Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus

Tuplin, A.; Evans, D. J.; Buckley, A.; Jones, I. M.; Gould, E. A.; Gritsun, T. S.

For the DENV subgroup, a marked region of SSSV was revealed in the C-coding region between positions 155-257 (start codon at position 95) when compared with the rest of the structural coding region (Figure 2) , consistent with RNA structure DV3 previously predicted between nucleotides 163-183 (28) (Supplementary Figure S1A) . Both ALIDOT-predicted DV2 and DV4 (28) fall immediately either side of the region of maximum SSSV suggesting that they are less conserved than DV3 (Supplementary Figure S1A) . STRUCTURE_DIST also predicts the formation of the DV2 and DV3 but not the SL6-like structure (Supplementary Figure S1A and Figure 2 ). However, a truncated SL6-like structure was predicted to form in all DENV serotypes, albeit at a suboptimal energy level, when the SL6-like region was folded independently from neighboring regions that form more stable overlapping structures (Supplementary Figure S1A) . Taken together, these data indicate that the DENV SL6-like structure was the least stable conformation among the MBFVs, potentially preventing its prediction by statistical approaches used here and elsewhere (28) . Despite this, the short-stem region of putative DENV SL6-like structures is highly conserved within the DENV group (DENV serotypes [1] [2] [3] [4] and also between DENV and JEV (Supplementary Figure S1A) suggesting that a linear or conformational signal at this location might have some functionality.