CROI 2020 Abstract eBook

Abstract eBook

Poster Abstracts

Results: The IPDA moderately correlated with QVOA measurements (Spearman r = 0.661, p < 0.0001). For 4/68 participants, no IPDA signal was observed despite moderate QVOA levels. For longitudinal measurements, there was significant interparticipant variability in the correlation between QVOA, intact DNA, and defective DNA measurements. In general, however, we observed a significant decay of both IPDA and QVOA measurements in the first 1 to 4 years following ART-initiation. After 4 years of ART, both IPDA and QVOA measurements generally remained stable or decayed more slowly. Packaging Signal (PS)- and Rev Response Element (RRE)-defective proviral DNA frequency tracked with intact and QVOA changes (or lack thereof) in most participants (17/25). However, in some participants there appeared to be expansion and/or decay of defective DNA species over time (8/25). Conclusion: This study provides a key comparison of QVOA and IPDA measurements longitudinally in a large cohort of ART-suppressed participants. In general, intact proviral DNA measurements correlated with QVOA measurements over time; some correlation was also seen in measurements of defective DNA species. The precision of correlation of IPDA with QVOA may vary across individuals. The recent description of proviral clones that contract and expand over time may explain some changes seen in IPDA over time. These findings suggest an advantage for the IPDA over traditional single-target assays that measure predominantly defective DNA. The utility of IPDA to monitor cure interventions designed to deplete persistent infection deserves further study. 314 HIV TRANSCRIPTION PROFILE IN BLOOD, GUT, LIVER, AND GENITAL TRACT IN SUPPRESSED WOMEN Sara Moron-Lopez 1 , Grace Xie 2 , Peggy Kim 3 , Joseph K. Wong 3 , Jennifer C. Price 1 , Najwa Elnachef 1 , Ruth Greenblatt 1 , Phyllis Tien 1 , Nadia R. Roan 2 , Steven A. Yukl 3 1 University of California San Francisco, San Francisco, CA, USA, 2 Gladstone Institutes, San Francisco, CA, USA, 3 San Francisco VA Medical Center, San Francisco, CA, USA Background: Sex-specific differences affect various aspects of HIV infection. However, few studies have quantified levels of HIV infection or expression in tissues from women. Here, we measured the extent of HIV infection and progression through the HIV transcriptional blocks in blood, gut, liver, and genital tissues from HIV-infected ART-suppressed women. Methods: Peripheral blood mononuclear cells (PBMC), liver, gut (ileum, colon, rectosigmoid), and genital tract biopsies (cervix, endometrium), and endocervical curettage (ECC) samples were collected from 5 women with plasma HIV RNA<200 copies/ml (median 10.4 years). Total and intact (IPDA) cell-associated HIV DNA and levels of read-through, initiated (TAR), 5’elongated, polyadenylated, and multiply-spliced HIV transcripts were measured by ddPCR. Phenotyping of immune cells was conducted by CyTOF. Results were analyzed using the Wilcoxon signed-rank test. Results: Total HIV DNA was detected in all tissues, with levels being comparable between the gut, liver and genital tract tissues. Intact HIV DNA was detected in PBMC, ileum, colon and cervix. HIV transcriptional initiation (TAR RNA per provirus) tended to be higher in PBMC and endometrium than in ileum, colon, rectosigmoid, cervix, and ECC (all p=0.06), and higher in rectum than either ileum or colon (p=0.06). Likewise, levels of elongated HIV transcripts per provirus were comparable in PBMC and endometrium, but higher than the gut and cervical samples (p=0.06). Polyadenylated HIV transcripts were detected in PBMC from all 5 individuals but were rarely detected in the tissues. Multiply- spliced HIV transcripts were detected in PBMC from 2 of 5 individuals, but not detected in any tissue. The phenotypes of CD4+ T cells were distinct between the blood, genital tract, and gut. Conclusion: The gut, liver, and genital tract are all sites of HIV persistence in women. The female genital tract contains a large pool of HIV-infected cells, with HIV DNA levels/million tissue cells that are similar to the gut. HIV-infected cells in the blood and endometrium showed higher levels of HIV transcription per provirus, while much lower levels were observed in the gut, cervix and liver. These results suggest tissue-specific differences in the mechanisms that govern HIV latency, with greater suppression of HIV transcription in most tissues than blood. Therapies aimed at disrupting latency, such as latency-reversing or latency-silencing agents, will be required to penetrate into multiple tissues and affect different blocks to HIV transcription.

