TY - JOUR T1 - The translational landscape of Zika virus during infection of mammalian and insect cells JF - bioRxiv DO - 10.1101/112904 SP - 112904 AU - Nerea Irigoyen AU - Adam M. Dinan AU - Luke W. Meredith AU - Ian Goodfellow AU - Ian Brierley AU - Andrew E. Firth Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/03/02/112904.abstract N2 - Zika virus is a single-stranded, positive-sense RNA virus of the family Flaviviridae, which has recently undergone a rapid expansion among humans in the Western Hemisphere. Here, we report a high-resolution map of ribosomal occupancy of the Zika virus genome during infection of mammalian and insect cells, obtained by ribosome profiling. In contrast to some other flaviviruses such as West Nile, we find no evidence for substantial frameshift-induced ribosomal drop-off during translation of the viral polyprotein, indicating that Zika virus must use alternative mechanisms to downregulate levels of catalytically active viral polymerase. We also show that high levels of ribosome-protected fragments map in-frame to two previously overlooked upstream open reading frames (uORFs) initiating at CUG and UUG codons, with likely consequences for the efficiency of polyprotein expression. Curiously, in African isolates of Zika virus, the two uORFs are fused in-frame into a single uORF. A parallel RNA-Seq analysis reveals the 5′ end position of the subgenomic flavivirus RNA in mammalian and insect cells. Together, these provide the first analysis of flavivirus gene expression by ribosome profiling.Author Summary Recent Zika virus outbreaks have been associated with congenital diseases and neurological complications. An enhanced understanding of the molecular biology of this pathogen may contribute towards the development of improved treatment and control methods. We present a single-codon resolution analysis of Zika virus translation in mammalian and mosquito cells using ribosome profiling. The analysis revealed two hitherto uncharacterized uORFs in the 5′ leader of Zika virus Brazilian isolate PE243, both of which are occupied by ribosomes during infection. In contrast, these two uORFs are fused into a single uORF in African isolates. This observation provides a new avenue for further investigations into potential factors involved in the emergence of Zika virus from a rarely detected pathogen into a major epidemic. ER -