CROI 2025 Abstract eBook

Abstract eBook

Poster Abstracts

Results: TRIM5α was a top hit for the screens using the N57A and A105T CA mutants. While CA mutants that lack CypA binding are known to be hypersensitive to TRIM5α the N57A and A105T TRIM5α-sensitive viruses maintain CypA binding. Therefore, other mechanisms are implicated in their TRIM5α susceptibility. Conclusions: Through screening of additional CA mutant viruses, we aim to map mutations and characteristics in CA that lead to changes in TRIM5α restriction. Additionally, we are determining the mechanism of TRIM5α recognition of the mutant viruses using depletion and binding assays. This insight into TRIM5α recognition of the CA will give us new understanding of how our host cellular defenses inhibit HIV. A Virus-Packageable CRISPR Screen to Uncover Genes Underlying SIVcpz Replication in Human Cells Michael Young, Molly Ohainle University of California Berkeley, Berkeley, CA, USA Background: Human immunodeficiency virus (HIV) is the result of the cross-species transmission of simian immunodeficiency viruses (SIVs) that endemically infect non-human primates. While pandemic HIV-1 M is the result of a chimpanzee lentivirus (SIVcpz) cross-species transmission to humans, lentiviruses from other non-human primates have also spilled over into humans. Since the emergence of HIV, the field has sought to characterize the cell-intrinsic determinants of primate lentivirus cross-species transmission. However, the factors that enable lentivirus zoonosis are not completely understood. Methods: Our lab developed a high-throughput HIV-CRISPR screen to unveil cell-intrinsic proviral and antiviral factors in the context of HIV infection. The approach involves a uniquely engineered sgRNA and Cas9 vector which allows for packaging of the sgRNA sequence from progenitor cells. We are now implementing the HIV-CRISPR screening methodology to reveal barriers specific to pre -pandemic lentiviruses, such as SIVcpz, in human cells. Results: We have screened 3 genetically diverse SIVcpz viruses using a genome wide sgRNA library in THP-1 cells. Among our hits are genes involved in the tethering of virions at the cell surface and the inhibition of broadly important transcriptional machinery for lentiviral replication. Conclusions: Our unbiased screening approach will help us better define the evolutionary barriers of SIV infection in human cells. We aim to identify key host factors that may underlie the evolutionary origins of HIV. Impact of Pre-Existing Immune Activation on SARS-CoV-2 Incidence and Disease During the First Wave Diana S. Yang 1 , Cong Xie 1 , Suji Udayakumar 1 , Sanja Huibner 1 , Karen Colwill 2 , Anne-Claude Gingras 2 , Joshua Kimani 3 , Rupert Kaul 1 1 University of Toronto, Toronto, Canada, 2 Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada, 3 Partners for Health and Development, Nairobi, Kenya Background: During the first wave of COVID-19 there was a relatively low burden of disease in many Sub-Saharan African (SSA) countries despite considerable SARS-CoV-2 transmission. Immune activation prior to pathogen challenge may protect against subsequent, unrelated infections. We hypothesized that female sex workers (FSWs) would experience frequent exposures to SARS-CoV-2 through social and physical contact early in the pandemic, and that pre-existing immune activation would protect against infection and/or symptomatic disease. Methods: FSWs from the Sex Worker Outreach Program (SWOP) clinics in Nairobi, Kenya had pre-pandemic blood and other biological samples collected mid-2019 (pre-pandemic), with follow up samples collected approximately 1 year later. SARS-CoV-2 infection was defined by the presence of antibodies against >=2 of 3 SARS-CoV-2 antigens (RBD, Spike, N). Plasma levels of pro inflammatory markers in pre-pandemic samples were quantified using the MSD V-PLEX proinflammatory panel 1. Immune activation was defined using a composite scoring system composed of the 7 pro-inflammatory markers: IL-1ß, IL-2, IL-6, IL-8, IL-12p70, IFNγ, and TNF. Cytokine levels were divided into quartiles and a score ranging from 1 (1st quartile) to 4 (4th quartile) was assigned to each marker and summed to generate the immune activation score. 100 cases who subsequently went on to acquire SARS-CoV-2, and 100 controls were matched 1 to 1 for age (±5 years), and visit date (±2 weeks). Results: Pro-inflammatory cytokines were detected robustly in cryo-preserved plasma. There was no significant difference in immune activation score between cases and controls (mean, 17.42 vs. 17.53; p = 0.86); furthermore, levels of the 7 individual cytokines were not significantly different between cases and controls

