CROI 2025 Abstract eBook

Abstract eBook

Poster Abstracts

567

Female Sex Is Associated With Continuous Decline in Intact HIV-1 Proviruses Yijia Li 1 , Nadia R. Roan 2 , Tom Medvec 1 , Sharon Riddler 1 , Greg Laird 3 , Albine Martin 3 , John W. Mellors 1 , Charles Rinaldo 1 , Bernard J. Macatangay 1 , Phyllis Tien 4 1 University of Pittsburgh, Pittsburgh, PA, USA, 2 Gladstone Institutes, San Francisco, CA, USA, 3 Accelevir Diagnostics, Baltimore, MD, USA, 4 University of San Francisco, San Francisco, CA, USA Background: Despite antiretroviral therapy (ART), HIV infection is not curable in most cases due to persistent HIV-1 reservoirs. Understanding the factors associated with long-term dynamics of intact HIV-1 proviruses during suppressive ART is critical for developing HIV-1 cure strategies. In this study, we aim to evaluate the association between sex assigned at birth and HIV-1 reservoir dynamics in people with HIV (PWH) on long-term suppressive ART. Methods: We leveraged a digital droplet PCR (ddPCR)-based platform, intact proviral DNA assay (IPDA), to measure intact and defective HIV-1 proviruses. Adult male and female participants from MWCCS cohort with ≥10 years of suppressive ART (HIV-1 viral load <50 copies/ml or contemporary level of detection) were included. Patterns of intact proviruses decline were categorized as continuous declines (D_C), decreasing initially then rising later (D_LR), and non-decline (ND). Correlation was evaluated using Spearman's rank correlation test. Results: Seventeen male and 18 female PWH were included, with a median follow-up duration of 12 years. Median age at ART initiation was 38 years. Median nadir CD4 cell count was 218 cells/μl. Sixteen participants demonstrated continuous decline in intact proviruses (D_C), while 8 had late increase (D_LR) and 11 had non-decline (ND) patterns (Figure 1). In the D_LR group, the inflection of proviral DNA took place approximately 10 years after viral suppression. There was no significant difference in follow-up duration, nadir intact proviral levels, and nadir CD4 cell count among the three groups. However, female sex was associated with a higher proportion of continuous decrease than male (66.7% vs. 23.5%, p=0.04). In contrast to intact proviral DNA, total and defective proviral DNA levels were not significantly different among the three groups throughout follow-up. Estradiol levels in female PWH were negatively correlated with interleukin 6 (IL6, rho=-0.53, p=0.001), and IL6 was negatively correlated to intact proviruses (rho=-0.38, p=0.01). In male PWH, D-dimer rather than IL6 was positively associated with intact proviruses (rho=-0.34, p=0.02). Conclusions: Among PWH with long-term suppressive ART, less than half of them had sustained proviral decline. Female sex is associated with the continuous decline pattern. Different proinflammatory pathways are related to HIV-1 intact proviral levels between male and female participants. The figure, table, or graphic for this abstract has been removed. A Virology Quality Assurance Program to Assess Inter-Lab Reproducibility of HIV-1 Reservoir Assays Maria Blasi 1 , Darin Weed 1 , Salvatore Scianna 1 , Bhavna Hora 1 , Thynn Thane 1 , Miranda Carper 1 , Raul Louzao 1 , Wes Rountree 1 , Mars Stone 2 , Michael P. Busch 2 , Elizabeth R. Wonderlich 3 , Keith Crawford 3 , Thomas Denny 1 1 Duke University School of Medicine, Durham, NC, USA, 2 Vitalant Research Institute, San Francisco, CA, USA, 3 National Institute of Allergy and Infectious Diseases, Baltimore, MD, USA Background: In recent years there have been significant advances in the development of assays to quantify and characterize the HIV-1 reservoir. As these assays are incorporated into HIV-1 cure clinical trials, ensuring the reliability and reproducibility of assay results across different laboratories becomes crucial. This study aimed to evaluate the inter-laboratory performance of assays measuring intact proviruses (AMIP) as part of the National Institute of Allergy and Infectious Disease (NIAID) Virology Quality Assurance (VQA) program at Duke (contract # 75N93019C00015). Methods: We conducted a multi-site study involving seven laboratories routinely performing AMIP. A panel of standardized samples comprising serial dilutions of HIV-1 infected cell lines with known proviral DNA levels were distributed blinded to the participating sites. Each laboratory performed the AMIP following their standard operating procedures. Results were collected and analyzed to establish the degree of concordance among laboratories and to identify discrepancies and potential sources of variability in assay outcomes. Results: We observed significant variability in AMIP results across laboratories, with several labs exhibiting discrepancies for both experimental and biological replicates. For some laboratories the reported results differed from the expected values by 3 to 10-fold. Factors such as sample handling, assay reagents, and

