CROI 2025 Abstract eBook

Abstract eBook

Poster Abstracts

responses track with features like spontaneous viral control. Previous studies addressed sex differences in the CD4 T cell reservoir and report that though men and women have similar HIV DNA levels in CD4s, there are sex-based differences in latency and reactivation. Therefore, we sought to assess if there were sex-differences in latency and reactivation in the monocyte reservoir in a large cohort of people with HIV (PWH). Methods: Viral reservoirs were assessed in 138 PWH (70% female[F], 74% Black, 98% viral load <200cp/mL). Monocytes and CD4 T cells were isolated from the same blood draw and used in cell specific intact proviral DNA (IPDA) and quantitative viral outgrowth assays (QVOA). Monocyte IPDAs were completed on 121 PWH (69%F) and monocyte-derived macrophage (MDM)- QVOAs completed on 75 PWH (49%F), 58 PWH(38%F) had cells available for both assays. A subset of participants had CD4 T cell IPDAs (n=118, 69%F) and QVOAs (n=27, 63%F) to determine if sex-based differences were specific to one cellular reservoir. T cell contamination was assessed by flow cytometry and TCRβ qPCR, and mathematically removed from the monocyte signal. Results: 92% of PWH had detectable provirus in monocytes in some form (median[md]= 42 copies[cp]/1e6) with 34% having detectable intact provirus (md=20cp/1e6). No sex differences were observed in the frequency of PWH that had detectable total or intact provirus or with the absolute quantities observed. 24% of PWH had reactivatable monocyte reservoirs as measured by MDM-QVOA. Notably, while the infectious units per million values did not differ between sexes, the frequency of reactivation was significantly lower in women compared to men with HIV (13% vs 32%, χ2=4.4, P=0.036 ). No sex differences were observed in HIV DNA levels or reactivation frequency in CD4 T cells. Conclusions: Our data suggest that the monocyte reservoir is less likely to reactivate in women with HIV despite having equivalent levels of HIV DNA compared to men with HIV. Further work is needed to determine if tissue specific macrophage reservoirs are also less likely to reactivate in women or if this is specific to monocytes. This sex-related difference in HIV reactivation has significant implications for the design and measurement of curative interventions in women with HIV. The figure, table, or graphic for this abstract has been removed. Well-Seeded Reservoirs in Gut Are Associated With Tertiary Lymphoid Structures With Activated ISR Ramon Lorenzo-Redondo 1 , Muhammad S. Arif 1 , Christopher T. Thuruthiyil 1 , Sean Pascoe 1 , Maryam A. Shaaban 1 , Yanique S. G. Thomas 1 , Jenna M. Hasson 1 , Muhammad R. Haque 1 , Flora A. Engelmann 1 , Isabelle Clerc 1 , Michael D. Raven 1 , Mariluz Arainga-Ramirez 2 , Elena Martinelli 1 , Francois Villinger 2 , Thomas J. Hope 1 1 Northwestern University, Chicago, IL, USA, 2 University of Louisiana at Lafayette, Lafayette, LA, USA Background: Despite effective antiretroviral therapy (ART), HIV-1 persistence is the major obstacle to a functional cure. Thus, understanding the tissue microenvironment during ART of the reservoirs that lead to a rapid viral rebound after treatment failure or analytical treatment interruption (ATI) is key. Methods: We have developed immunoPET/CT-guided spatial transcriptomics, combined with immunofluorescence detection of viral proteins and viral sequencing using the SIV/rhesus macaque model. With this approach we can find and study foci of viral replication in tissues of all animals. Here we compare the local neighborhood of the rebound eclipse-phase foci (4-6 days post-ATI) from animals initiating ART 4-days (early-seeded reservoir with short lifespan) or 10-weeks (well-seeded reservoir) after high-dose challenge, as well as early-seeded tissues from animals on ART for 3-or-7-weeks. Additionally, we performed viral long-read deep sequencing and population dynamics analysis in the same tissue sections. Results: Overall, SIV presence in every condition was associated with higher transcriptional levels and up-regulation of genes related to SIV infection. Activation of innate immune responses was observed only in the eclipse phase of the rebound for both types of reservoirs and not during therapy indicating the specificity of the analysis. Notably, we also detected significant differences between early- and well-seeded reservoirs. Translation activation was associated with SIV presence in early-seeded but downregulated in well-seeded reservoirs, while mitochondrial translation was activated in all cases. This is consistent with integrated stress response (ISR) induced decreased protein synthesis in well-seeded reservoirs. Inference of cell type frequency per foci indicated that SIV presence was always associated with epithelial cells. SIV in well-seeded reservoirs was distinctly associated with IgA plasma cells, monocytes, and cycling gamma-delta T-cells. Analysis of intra-host viral

