Zika virus RNA structures act cooperatively to regulate the production of viral non-coding RNAs with different impact in mosquito and human hosts

Abstract

The explosive epidemic of Zika virus (ZIKV), together with the unique properties of this virus regarding transmission and disease, posed a tremendous challenge to understand the molecular processes that lead to infection and pathogenesis. ZIKV is an enveloped RNA virus, member of the Flaviviridae family, together with other important human pathogens transmitted by mosquitoes, such as dengue and yellow fever.In order to dissect functions and mechanisms of viral RNA structures during ZIKV infection, we constructed infectious clones and reporter viruses from local Argentinean isolates. Using these tools, we analyzed the role of each 3’UTR element and found a domain comprised by two stem loops (SL1 and SL2) that was essential for infection in human cells. Surprisingly, a virus lacking this domain was able to infect and propagate in mosquitoes and mosquito cells. We studied the mechanisms by which the virus displayed different host restrictions and found the absolute requirement of accumulation of non-coding viral RNAs, known as sfRNAs, in human cells.The sfRNAs have been previously involved in evasion of antiviral responses and are products of partial degradation of the viral genome. Construction of a battery of recombinant viruses tested in adult Ae aegypti mosquitoes and human cells indicated that SL1 and SL2 function in a cooperative manner to generate sfRNAs. In this regard, the presence of SL2 was found to be essential for SL1 function. Our results support a model in which the two RNA elements at the ZIKV 3’UTR control both sfRNAs production and differential replication in the two hosts. These findings are unique for ZIKV, because even though the SL domain modulates differential host replication in other flaviviruses, only in ZIKV the function is essential for productive infection in human cells. This work provides new ideas regarding the impact of 3’UTR elements on host adaptation, with possible implications in viral transmission.