PROJECT SUMMARY/ABSTRACT –VIRAL PATHOGENESIS & PERSISTENCE CORE E Viral Pathogenesis & Persistence Core E supports the needs of CFAR investigators and their innovative projects, while maintaining strong capacities to assist researchers with more traditional basic and translational virology research. The Core leverages the combined strength of virologists from both Case and Pitt to facilitate research on HIV-1 pathogenesis and persistence by RUSTBELT CFAR investigators. Core E provides investigators with innovative services to measure HIV-1 persistence with assays that identify and quantify latent, expressed, and inducible HIV-1, paired with pioneering ex vivo methods to examine the efficacy of novel Latency Reversal Agents (LRA) and other curative strategies in fully autologous systems, making deeper characterization of HIV-1 reservoir dynamics and clonality widely available. Case and Pitt also have complementary systems to quantify HIV-1 persistence, having originally pioneered ultrasensitive single copy quantitative PCR (qPCR) assays targeting HIV-1 gag/pol and established novel techniques to measure HIV-1 env RNA transcripts by induced transcription–based sequencing. These methods have been continually refined and expanded to now quantify intact vs. defective proviral DNA and automated for sensitive detection of HIV-1 RNA in plasma or culture supernatants. Core E also provides advanced viral outgrowth assays to assess inducible, infectious HIV-1 in new ways, such as using a fully autologous system whose performance characteristics meet or exceed the gold standard in the field. Advances in automation have also increased the throughput, consistency, and quality of near full-length HIV-1 sequencing, while new technologies have enabled integration site analysis from the same sample at a single cell level. Core E also provides advanced imaging platforms to study HIV-1 infection at single virion resolution, including real-time live cell imaging. The focus of Core E on cutting edge virology is designed to complement our second laboratory core, Core F (Systems Biology & Biostatistics), which focuses on the host through offerings in single host cell genomics and immunology. The combination of the transcriptomic and proteomic capabilities of Core F with the validated HIV latency and reversal models made available by Core E opens the door to applying these detailed analytical techniques to cutting edge studies of basic virology, prevention, treatment, and cure research. Core E will also support HIV prevention initiatives in coordination with the Clinical Sciences Core D, and the EHE SWG2. The Core will continue to work closely with Uganda Core C, which is now one of two national sites for HIV drug resistance testing in Uganda, to transfer advanced technology to our partner organizations in Kampala, Uganda, and enhance the ability of Ugandan investigators to conduct informative virological studies including Cure research. Finally, and most importantly, Co...