A conserved RNA structure at the capsid-coding sequence of Zika virus genome is required for viral replication in a host-dependent manner

Flaviviruses are important human pathogens mainly vectored by arthropods. They contain RNA genomes that fold into complex structures with biological functions in viral infection. Zika virus is a flavivirus that has caused significant outbreaks and epidemics around the world. In this study, we used Zika virus to identify functional RNA structures present in the viral coding sequence. We manipulated an infectious clone from an Argentinean Zika virus isolate to dissociate protein-coding sequences from cis-acting RNA structures and discovered an RNA element in the capsid coding region that is essential for Zika virus replication in mosquito cells. Point mutations, disrupting the identified structure, impaired infection in mosquito cells and rendered viral attenuation in mammalian cells. Selection of revertant viruses in cell culture restored the RNA structure and the viral replication capacity. Our studies provide a basic understanding of the flavivirus genome organization, which is necessary for designing rational antiviral strategies.