Fig. 2: ZIKV 5′ region.

The 5′ region of the ZIKV American isolate PE243 genome shows two non-AUG uORFs in Vero cells pre-treated with CHX (A), flash-frozen Vero cells (B, upper panel) and flash-frozen U251 cells (B, lower panel). Note that in order to visualise RPFs across the uORFs properly, the y-axis has been truncated at 10 RPM for the Ribo-Seq samples for Vero cells and 3 RPM for U251 cells, leaving some RPF counts, mainly for the main ORF, off-scale. C The 5′ region of the ZIKV African isolate Dak84 genome shows the African uORF in flash-frozen Vero (upper panel) or flash-frozen U251 cells (lower panel). Note that in Vero-infected cells, the peak marked with a red asterisk, unlike all other peaks, has an unusual read-length distribution centred on 26 nt, and this is not seen in U251-infected cells. For U251 cells infected with Dak84, only RPFs with a read length of 28 and 29 were plotted. Histograms show the positions of the 5′ ends of reads with a +12 nt offset to map the approximate P-site. Reads whose 5′ ends map to the first, second or third phases relative to codons in the polyprotein reading frame are indicated in blue, orange or purple, respectively. Capsid (C) denotes the initiation of the polyprotein (main ORF). D–F Bar charts of the percentage of ribosome-protected fragments (RPFs) in each phase relative to the polyprotein ORF. Regions with the least amount of overlapping, (coordinates given in plot titles), were selected. Reads whose 5′ ends map to the −2, −1 or 0 phases are indicated in blue, orange or purple, respectively. CHX-treated Vero cells infected with American isolate PE243 (D); flash-frozen Vero (E, upper panel) and U251 (E, lower panel) cells infected with PE243; and flash-frozen Vero (F, upper panel) and U251 (F, lower panel) cells infected with African isolate Dak84.