Figure 1.

(A) Representations of ZIKV, TBEV, MODV and RBV xrRNA structures, illustrating two- (above) and three-dimensional (below) contacts. The proposed stem-interactions α, β, γ, δ and ε are given in blue, green, magenta, red and orange, respectively. Nucleotides involved in the base triple interactions are shown in bold. (B) Sequences of ZIKV and CFAV xrRNA, in structural alignment with a collection of various tick-borne and no-known-vector flaviviruses, revealing covariations in this region. Grey columns in the background depict which nucleotides are involved in the base triple interaction. Accession numbers used for sequences were: Zika virus isolate 15555 (ZIKV), MN025403; Cell fusing agent virus isolate Guadeloupe (LR694081); Tick-borne encephalitis virus Sofjin-HO (TBEV), AB062064; Spanish goat encephalitis virus (SGEV), NC_027709; Tick-borne encephalitis virus Neudoerfl (WEST), U27495; Langat virus strain TP21 (LANG), AF253419; Louping ill virus LI3/1 (LOUP), KP144331; Karshi virus strain LEIV 2247 (KARS), AY863002; Deer tick virus strain ctb30 (DEER), AF311056; Powassan virus strain LB (POWA), L06436; Modoc virus (MODV), NC_003635; Rio Bravo virus (RBV), JQ582840; Montana myotis leukoencephalitis virus (MMLV), NC_004119; Apoi virus (APOIV), AF452050