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The quest for conserved RNAs in viral genomes
Arthropod-borne RNA viruses (arboviruses) represent a global health threat, causing millions of human and animal infections every year. Recent outbreaks of emerging and re-emerging viruses have revealed new clinical manifestations, e.g., the accumulation of congenital microcephaly cases during the Zika virus epidemic in the Americas 2015-2016. While vaccines against many of these viruses are still under development, experimental data suggest an involvement of RNA structure in viral pathogenesis. Comparative studies of RNA structure combine thermodynamic modeling, phylogenomics and homology search, thereby providing a powerful approach for characterizing the evolutionary conservation of viral genomes. In particular, untranslated regions (UTRs) of arboviruses harbor functional RNA elements, which play vital roles in virus replication and often mediate tropism. Here, the availability of large amounts of genome data allows building fine-grained models of homologous RNA structures in phylogenetically related viruses. On a broader scale, these data reveal common patterns and evolutionary traits of non-coding viral RNAs.