RT Journal Article
SR Electronic
T1 Updated phylogeny of Chikungunya virus suggests lineage-specific RNA architecture
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 698522
DO 10.1101/698522
A1 Adriano de Bernardi Schneider
A1 Roman Ochsenreiter
A1 Reilly Hostager
A1 Ivo L. Hofacker
A1 Daniel Janies
A1 Michael T. Wolfinger
YR 2019
UL http://biorxiv.org/content/early/2019/08/23/698522.abstract
AB Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are 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 nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3’UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3’UTR architecture among different CHIKV lineages.