CROI 2025 Abstract eBook

Abstract eBook

Poster Abstracts

transcriptomics (Illumina HiSeq3000) was performed on rectal biopsies and analyzed for differential gene expression and with gene set enrichment analysis (GSEA). Results: Blood analyses revealed a significant global difference between TGW and CGMSM in cellular composition (p=0.002). Several individual blood cell subsets contributed to this difference, including an increase in activated memory CD4+ T cells (q=0.004), decreases in CD56+CD16+ NK cells (q=0.028) and perforin+ cells (q=0.004) among TGW. Analyses of rectal tissues also identified a significant global difference in cellular composition (p=0.0002) between TGW and CGMSM, and an increase in CCR5+ (q=0.01), Th17 (q=0.002), and Th1Th17 (q=0.02) memory CD4+ T cells among TGW. Ex vivo challenge assays revealed a higher slope of p24 production among TGW compared to CGMSM (p=0.04). Among TGW after FHT initiation, differences in cellular composition were apparent in blood, but not the rectal mucosa. GSEA identified several highly relevant immune pathways that were downregulated in rectal mucosa among TGW compared to CGMSM, while others were increased after initiation of FHT. Conclusions: The rectal mucosal immune environment among TGW using FHT is distinct from CGMSM and may support higher HIV replication, underscoring the need for further study of this unique population. Our data suggest that cellular changes in blood, but not rectal tissues, are apparent after short-term FHT use. Understanding the effects of FHT on HIV acquisition risk in the context of rectal exposure merits urgent investigation.

for ΔVpr versus 38.5% for WT (p<0.05). In the presence of E. coli , WT and ΔVpr virus had no significant difference in cellular infection levels or infectious titers. However, ΔVpr induced significantly lower levels of CD4 T cell depletion relative to WT (20.8% versus 42.3%, p<0.05). Total and HIV p24hi CD4 Ts from ΔVpr infected cultures had lower levels of GZB versus WT. Conclusions: Our findings demonstrate that Vpr is critical for robust HIV replication and depletion of gut CD4 T cells. In the context of microbial exposure, Vpr was dispensable for gut CD4 T cell replication, but still contributed to death, possibly by upregulating GZB expression. These data underscore Vpr as an essential component of the HIV life cycle in gut CD4 T cells and highlight novel functional attributes of HIV-Vpr in gut pathogenesis. Early HIV-1 Genetic Diversity Includes CTL and Drug Resistance Mutations Adam A. Capoferri 1 , Valerie F. Boltz 1 , Wei Shao 2 , Clarissa Halpern 1 , Rasmi Thomas 3 , Morgane Rolland 3 , Nittaya Phanuphak 4 , Lydie Trautmann 5 , Julie Ake 3 , Carlo Sacdalan 6 , Somchai Sriplienchan 6 , Jason W. Rausch 1 , John W. Mellors 7 , John Coffin 8 , Mary Kearney 1 , for the RV254/SEARCH 010 Study Team 1 National Cancer Institute at Frederick, Frederick, MD, USA, 2 Leidos Biomedical Research, Inc, Frederick, MD, USA, 3 US Military HIV Research Program, Bethesda, MD, USA, 4 Institute of HIV Research and Innovation, Bangkok, Thailand, 5 Henry M Jackson Foundation, Bethesda, MD, USA, 6 SEARCH, Bangkok, Thailand, 7 University of Pittsburgh, Pittsburgh, PA, USA, 8 Tufts University, Boston, MA, USA Background: Genetic analysis of HIV-1 during acute infection can reveal early drivers of diversity and evolution. Here, we used ultrasensitive single-genome sequencing (uSGS) on plasma virus collected from participants in the early weeks after transmission to determine the relative roles of mutation and selection in shaping the pol and env genes. Methods: HIV-1 RNA was extracted from plasma of 10 participants with acute infection (Fiebig II-III) enrolled in the RV254/SEARCH010 Trial. Participant HLA types were previously determined. Our uSGS method used primer IDs and Illumina sequencing (234bp) to characterize the genetics of >10,000 pol (RT) and env (C2-V3) genomes per sample. We measured average pairwise distances (APD), substitution rates, transition/transversion ratios (Ti/Tv), non synonymous/synonymous ratios (dN/dS), frequencies of amino acid reversions back to consensus CRF01AE (conAE), CTL mutations away from conAE, and drug resistance mutations. Results: Sequences from an average of 11,733 pol and 12,096 env single genomes were obtained from each participant. In these 10 single transmitted founder (TF) infections, an average 93% of the genomes were identical. APD was a median of 0.07% in pol and 0.05% in env (p=0.10), or ~6-fold lower than expected from the HIV-1 mutation rate and time since transmission. A preference toward transitions was observed with a median Ti/Tv of 5.1 in pol and 3.8 in env (p=0.21). In pol , 52% of transitions were G>A and in env , 42% were G>A, with the split divided over the other 3 mutations. The average dN/dS was 0.38 in pol and 1.0 in env (p=0.02). Reversions to conAE were observed at 57% of sites that varied from the TF, but these mutations only comprised 0.3% of all amino acid changes in pol and 2.8% in env (p<0.0003). The remainder were mutations away from conAE, with 42% in pol and 51% in env falling within CTL epitopes that matched the participants’ HLA. Drug resistance mutations were detected in all participants (0.2-4.0% of genomes), but were not linked to one another. Conclusions: Genetic diversity in Fiebig II-III was ~6-fold lower than expected from the HIV-1 mutation rate over the first 21.5 days of infection, implying purifying selection during acute infection. While many transmitted amino acid mutations reverted to conAE; these mutations were a small contribution to the overall genetic diversity. The main drivers of early HIV-1 diversity were synonymous mutations and amino acid changes in CTL epitopes, suggesting the possibility of early CTL escape. Tuberculosis Promotes the Persistence of Genetically-Intact HIV in People With HIV and Tuberculosis Samantha K. Cronin 1 , Andrea Pereyra Casanova 2 , Eunok Lee 2 , Katie Fisher 2 , Anthony D. Kelleher 3 , Natalia Laufer 4 , Gabriela Turk 4 , Maria Florencia F. Quiroga 4 , Christel Vérollet 5 , Luciana Balboa 4 , Sarah Palmer 2 , Gabriel Duette 2 1 The University of Sydney, Sydney, Australia, 2 The Westmead Institute for Medical Research, Westmead, Australia, 3 University of New South Wales, Darlinghurst, Australia, 4 Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, Buenos Aires, Argentina, 5 Institut de Pharmacologie et Biologie Structurale, Toulouse, France Background: The persistence of HIV-infected cells containing genetically intact and replication-competent virus remains the main obstacle to achieving