population dynamics from the same “hot” tissues indicates that the highest viral diversity levels are consistently detected in GALT reservoirs where our spatial transcriptomics show activation of stress responses. Conclusions: Our results indicate that persistent reservoirs are associated with gut tertiary lymphoid structures and might be characterized by a status of low translation consistent with ISR which could be favoring long-term viral persistence during ART and rapid rebound of robust viral populations post-ATI. HIV-1 Clade C Reservoir Traits in Blood and Lymph Node Tissue in Acute and Chronic Treated Infection Kavidha Reddy 1 , Chantal Molechan 2 , Guinevere Lee 3 , Tatenda Chikowore 1 , Nicole Reddy 1 , Krista Dong 4 , Zaza Ndhlovu 1 , Thumbi Ndung'u 1 1 Africa Health Research Institute, Mtubatuba, South Africa, 2 University of KwaZulu-Natal, Durban, South Africa, 3 Weill Cornell Medicine, New York, NY, USA, 4 Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA Background: HIV-1 latently infected cells that persist in tissues during antiretroviral therapy (ART) are a barrier to HIV-1 cure, but these reservoirs are hard to reach and therefore poorly characterized. In this study we performed a comparative cross-sectional analysis of HIV-1 reservoir characteristics in paired blood and excised lymph node (LN) tissue. Methods: We studied 12 individuals from South Africa identified with acute infection by virtue of being HIV-RNA positive and antibody negative with subsequent seroconversion. At the time of sampling 5 participants had initiated ART during chronic infection (CT) (median days after diagnosis =424, IQR 141-719; median days on ART =899, IQR 405-1567), 5 during acute infection (AT) (median days after diagnosis =1, IQR 0.5-1; median days on ART =428, IQR 64-843) and 2 remained untreated (UT). One AT was not virologically suppressed at the time of sampling (days after treatment initiation =8). We measured total proviral DNA by ddPCR (n=12) and sequenced viral genomes by full length individual proviral sequencing (FLIP-seq) (n=8) in paired PBMC and excised LN samples. Results: In CT (n=5) and AT (n=5), LNs had 1.5 and 1.1-fold higher median total HIV DNA load than PBMCs (p=0.04). By FLIP-seq we obtained 65 single genome sequences from PBMCs and 159 from LN samples. Around 50% of participants well-suppressed on ART for more than 2 years had detectable intact HIV-1 DNA in LN but not in PBMC. Pooled analysis revealed that relative to PBMC, LN had higher proportions of intact viral genomes in both CT and UT individuals (CT: 5% vs 0% intact, sampling depth 66 and 20 genomes from 258 888 and 231 501 cells; UT: 54% vs 29% intact, sampling depth 22 and 21 genomes from 11 585 and 12 686 cells, in LN and PBMC respectively). In contrast, in AT, proportions of intact HIV-DNA were similar between compartments: LN and PBMC was 20% vs 25% intact respectively (sampling depth 64 and 24 genomes from 630 293 and 214 561 cells). Conclusions: Genetically intact proviruses are found at higher frequencies in lymphoid tissues compared to PBMC in both chronic-treated and untreated infections but were similar in acute treated infections. These data suggest that depending on treatment status/stage, HIV DNA genome profiles in peripheral blood may not reflect those in tissue and that viral compartmentalization persists during suppressive ART. Design of HIV curative strategies should target all relevant organ systems. HIV Burden Is Associated With Specific Bacteriome Profiles Relative to Specific Gut Segments Mattia Trunfio 1 , Davey Smith 1 , Noah Gaitan 1 , Mina Awad 1 , Magali Porrachia 1 , Alan Wells 1 , Jesus Rivera-Nieves 1 , Elizabeth Hastie 1 , Patricia K. Riggs 2 , Antoine Chaillon 1 , Sara Gianella Weibel 1 1 University of California San Diego, La Jolla, CA, USA, 2 University of California San Diego Medical Center, La Jolla, CA, USA Background: We assessed whether the gut bacteriome affects the size and activity of HIV reservoir in the human gut. Since each gut segment has a different immune and bacteriome environment, we also aimed at identifying a core bacteriome that is associated with HIV reservoir consistently and similarly across all the segments. Methods: Tissue samples of 5 segments (small bowel: duodenum, jejunum, ileum; large bowel: right colon, rectum) were collected during rapid autopsies (≤6 hour from death) from people with HIV (PWH). For each segment, we determined the bacteriome composition by 16SrRNA sequencing and measured cell-associated HIV DNA and RNA by ddPCR. The α and β diversity were analyzed (Phyloseq) after dimension reduction of taxa. Mixed-effect models assessing the associations between the relative abundance (RA) of taxa and HIV DNA and

521

Poster Abstracts

520

522

CROI 2025 134