315 INTACT PROVIRUSES FROM NAIVE AND EFFECTOR MEMORY T CELLS MATCH PERSISTENT VIREMIA Katie Fisher 1 , Bonnie Hiener 1 , Bethany A. Horsburgh 1 , Timothy E. Schlub 2 , Eunok Lee 1 , Vincent Morcilla 1 , John-Sebastian Eden 1 , Susanne Von Stockenstrom 3 , Jeffrey M. Milush 4 , Rebecca Hoh 4 , Rémi Fromentin 5 , Nicolas Chomont 5 , Steven G. Deeks 4 , Frederick M. Hecht 4 , Sarah Palmer 1 1 The Westmead Institute for Medical Research, Westmead, NSW, Australia, 2 University of Sydney, Camperdown, NSW, Australia, 3 Karolinska Institute, Stockholm, Sweden, 4 University of California San Francisco, San Francisco, CA, USA, 5 Université de Montréal, Montreal, QC, Canada Background: Genetically intact, and potentially replication competent, proviruses are a likely source for viremia during antiretroviral therapy (ART). Identifying the CD4+ T cell subsets that harbour these proviruses within different anatomic sites is important for future eradication strategies. Methods: Near full-length proviral sequences were obtained from naïve (NV), central (CM), transitional (TM) and effector memory (EM) CD4+ T cells (sorted based on their expression of CD45RA, CD27 and CCR7), which were isolated from both the peripheral blood (PB, 13 participants) and lymph nodes (paired LN, 5 participants), using the Full-Length Individual Proviral Sequencing Assay (FLIPS). Proviral sequences were identified as genetically intact if they lacked inversions, stop codons/hypermutation, insertions, deletions or frameshifts. Genetically intact proviruses from 10 participants were compared to on-therapy plasma RNA (p6-RT region obtained by single-genome sequencing (SGS)). Results: We sequenced 1913 proviruses, and genetically intact proviruses were found in all cell subsets except for LNEM (n=3). We found that the infection frequency of genetically intact proviruses differed across the subsets in both PB and LN (P<0.001). In PB, the order of intact genomes was found to be EM>TM/ NV>CM (all P<0.02), while in the LN the trend was NV>TM>CM>EM, with evidence for NV>CM (P=0.01). All 22 intact LN sequences were genetically unique. For the subsets that had more than 10 genetically intact DNA sequences (PBEM, PBNV and LNNV), we compared the genetically intact proviruses obtained by FLIPS to the on-therapy plasma RNA p6-RT sequences obtained by SGS. PBEM had the highest frequency of genetically intact DNA sequences matching 100% to the on-therapy RNA sequences (13/23, 57%). This was followed by PBNV, with 6/19 (32%) DNA sequences matching RNA, and LNNV, with 3/16 (19%) DNA sequences matching RNA. Conclusion: The distribution of genetically intact proviruses differs between PB and LN. For the five participants with paired PB and LN cells available, NV cells had the highest frequency of intact proviruses in LN. In PB, however, the highest levels of intact genomes were found in EM cells. PBEM, PBNV and LNNV also had a high frequency of genetically intact proviruses matching to on-therapy plasma RNA p6-RT sequences, suggesting that the intact proviruses within these T cell subsets from different anatomic sites may contribute to ongoing viremia during ART. 316 HIV Gag p24 PERSISTS IN TISSUE AND CORRELATES WITH IMMUNE RESPONSE Guoxin Wu 1 , Paul Zuck 1 , Shih Lin Goh 1 , Timothy Schacker 2 , Steven G. Deeks 3 , Daria Hazuda 1 , Peter W. Hunt 3 , Bonnie J. Howell 1 , Schuyler Metzger 1 , Dhrupal Patel 1 , Ashley Haase 2 1 Merck & Co, Inc, West Point, PA, USA, 2 University of Minnesota, Minneapolis, MN, USA, 3 University of California San Francisco, San Francisco, CA, USA Background: Gut tissue and lymph nodes (LN) harbor HIV DNA and RNA during antiretroviral therapy (ART)–mediated viral suppression, but less is known about HIV protein expression. The goal of this study is to apply a sensitive immunoassay for detecting HIV p24 antigen in lymphoid tissues during ART and to assess the relationships between immune phenotypes and HIV control to inform on HIV cure strategies. Methods: HIV gag p24 protein was measured by an in house optimized digital ELISA in cells isolated from either rectal tissue, LN biopsies, or LN fine needle aspirates from HIV participants in the UCSF and University of Minnesota cohorts. HIV gag protein was assessed from study participants with variable levels of plasma viremia levels, ranging from fully suppressed to viremic, either naturally controlling or on ART. Results: HIV gag p24 protein persists in lymph node and rectal biopsies in well-suppressed participants. HIV p24 levels in rectal and peripheral blood CD4+ T cells were moderately correlated among all participants (r: 0.54, P=0.0169); Rectal p24 levels discriminated between viremic, ART-suppressed, and HIV-uninfected participants much better than peripheral blood p24 levels.

Poster Abstracts

CROI 2020 108