FIG 6. Models of predicted secondary and tertiary structures of kobuvirus Type IV IRESs.

The model of the Ferret kobuvirus (FKV) IRES (A) was derived as described in the text and the model of the IRES of PKV-1 strain sw/S-1-HUN/2007 (B) is based on previous proposals (Reuter et al., 2009). Nucleotide differences between the 22 current PKV strains are assigned to different classes as indicated in the inset key, and as defined in the legend for Fig. 2. Domains are labeled II and III; individual helical segments are labeled II1, II₂, III1; hairpins are labeled IIIb, IIId, etc. For consistency with the current nomenclature, the additional hairpin element in the FKV and PKV IRESs was named “IIIb2”. Stem 1 and stem 2 are elements of the pseudoknot. AUG triplets marked with a solid black bar represent the translation initiation site for the viral polyprotein. Sequence motifs in domain II and III of FKV and PKV-1 IRESs that are conserved in other Type IV IRES, as indicated by grey shading. (C) Secondary and tertiary 5’-terminal structures of ovine kobuvirus 1 (OKV-1) strain sheep/TB3/HUN/2009 and (D) Ferret kobuvirus, predicted using pKnotsRG. This OKV-1 model has been described elsewhere (Sweeney et al., 2012). Domains A, B, and C are labeled, and nucleotides are numbered in both models. (E) Schematic representations of the 5’ UTRs and adjacent L protein coding region of caprine kobuvirus, porcine kobuvirus, ferret kobuvirus and ovine kobuvirus. 5’-UTRs are divided into domains to show the Type IV IRES in FKV and PKV-1 (orange), the type V IRESs in caprine kobuvirus and ovine kobuvirus and the conserved domain A/B/C/pseudoknot region (blue), which in Aichi virus constitutes the 5’-terminal ori (Sasaki et al., 2001). The L protein region is shaded pink. The ori region, nucleotides forming the Type IV and Type V IRESs and the L protein coding region are labeled; the nucleotides at the borders of conserved regions or defined functional domains are indicated, as are nucleotide sequence identities (ori, IRES) or amino acid sequence identities (L protein). The FKV 5’-UTR is suspected to be incomplete.