Viruses encode novel subsets of uncharacterized genes (predicted and hypothetical ORFs and noncoding RNAs) which can be expressed to modulate virus replication efficiency and/or host antiviral responses both in vitro and in vivo. Using highly pathogenic human respiratory and systemic viruses which cause acute and chronic life-threatening disease outcomes, we test the hypothesis that RNA and DNA viruses encode common and unique mechanisms to manipulate virus replication efficiency and host responses to determine severe disease outcomes. To address this hypothesis, the proposal takes advantage of novel expression vector platforms, synthetic gene design, reverse genetics, animal models of human disease, and a defined set of biochemical and immunologic assays to identify, characterize and then determine the role of uncharacterized genes in the lung (e.g., H5N1, SARS-CoV and human coronavirus EMC-1) and in systemic infections (e.g., Ebola and Human Herpes virus 8) both in vitro and in some instances, in vivo. Specifically, we test the hypothesis that these viral uncharacterized genes may function to auto-regulate virus replication efficiency, and/or function as an agonist or antagonize the host intracellular milieu to enhance virus replication, most likely be altering p53, innate immune sensing, inflammasome, apoptosis, and/or NF-? signaling. To achieve these goals, a highly interactive group of experts in RNA and DNA virus pathogenesis and immunity work collectively to create a robust screening platform that rapidly identifies and characterizes the function of these uncharacterized genes in replication and pathogenesis. By identifying common key host bottleneck genes that are targeted by disparate virus pathogens, we identify rationale broadly relevant therapeutic targets for ameliorating disease outcomes in vivo. Importantly, this platform is: a) portable, b) can be rapidly applied to other highly pathogenic respiratory and microbial pathogens, c) will rapidly identify novel targets for therapeutic intervention, d) improve strategies for live attenuated or vectored virus vaccine design, and e) improve global responses to newly identified, epidemic disease outbreaks in human populations.
H5N1, SARS-CoV, human coronavirus EMC-1, Ebola, and human herpesvirus 8 are on the list of NIAID Category A-C pathogens and Emerging/Re-Emerging pathogens. We propose to decipher the function of uncharacterized genes (unknown ORFs, hypothetical ORFs, non-coding RNAs) expressed by these RNA and DNA viruses in viral pathogenesis and evasion of host immunity. This will expand our understanding of the biology of these pathogenic human viruses and improve our ability to treat these viral infections.
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