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.

In silico analysis of SL6 in the TBFV subgroup It was found that the overall folding of the first 333 nt of TBFV was highly conserved among several members of the mTBFV subgroup (16, (26) (27) (28) , with six stable SLs (enumerated 1-6 in Figure 1A ). This analysis was extended to investigate the conservation of SL6 in the larger group of distantly related mTBFV, sTBFV and KADV (37) . A nucleotide alignment of the C region was generated and optimized by the introduction of numerous gaps (Supplementary Figure S1A) ; it shows that divergent RFV, GGYV and KSIV (distant virus species of the mTBFV) maintained homology in the SL6 region. However, some nucleotide perturbations in the SL6 region were observed between mTBFV, sTBFV (MEAV, TYUV and SREV) and KADV proving that the region between the initiation codon and SL6 had evolved with frame shifts as we previously demonstrated (16) . We conducted MFold analysis to investigate the presence of SL6-like structures in the distantly related mTBFV (RFV, GGYV and KSIV), sTBFV and KADV groups ( Figure 1B) .