differences in analytical protocols were identified as potential contributors to this variability. Recommendations for standardization and training are currently being evaluated to mitigate these issues. Conclusions: The establishment of a virology quality assurance program is essential in harmonizing inter-laboratory performances of assays to measure the size and expression of the HIV-1 reservoir. Enhanced quality assurance measures are necessary to ensure consistent and accurate results across laboratories, thereby strengthening the utility of these assays in clinical and research applications. Further investigations will focus on rigorous inter laboratory training and the development of standardized protocols to minimize variability and improve assay performance and data comparability. The Cross Subtype Intact Proviral DNA Assay Detects 97% of Proviruses From Diverse HIV Clades Morgan Litchford 1 , Carolyn Fish 1 , Noah Cassidy 1 , Pavitra Roychoudhury 2 , Ethan Nunley 3 , Agnes Langat 4 , Helen Moraa 4 , Daniel B. Reeves 1 , Elizabeth M. Obimbo 4 , Grace John-Stewart 3 , Dalton Wamalwa 4 , Julie Overbaugh 1 , Dara A. Lehman 1 1 Fred Hutchinson Cancer Center, Seattle, WA, USA, 2 Washington DC VA Medical Center, Washington, DC, USA, 3 University of Washington, Seattle, WA, USA, 4 University of Nairobi, Nairobi, Kenya Background: Intact proviral DNA assays (IPDA) are high-throughput methods to quantify intact and defective HIV proviruses during ART, with the former providing estimates of rebound-competent HIV reservoir. However, most IPDAs have been designed for subtype B and have ~28% false negative rate due to polymorphisms in the primer/probe sites 1 . The cross-subtype IPDA (CS-IPDA) was designed to tolerate diversity across subtypes A, B, C, D and CRF01_AE, 2 but has not yet been validated on large cohorts. Methods: CS-IPDA is a multiplex droplet-digital PCR assay that targets 3 genomic regions ( gag , pol and env ) of HIV. The number of triple-positive droplets is used to estimate intact proviruses, while single- and dual-positive droplets are indicative of defective proviruses. We used the CS-IPDA on PBMCs collected during ART from 191 children living with HIV from 2 cohorts in Kenya, where subtypes A, C and D are prevalent. Each sample was tested in 3 or more replicates and included here if >1e5 cell equivalents (median 4.2e5, range 1e5 - 4.3e6) were tested and if the shearing index was <40% (median 3%, range 2% - 31%). Results: Across all 696 samples collected longitudinally from 191 ART-treated participants, there was a median 1.4e3 defective (range: 0 – 6.8e4) and 145 intact (range: 0 – 5.2e4) HIV DNA copies per million T cells. In 91 (13.1%) samples there were no intact proviruses detected, which could indicate intact levels truly below detection, or false negatives due to primer/probe mismatches. In 75 (10.7%) samples intact HIV DNA was undetectable, however all 3 genomic targets were detected in the defective proviral population (in single- or dual-positive droplets), suggesting the negative intact result was not due to polymorphisms causing failure of the PCR to detect a region of the provirus. In only 16 (2.3%) of the 696 samples tested, the CS-IPDA failed to detect any signal for one of the targets, likely due to polymorphisms in the primers and/or probe binding sites. Conclusions: The CS-IPDA has a very low (<3%) false-negative rate due to PCR failure in samples from Kenya, where the most prevalent global subtypes circulate, suggesting it effectively tolerates diversity across multiple subtypes. References: 1. Kinloch, NN, et al. (2021) HIV-1 diversity considerations in the application of the Intact Proviral DNA Assay (IPDA). Nat Commun 12, 165. 2. Cassidy, NAJ, et al. (2022) HIV reservoir quantification using cross-subtype multiplex ddPCR. iScience 25, 103615. Impact of Early ART Initiation With BIC/FTC/TAF on HIV-1 Reservoir Decay During Primary Infection Sònia Vicens-Artés 1 , Elisa Moraga 1 , Juan Ambrosioni 1 , Elisa De Lazzari 2 , Lucía Bailón 3 , Paula Suanzes 4 , Carmen Busca 5 , Beatriz Mothe 6 , Jorge Del Romero 7 , Vicenc Falco 4 , Anna Cruceta 1 , Josep Mallolas 1 , Jose Alcami 1 , José M. Miró 2 , Sonsoles Sánchez-Palomino 1 , for the BIC-PHI Study Group 1 August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain, 2 Hospital Clinic of Barcelona, Barcelona, Spain, 3 Fundació Lluita contra les Infeccions, Barcelona, Spain, 4 Hospital Vall d'Hebron, Barcelona, Spain, 5 Hospital La Paz Institute for Health Research, Madrid, Spain, 6 Fundació Lluita contra la SIDA, Badalona, Spain, 7 Centro Sandoval, Madrid, Spain Background: Viral reservoir is established early during primary HIV infection (PHI). Early antiretroviral therapy (ART) is essential to limit reservoir development. The aim of this work was to evaluate the impact of rapid

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CROI 2025 150