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.

Thermodynamic and phylogenetic analysis of large sequence data sets indicated that all TBFVs including even the distantly related mTBFV, KADV and sTBFV form an SL6-like structure with an exposed conserved hexanucleotide although the molecular details of the predicted stem-loop varied among the mTBFV, sTBFV and KADV subgroups ( Figure 1B) . In similar manner, an SL6-like structure has been predicted for MBFV although with less stability in comparison to SL6 in TBFV. Two other flavivirus groups NKV and PABV demonstrated no significant sequence homology with the TBFV SL6 region although the genome of KRV (PABV group) formed a thermodynamically stable structure in close vicinity to the TBFV SL6 with a similar terminal loop motif CCAA (TBFV-UGCCAA) (Supplementary Figure S1) .