs once seeded in the body, e.g., by intrauterine infection, is likely difficult to fully eradicate by early interventions, thus predisposing to a high risk of viral persistence and viral rebound once treatment is discontinued. A small proportion of the HIV-infected infants develop de novo potent and broadly neutralizing antibodies (bnAbs) that respond to different and perhaps new epitopes of HIV-1 Env as early as one year post infection, compared with bnAbs development in HIV+ adults after 2-3 years of infection 92. However, neutralizing Abs against SIV Env were not detected in any of five SIV-infected infant macaques on early ART, likely because SIV Env does not effectively elicit nAbs 93. Interestingly, neither nAbs nor CTLs are responsible for protection against SIV in the four infant macaques with viral remission, the mechanisms behind discrepant proviral reservoir seeding in infants at very early infection need to be further investigated.
In summary, our data suggest that onset of proviral reservoir seeding in tissues, timing and regimen of early intervention may determine the outcome of pediatric HIV therapy. These findings demonstrate that sustained HIV remission and even a cure are possible in infants postnatally exposed to HIV by early treatment regimens, providing a rational and translatable pediatric cure strategies to the clinic.