Ensuring a world safe from microbial threats remains a pressing challenge. However, significant gaps remain in our understanding of viral diseases. This proposal employs genomics to address these three major needs: Genomic detection and epidemiology of emerging viral threats in humans and vectors​. For emerging viruses, such as Lassa, Ebola, Zika, Powassan, and other NIAID Category A-C Priority Pathogens, the natural prevalence, evolution, genetic diversity, and transmission among and between humans and zoonotic hosts are not well characterized, which threatens our ability to prepare for and even identify human cases when they occur. Pathogen genomics provides critical public health insight into the movement of viral threats. In partnership with established clinical, public health, and academic collaborators in West Africa and Massachusetts, this project will sequence viruses both human patients and zoonotic reservoirs (African rodents, American ticks and mosquitoes), publicly distribute genomic and metagenomic datasets, and rapidly deliver analyses relevant to the evolution, epidemiology and ecology of these viruses, with a focus on insights that may inform the ongoing development work of diagnostics, therapeutics, and other intervention strategies. Tissue-specific and single-cell characterizations of host response and viral dynamics during viral hemorrhagic fever infection​. Viral hemorrhagic fevers (VHFs) like Ebola and Lassa are highly fatal, but how the molecular and cellular host response mechanisms differ between fatal and non-fatal cases is poorly understood. In partnership with NIAID’s Integrated Research Facility in Frederick, MD (BSL-4), this project will sequence ​in vivo​ VHF infections in animal model organisms, simultaneously profiling both the host transcriptional response and viral replication and evolution within different host tissues, and utilizing single-cell RNA-seq approaches to interrogate individual host PBMC types. This will provide a new understanding of cell-specific host response to VHF infections, with insights into the differing mechanisms behind fatality and recovery and inform the development of countermeasures for VHFs. Systematic discovery of viral antigens using thousands of rationally designed oligonucleotides​. For most viral threats, our ability to respond is hampered by a lack of systematic, high-throughput methods that evaluate and inform the development of therapeutics and vaccines. Although cytotoxic T lymphocytes can afford protection against a wide range of viral antigens, there has not been a systematic investigation of all possible immunogenic peptides. Utilizing a “systems virology” approach, we will design, create, evaluate, and test a large synthetic library of oligos that span large portions of hundreds of human viral pathogens and produce novel candidate targets for vaccine design.