CROI 2020 Abstract eBook

Abstract eBook

Poster Abstracts

Background: Identifying the source of viral rebound during a monitored analytical treatment interruption (ATI) would reveal potential targets for cure strategies. Therefore, we examined the genetic composition of proviral DNA in different subsets from participants on antiretroviral therapy and compared this to rebounding virus after an ATI. Methods: Eleven participants underwent a monitored ATI and were sampled from different anatomical sites prior to and after the ATI. From the peripheral blood, Naïve (TNA), central (TCM), transitional (TTM) and effector (TEM) memory CD4+ T cells were sorted as were CD45 cells from gut-associated lymphoid tissue (GALT). Using single-genome sequencing (SGS) the env region of HIV DNA and plasma-derived RNA was sequenced. In an ongoing study, Full-Length Individual Proviral Sequencing (FLIPS) and Integration Site Loop Amplification (ISLA) assays were performed on the T cell subsets from 2 participants. Results: For participant STAR10, 87 integration sites (IS) and 113 proviral genomes were sequenced while only 3 unique intact proviruses (3%) were identified. A cluster of 17 identical defective proviruses were linked to an IS (9% of all IS) in STAT5B located in TCM, TNA, TEM and TTM. When comparing the FLIPS to SGS env sequences a 100%match was found between one defective provirus and one plasma HIV RNA sequence after rebound. For participant STAR11, 37 IS and 105 proviral genomes were sequenced yielding 14 intact proviruses (13%) with the highest proportion found predominantly in the TEM subset (n=13, 45%). Four different clusters of identical sequences could be identified of which 2 (n=3 and n=9) consisted of intact TEM sequences with the smaller cluster linked to an IS in ZNF274. A 99%match between 2 env from rebounding plasma RNA and this smaller cluster of intact proviral genomes was identified. Conclusion: Comparing proviral sequences and their IS to plasma-derived RNA sequences after an ATI reveals additional information in terms of the source of viral rebound. However, this comparison is complicated by multiple factors. For example, we found a plasma-derived RNA sequence obtained during viral rebound matched a defective proviral sequence which highlights the problem of using one HIV RNA subgenomic region for identifying replication-competent virus. In addition, ongoing viral replication during rebound may prevent a 100% match with genetically intact proviral sequences making it challenging to determine the absolute source of rebound. 325 HIV POSTTREATMENT CONTROL DESPITE PLASMA VIRAL EVOLUTION AND DUAL INFECTION Behzad Etemad 1 , Golnaz Namazi 1 , Ying Wen 2 , Nikolaus Jilg 3 , Elmira Esmaeilzadeh 1 , Xin Zhang 1 , Radwa Sharaf 1 , Daniel MacMillan 4 , Ronald Bosch 5 , Evgenia Aga 5 , Jeffrey A. Johnson 6 , Rajesh T. Gandhi 7 , Zabrina Brumme 4 , Mary F. Kearney 8 , Jonathan Z. Li 1 1 Brigham and Women's Hospital, Boston, MA, USA, 2 China Medical University, Shenyang, China, 3 Massachusetts General Hospital, Boston, MA, USA, 4 Simon Fraser University, Burnaby, BC, Canada, 5 Harvard T.H. Chan School of Public Health, Boston, MA, USA, 6 CDC, Atlanta, GA, USA, 7 MGH Institute of Health Professions, Boston, MA, USA, 8 NIH, Frederick, MD, USA Background: HIV post-treatment controllers (PTCs) serve as models for sustained HIV remission. These individuals frequently have early HIV rebound before viral control and subsequent periods of intermittent low-level viremia. Little is known about the viral composition during these periods of viremia. Methods: We extracted longitudinal plasma HIV RNA from PTCs and post- treatment non-controllers (NCs) from AIDS Clinical Trials Group (ACTG) analytic treatment interruption (ATI) trials. Single-genome sequences (SGSs) of HIV-1 pol were obtained at pre- and multiple post-ATI time points (median 90 wks at the late time point for the PTCs). Sequence analysis included calculations of viral genetic diversity by average pairwise distance (APD), root-to-tip distances, percent of HLA-escape mutations, and panmixia testing. Results: Despite low plasma viremia, >1200 SGSs were obtained for 20 PTCs and 13 NCs. Early after ATI, chronic-treated NCs had the highest levels of plasma HIV diversity while viral diversity was limited for both early-treated PTCs and NCs. Over time, increasing viral diversity was detected in almost all PTCs, but rates of diversification were significantly slower in PTCs compared to NCs (median 0.05% vs 0.27% per year, p=0.007). PTCs were also able to maintain viral control despite evidence of viral evolution. This included increasing root-to-tip distances of HIV sequences by phylogenetic analysis over time for all PTCs, divergent population structures by the panmixia test in 73% of PTCs, and accumulation of HLA escape mutations in longitudinal sampling for 2 chronic- treated PTCs (Figure). The proportion of HLA-escape mutations were common in

