Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the Togaviridae family, has recently emerged in the Americas from two originating continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent re-emergence patterns, and the current status of the CHIKV spread, an updated ... [Show full abstract] phylogeny of the virus is needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from full open reading frame nucleotide sequences. Within this phylogeny, we propose the presence of several distinct lineages in Africa which were once considered a single lineage. In parallel, thermodynamic modeling of CHIKV untranslated regions (UTRs) reveals a cascade of evolutionarily conserved RNA structures, in particular in the 3' UTR. We provide evidence for the duplication of non-coding RNAs (ncRNAs) in recently emerged Carribean CHIKV isolates and propose the existence of lineage-specific duplicated ncRNAs in different CHIKV lineages.