Viruses with RNA based genomes often contain structurally defined regions that are engaged in the viral infection cycle. The unpacking of viral RNA genomes to a deployed state is likely a structurally dynamic event that establishes the first intracellular host-pathogen interactions via viral and cellular RNA binding proteins. My research aims to explain and relate the structural changes of viral genomes using chemical biology, high-throughput sequencing, and computational structural methods. The Rosetta software suite will augment current viral RNA structural workflows to generate high-resolution structural models from experimentally derived data. These models will be utilized to guide research efforts characterizing the relationship between viral RNA structure and host-pathogen interactions.