Project Summary: Virology and Molecular Biomarkers Core (Core J) The Virology and Molecular Biomarkers Core of the Emory CFAR provides state-of-the-art viral quantification and characterization services in support of the extensive basic, clinical, and translational HIV/SIV research being conducted at Emory University. Core J has been extremely successful in its provision of these services because 1) it limits costs to researchers through an economy of scale, 2) it is effective at responding to the constantly evolving needs of HIV/SIV researchers, and 3) it serves as a resource for training and consultation in molecular virologic assays. This proposal provides a detailed blueprint for the Core's future service provision as well as for a Tier-2 funded expansion of services and expertise that will support the growing number of investigators focused on HIV cure research. Core J will be divided into three main laboratories. The Translational Virology (TV) laboratory develops and implements quantitative viral assays that support research using nonhuman primate models of AIDS pathogenesis, prevention, and therapy. Additionally, the Core's expertise in molecular viral diagnostics has led to the validation and implementation of several new assays in response to the needs of AIDS researchers at Yerkes, including notably, cell-associated HIV and SIV DNA assays with single copy sensitivity and viral amplicon deep sequencing. The primary focus of the Core Clinical Virology (CV) laboratory is to provide virologic and molecular diagnostic assays for clinical studies of HIV infection, STIs, and co-infections in a CLIA/CAP-certified environment, as well as microbiome sequencing. These highly utilized functions will be maintained in the next project period. During the next funding period, the Core will expand its scope and menu of services in order to meet the demands of HIV/SIV/AIDS researchers that require new tools to study the establishment, maintenance, and eradication of the persistent reservoir of latently infected cells during antiretroviral therapy. It will establish a third Core laboratory, the Viral Reservoir (VR) Laboratory, with the purpose of validating and implementing quantitative, cell culture-based assays of replication competent virus in HIV- and SIV-infected CD4+ T cells. In addition, Core J will expand its menu of tests utilizing its recently acquired Illumina MiSeq deep sequencing platform to provide virus and more detailed microbiome sequencing services in support of initiatives to characterize virus integration sites, viral evolution in response to new therapies, and the relationship between the genital/gut microbiomes and HIV transmission/pathogenesis. The new activities proposed herein will significantly impact the outcomes of a large number of new and ongoing research programs at Emory University by providing the state-of-the-art virological services that are crucial for characterizing the latent viral reservoir and evaluating novel HIV cure treatment strategies.