Alphaviruses are globally distributed +ssRNA viruses which are transmitted by mosquito vectors. Viral determinants which impact the transmission and pathogenesis of numerous alphaviruses have been identified, including amino acid coding changes in the viral attachment protein (E2). However, the role of viral RNA secondary structure in viral emergence is still poorly defined. We have developed a computational approach to compare RNA structures across the alphavirus genus in order to identify RNA structure signatures associated with specific viral properties (e.g. RNA structures unique to epidemic viruses). Using this approach we have identified several regions in the Venezuelan equine encephalitis virus (VEEV) and Sindbis virus (SINV) genomes that are predicted to contain RNA structures relevant for emergence and pathogenesis of these viruses. Surprisingly, despite encoding distinct viral RNA structures, pathogenic/epidemic strains were all observed to replicate differentially in myeloid cells, suggesting that myeloid cell replication fitness may be a hallmark of viral emergence. Recently, we compared replication of epidemic and non-epidemic strains of VEEV and observed that myeloid cell replication phenotypes were predictive of epidemic status. Presently we are using computational approaches to identify key RNA structure and mutations that drive changes in myeloid cell replication, thus contributing to emergence of epidemic VEEV.