346

Poster Abstracts

345

HIV-1 Vpr Promotes Viral Replication, Granzyme B Expression, and Death of Gut CD4 T Cells Ex Vivo Kaylee Mickens, Kejun Guo, Brad Barrett, Stephanie M. Dillon, Ashley Thompson, Cara C. Wilson, Mario L. Santiago University of Colorado Anschutz Medical Campus, Aurora, CO, USA Background: In the gut, early HIV-1 (HIV) infection is associated with high HIV replication, CD4 T cell death, and microbial translocation. Among HIV proteins, Vpr remains enigmatic. In vitro , Vpr is linked to cell cycle arrest, DNA damage, apoptosis, and HIV replication in myeloid cells. Consistent Vpr phenotypes are lacking in CD4 T cells (CD4 Ts) when mitogen-activated blood cells or cell lines are utilized. These data are incongruous with Vpr being packaged in virions as it should exert influence early in infection, where CD4 Ts, particularly in the gut, are critical. To study interactions between primary gut T cells, transmitted/ founder (TF) HIV, and translocating enteric bacteria ex vivo , we developed the Lamina Propria Aggregate Culture (LPAC) model. We previously demonstrated bacteria enhance HIV infection and contribute to HIV-mediated CD4 T cell death by inducing Granzyme B (GZB). Here, we investigated if Vpr plays a role in HIV replication and death in gut CD4 Ts using the physiologically-relevant LPAC model. Methods: Jejunal LP mononuclear cells (n=8 donors) were infected with TF HIV (CH040) wildtype (WT), Vpr-deleted (ΔVpr), or mock in the presence or absence of commensal Escherichia coli lysate (10μg/ml). At 4 dpi, infection (p24), GZB, and total CD4 T cell counts were determined by flow cytometry. Infectious titer in supernatants was determined by TZM-bl assay. Results: In the absence of bacteria, ΔVpr replicated to significantly lower levels than WT, with an 8.3-fold (p<0.05) reduction in the frequency of p24+ CD4 Ts and 7.4-fold (p<0.01) reduction in infectious titer. The lack of ΔVpr replication significantly rescued CD4 Ts from HIV-mediated death, with 8.9% depletion

347

74

CROI 2025