Fig 5. Secondary structure at the 5´-termini of the PEDV RNA genome.

Multiple stem-loop (SL) structures have been predicted to be present in the 5´-terminal region of the PEDV genome [21]. The structure, termed SL1, closest to the terminus, in the CV777 reference strain is indicated in panel (a). A similar structure, predicted for the consensus Br1/87 sequence, is shown in panel (b). Note, the sequence marked in blue is the “reverse complement” of the sequence marked in red from panel (a). The conserved stems within SL1 are boxed but the apical loop region is distinct. In panel (c), a comparison of secondary structure predictions derived by M-fold for the CV777 5´-terminal sequence (i) and the consensus Br1/87 sequence (ii), are shown. The structures have the same apical loops as the SL1 structure shown in panels (a) and (b). The extended sequences (in blue), that include self-complementary regions extending beyond the TRS are indicated in panel (c) (iii). The complementary sequences (e.g. the sense and anti-sense SL2 regions) can simply base pair to each other to form an extended stem-loop structure that can be present at the 5´-terminus of the genomic and sub-genomic mRNAs (see also Fig 6).