plasma HIV sequences from PTCs and not significantly different than NCs (47% vs 59%, p=0.16). Unexpectedly, the presence of dual HIV infections (populations of HIV variants with ≥5% sequence divergence) was detected in the plasma SGSs for 3 PTCs (1 early-treated, 2 chronic-treated) and for none of the NCs. In two participants, dual infection was detected at the early ATI time point with one variant becoming dominant over time. One individual was found to have an apparent superinfection with a late post-ATI viral rebound of a second HIV variant before subsequently regaining HIV control. Conclusion: PTCs exhibit sustained HIV remission despite evidence of slow plasma viral diversification and evolution. The detection of dual HIV infection in a subset of PTCs suggests the presence of an antiviral response that can control a diverse viral population.

Poster Abstracts

' 326 EVALUATING BIOMARKERS FOR HIV REBOUND DURING TREATMENT INTERRUPTION Marie-Angélique D. De Scheerder 1 , Clarissa Van Hecke 2 , Henrik Zetterberg 3 , Dietmar Fuchs 4 , Nele De Langhe 1 , Sofie L. Rutsaert 2 , Bram Vrancken 5 , Wim Trypsteen 2 , Sarah Palmer 6 , Philippe Lemey 5 , Magnus Gisslén 3 , Linos Vandekerckhove 7 1 Ghent University Hospital, Ghent, Belgium, 2 HIV Cure Research Center, Ghent University, Ghent, Belgium, 3 Sahlgrenska University Hospital, Gothenburg, Sweden, 4 Innsbruck Medical University, Innsbrusk, Austria, 5 Katholieke University Leuven, Leuven, Belgium, 6 The Westmead Institute for Medical Research, Westmead, NSW, Australia, 7 Ghent University, Ghent, Belgium Background: Validated biomarkers to evaluate HIV-1 cure strategies are currently lacking, therefore requiring analytical treatment interruption (ATI) in study participants, potentially impacting their health. Here we assessed these patients safety concerns by evaluating viral reservoir size in blood and inflammatory levels in the brain. Furthermore, restriction factor (RF) expression levels and cell-associated (CA) HIV-1 RNA transcripts were assessed as potential biomarkers for predicting viral rebound. Methods: In the HIV-STAR study, we collected peripheral blood mononuclear cells (PBMC), plasma and cerebrospinal fluid (CSF) from 11 participants at 4 time-points on-and off-treatment to assess these safety concerns and screen potential biomarkers for predicting viral rebound. Total and integrated HIV-1 DNA, CA HIV-1 RNA transcripts and restriction factors (RF) expression were measured. Markers of neuro-inflammation and neuronal injury were measured in CSF and immune activation was assessed in plasma and CSF. Results: Total HIV-1 DNA, integrated HIV-1 DNA and CA viral RNA transcripts did not differ pre- and post-ATI. Similarly, no significant NfL or YKL-40 increase in CSF was observed between baseline and viral rebound. Furthermore, markers of immune activation did not increase during ATI. Interestingly, RF SLFN11 and APOBEC3G increased after ATI before viral rebound was observed. Similarly, Tat-Rev transcripts were increased preceding viral rebound after interruption. Conclusion: ATI did not increase viral reservoir size, nor did it reveal signs of increased neuronal injury or inflammation, suggesting that these well- monitored ATIs are safe. Elevation of Tat-Rev transcription and induced expression of RF SLFN11 and APOBEC3G after ATI prior to viral rebound indicates

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