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We previously reported that deletion of a 44-nucleotide element in the 3′ untranslated region (UTR) of the Chikungunya virus (CHIKV) genome enhances the virulence of CHIKV infection in mice. Here, we find that while this 44-nucleotide deletion enhances CHIKV fitness in murine embryonic fibroblasts in a manner independent of the type I interferon response, the same mutation decreases viral fitness in C6/36 mosquito cells. Further, the fitness advantage conferred by the UTR deletion in mammalian cells is maintained in vivo in a mouse model of CHIKV dissemination. Finally, SHAPE-MaP analysis of the CHIKV 3′ UTR revealed this 44-nucleotide element forms a distinctive two-stem-loop structure that is ablated in the mutant 3′ UTR without altering additional 3′ UTR RNA secondary structures.