CROI 2024 Abstract eBook

Abstract eBook

Poster Abstracts

sites (HIVIS), and to evaluate immunologic biomarkers and HIV-specific immune responses. Results: Plasma HIV RNA levels ranged from 79-9176c/mL in P1 and 440 15600c/mL in P2; with levels decreasing over time although neither had specimens with undetectable viral loads. No drug resistance was detected in P1, and no novel mutations were detected in 73 single-genome-sequences (SGS) from P2 after immigration to the USA. C2V5 env SGS from P1 and P2 revealed no evidence of HIV evolution over time. P1's 448 sequences and P2's 816 sequences revealed 69 and 175 unique indels in the vpr and/or tat1 sequences, with 447/448 (99.8%) and 809/816 (99.1%) genomes having defects in one or both genes. In contrast, 0% of vpr and 0.5% of tat1 genes were defective in 394 DNA sequences from 4 individuals matched for ART-suppression. Elevated immune biomarkers included C-reactive protein and myeloid-derived-suppressor-cells in P1. The largest HIV cell clones comprised 5% of P1's 235 and 3% of P2's 287 HIVIS. Interferon-gamma ELISpots with (1) non-escaped predicted HIV HLA binding peptides (76 for P1 and 25 for P2), (2) HIV Gag, Pol, and Nef potential T-cell epitope peptide pools from the NIH and (3) control antigens, detected reactive T cells to control antigens, but no reactive T cells to HIV (1) or (2) in P1 or P2 across multiple timepoints. Conclusion: Our data suggest that the persistent LLV in these two individuals is unlikely to have originated from proliferating HIV-infected clones or from ongoing HIV replication. Rather, their lack of HIV-specific T cell responses suggests that immune tolerance to HIV causes a failure to eliminate infected cells expressing HIV proteins. Furthermore, the near absence of intact vpr or tat1 and the high frequency of unique inactivating mutations in these genes suggests that ongoing selection maintains the cells with vpr- and tat1-deleted viruses, possibly by conferring resistance to apoptosis. Proviral Landscape in Neonates With In Utero HIV-1 on Very Early ART in IMPAACT P1115 Soumia Bekka 1 , Priya R. Khetan 2 , Yufeng Liu 3 , Adit Dhummakupt 3 , Bryan S. Nelson 4 , Camlin Tierney 4 , Ellen G. Chadwick 5 , Jennifer Jao 5 , Yvonne Bryson 6 , Anne Coletti 7 , Nicol Nicodimus 8 , Lynda Stranix-Chibanda 8 , Guinevere Q. Lee 9 , Stuart Ray 3 , Deborah Persaud 3 1 The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA, 2 University of North Carolina at Chapel Hill, Chapel Hill, NC, USA, 3 The Johns Hopkins University School of Medicine, Baltimore, MD, USA, 4 Harvard TH Chan School of Public Health, Boston, MA, USA, 5 Northwestern University, Chicago, IL, USA, 6 University of California Los Angeles, Los Angeles, CA, USA, 7 FHI 360 , Durham, NC, USA, 8 University of Zimbabwe, Harare, Zimbabwe, 9 Weill Cornell Medicine, New York, NY, USA Background: We studied the proviral landscape of neonates with in utero HIV-1 who initiated antiretroviral treatment (ART) within 48 hours of birth in the IMPAACT P1115 study. Methods: 21 neonates with in utero HIV-1 in IMPAACT P1115 met criteria for near full-length single genome sequencing (nFLSGS) at either Step 1 (within 48 hours post-birth; N=16), Step 2 (7-18 days post-birth when infection was confirmed; N=17) or both (N=12). Of the 13 neonates excluded at either timepoint, 11 had low proviral DNA loads (<20 copies/10 6 PBMCs) and 2 had low sample volumes (<5 uL) insufficient for nFLSGS amplification. nFLSGS was performed using a standard input of HIV-1 DNA per neonate to ensure single proviral genome amplification. nFLSGS data were classified with HIVSeqinR as intact, defective, or hypermutated, and copy numbers were standardized and efficiency adjusted to c/10 6 PBMCs. The limit of detection was set to 0.5 copies per number of cells assayed. ART drug resistance was evaluated using the Stanford HIV Drug Resistance Database. Results: In the 21 neonates analyzed, median log 10 HIV-1 DNA load was 2.8 at Step 1 and 2.9 at Step 2 (median 15 days). nFLSGS examined 93 genomes at Step 1 and 111 genomes at Step 2 (median 6 genomes per neonate in median 50000 cells). At our sampling depth, we detected intact proviruses in 13/16 (81%) neonates at Step 1 and 14/17 (82%) at Step 2. Intact proviruses comprised a median of 50% of each neonate's observed genomes at Step 1 and 33% at Step 2. Median log 10 intact proviral load was 2.0 at Step 1. Among the 12 neonates with data at both timepoints (median 14 days apart), intact proviruses shared >99.8% sequence identity. Defective and hypermutated proviruses were detected at either timepoint in 20/21 and 9/21 neonates. The K103N resistance mutation was detected in all intact proviruses at both timepoints for one neonate, confirmed with maternal genotyping. No other major resistance mutations were identified in the 21 neonates.