(p>0.05). When looking at symptoms after SARS-CoV-2 infection, there was no significant difference in immune activation score nor in the individual cytokines between symptomatic vs. asymptomatic cases (p>0.05). Conclusions: Levels of preceding systemic immune activation, as defined by plasma inflammatory markers, did not predict SARS-CoV-2 infection nor symptomatic disease in those who did become infected. This suggests that the low burden of severe COVID-19 disease in many SSA countries was not due to increased immune activation in this region. Future studies should investigate the role of immune activation at mucosal infection sites more proximal to viral entry. Unique SARS-CoV-2 Variants and Inflammatory Milieu in Urine of Severe COVID-19 Participants Aarthi Subramani 1 , Tatianna Travieso 1 , Zeguo Sun 2 , Danai Psaradelli 1 , Mary Klotman 1 , Weijia Zhang 2 , Maria Blasi 1 1 Duke University School of Medicine, Durham, NC, USA, 2 Icahn School of Medicine at Mount Sinai, New York, NY, USA Background: Acute kidney injury (AKI) is a common complication in people hospitalized with COVID-19. The etiology of AKI is likely multifactorial, with potential contributions from hemodynamic compromise, systemic inflammation, cytokine release, and local viral infection. People with COVID-19 and AKI have higher levels of systemic markers of inflammation than those with normal kidney function. To understand the pathophysiology of AKI in people with COVID-19, we investigated the presence of SARS-CoV-2 RNA in urine samples from participants with mild or severe disease and explored the associated inflammatory profiles. Methods: Urine specimens were obtained from 66 people with COVID-19 hospitalized in the intensive care unit (ICU) and 26 with mild symptoms. We performed single genome amplification of viral RNA in urine and respiratory tract samples. We also performed scRNAseq and a multiplexed analysis of inflammatory markers in the urine to compare renal inflammatory signatures between people with mild symptoms and those with severe COVID-19 with or without AKI. Results: Viral RNA was detected in urine samples from a small number of COVID-19 people hospitalized in the ICU. Single viral genome analysis demonstrated a predominant pattern of deletions and mutations at the furin-cleavage site of the SARS-CoV-2 spike gene, which provided a replicative advantage in renal podocytes but not in airway epithelial cells grown at the air-liquid interface. People with AKI showed elevated levels of IL-6, IL-8, IL-18, MCP-1, Renin, TIMP-1, and Clusterin, suggesting an association between these inflammatory markers and renal disease. scRNAseq analysis of urine-derived cells revealed a higher frequency of macrophages, T cells, podocytes, and tubular cells in people with severe COVID-19, AKI, and viral shedding in urine. Pathway analysis of tubular cells from people with AKI showed enrichment of DNA damage-responsive pathways compared to those without AKI. Conclusions: We identified unique SARS-CoV-2 variants in urine samples from participants with severe COVID-19, which demonstrated a replicative advantage in renal podocytes, raising the possibility of organ-specific selection of viral variants. We also observed higher levels of inflammatory markers and inflammatory cells in urine samples of people with severe COVID-19 and AKI. Our data demonstrate the ability to use urine samples to noninvasively study renal infection, characterize cellular diversity, and identify altered pathways in the setting of COVID-19 AKI. Bile Acids in the Modulation of Antiviral Immune Response Eileen F. Serrano 1 , Diego A. Diaz-Dinamarca 1 , Paul Dawson 1 , Ali Muhammad 1 , Grace A. McComsey 2 , Rafael F. Medina 1 , Elias Haddad 3 , Nadine Rouphael 1 , Slim Fourati 4 , Jeffrey A. Tomalka 1 , Rafick P. Sekaly 1 1 Emory University, Atlanta, GA, USA, 2 Case Western Reserve University, Cleveland, OH, USA, 3 Drexel University, Philadelphia, PA, USA, 4 Northwestern University, Chicago, IL, USA Background: Bile acids (BAs) are produced from cholesterol in the liver as primary BAs and modified by gut microbiota becoming secondary BAs. Besides their primary role in solubilizing fats, these metabolites have been shown to modulate innate and adaptive immune function, making BAs a link between host metabolism and immune response. BAs regulation of immunity is increased by the multiple modifications that BAs can undergo, like sulfation. Methods: In this study, we used a multi-omic approach to identify mechanisms of pathogenesis during acute SARS-CoV-2 in a subset of 270 COVID-19 volunteers from the IMPACC cohort. To understand how BAs, and their modifications,

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CROI 2025