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.

An annotated nucleotide alignment of the C-coding region between TBFV and three MBFV groups (JEV, DENV and YFV) was constructed based on a previously presented alignment (16) but modified to include newly sequenced distantly related mTBFV, sTBFV and KADV isolates (Supplementary Figure S1A ). The C protein TBFV/MBFV alignment (available on request) was used to anchor the divergent nucleotide sequences. The annotations include the 5 0 -CYCL of MBFV, an 8-nt long cyclisation domain highly conserved between all MBFVs (16) . The 5 0 -CYCL interacts with a complementary sequence 3 0 -CYCL in the 3 0 -UTR to form a dsRNA panhandle, a vital element of the replication promoter that initiates viral RNA synthesis (16) . For the TBFV the 21-nt long 5 0 -CYCL is located in the 5 0 UTR (i.e. outside the alignment in Supplementary Figure S1A ; highlighted in Figure 1A ). The 5 0 -CYCL for MBFV mapped to the capsid gene and, among the TBFV, aligns optimally with a region that is identified only in TUYV (Supplementary Figure S1A) .