GZMA, PFN1) compared to other NK cells, suggesting reduced functional capacity. The enriched CD8+ T cell population in HEI constituted 8% of cells analyzed per donor (median, IQR 1.4-17.4) compared to 0.1% of cells from HEU and V(D)J analysis showed clonal hyperexpansion in this cluster only. These cells were characterized as cytotoxic T lymphocytes (CTL) effectors based on NK-like transcriptomes and high expression of CD57, a marker of terminal differentiation. CTL also expressed FCG3RA/CD16 suggesting potential for ADCC function. Conclusion: Perinatal HIV infection is associated with expanded CTL and NK cells in early life that may play an important role in establishment or shaping of the HIV reservoir. Distinct Populations of HIV-Infected Naive and Memory CD4+ T-Cell Clones in Children on ART Victoria Neer 1 , Mary Grace Katusiime 1 , Shuang Guo 2 , Sean Patro 2 , Wenjie Wang 2 , Xiaolin Wu 2 , Anna Horner 3 , Ann Chahroudi 3 , Jason W. Rausch 1 , Maud Mavigner 3 , Mary F. Kearney 1 1 National Cancer Institute, Frederick, MD, USA, 2 Leidos Biomedical Research, Inc, Frederick, MD, USA, 3 Emory University, Atlanta, GA, USA Background: Pediatric HIV remains a major public health issue with 1.7 million children living with HIV (CLWH) worldwide. The key obstacle to cure HIV infection is a reservoir of latently infected CD4+ T cells that persist despite long-term antiretroviral therapy (ART). Although HIV primarily infects memory CD4+ T cells, recent studies suggest that naïve CD4+ T cells are a significant contributor to the reservoir. Here, we characterized HIV persistence in naïve CD4+ T cells from CLWH on long-term ART. Methods: The cohort consisted of 8 children aged 5-11 years who initiated ART at a median of 4 weeks of age (range 0-39) with suppressed viremia for a median of 8.5 years. PBMC were sorted into naïve (CD45RO-CD28+CD27+CD95 CCR7+CD45RA+) and memory (CD45RO+ CD95+) CD4+ T cells. Multiple displacement amplification (MDA) was used to amplify single proviruses in a background of genomic DNA from the sorted cell populations. MDA products were screened for HIV-1 LTR, Psi (ψ) and the Rev response element (RRE) to identify proviruses that may be intact. Intactness was verified in one donor by full length sequencing. All HIV LTR+ MDA products were also used for HIV integration site analyses. Results: HIV infected naïve CD4+ T cells were detected in all 8 children at a median frequency of 38 infected cells/million (range 6-231), a mean of 12-fold lower than the infected memory CD4+ T cells (median 464 cells/million, range 178-506). Of the 200 total proviruses detected in the naïve cells, 8 were predicted intact by amplification of Psi and RRE. HIV integration site analyses identified 8 clones of infected naïve T cells, but none of these harbored the predicted intact proviruses. In the child with the greatest depth of sampling (85 integration sites from naïve cells and 174 from memory cells), no matching integration sites were found across subsets, including from the largest infected clones (p<10-4). Conclusion: Infected naïve CD4+ T cells in children can proliferate into cell clones, contain proviruses with integration sites distinct from those of infected memory CD4+ T cells, and contain intact proviruses. Our findings suggest that naïve and memory T cells may be distinct reservoirs for HIV infection and therefore may require different approaches for targeting and eradication. The figure, table, or graphic for this abstract has been removed. Persistent Viremia With vpr/tat-Deleted HIV and No T-Cell Responses to HLA-Predicted HIV Peptides Alyssa R Oldroyd 1 , Mariam Aziz 2 , Sheila Styrchak 1 , Lennie Chen 3 , Wenjie Deng 3 , Melanie Gasper 1 , Marley Bishop 1 , Cooper James 1 , Madelyn Shapiro 1 , Ewelina Kosmider 4 , Judith A. Guzman-Cottrill 5 , Farah Cassis-Ghavami 6 , James Mullins 3 , Lisa Frenkel 1 , Ana Gervassi 1 1 Seattle Children's Research Institute, Seattle, WA, USA, 2 Rush University, Chicago, IL, USA, 3 University of Washington, Seattle, WA, USA, 4 Fred Hutchinson Cancer Center, Seattle, WA, USA, 5 Oregon Health and Sciences University, Portland, OR, USA, 6 Children's Minnesota, Minneapolis, MN, USA Background: Two children, P1 and P2, living with HIV have persistent low-level viremia (LLV) despite adherence to ART documented by directly-observed therapy and/or therapeutic drug monitoring. We hypothesized that their persistent viremia was due to clones of HIV-infected cells harboring HIV epitopes that escaped immune surveillance. Methods: Plasma HIV RNA was monitored. Blood RNA and DNA from P1 over 7 years and P2 over 6 years was used to generate HIV sequences (env, pol, HIV 5' and 3'-half and 3Kb central region genomes), to determine HIV integration

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