Figure 1 (A) Transmission electron micrograph of negative-stained virion of gill-associated virus (GAV). (B) Transmission electron micrograph of partially disrupted yellow head virus (YHV) virion displaying the internal nucleocapsid and a ring-like structure which appears to be a disrupted virion in cross-section. (C) Schematic illustration of an okavirus virion. (D) Transmission electron micrograph of unenveloped cytoplasmic nucleocapsids in a thin section of GAV-infected shrimp cells. The bars represent 100 nm.
(Electron micrographs provided by K.M. Spann, P. Loh, J.A. Cowley and R.J. McCulloch and reproduced with permission.)
Figure 2 Schematic representation of the 26,662 nt polyadenylated (+) ssRNA genome of YHV (g RNA1) and the two 3′-coterminal sub-genomic RNAs sg mRNA2 and sg mRNA3. Functional domains in ORF1a: hydrophobic regions (HD1-HD4), 3C-like protease (3CLP), papain-like protease (PLP1) and a domain with homology to PLP1 but lacking the canonical α + β fold of papain-like proteases (PLPx). Functional domains in ORF1b: RNA polymerase (RdRp), cysteine- and histidine-rich zinc finger and helicase (Zn-Hel), exoribonuclease (ExoN), uridylate-specific endoribonuclease (N) and ribose-O-methyl transferase (MT). ORF2 encodes the nucleoprotein (p20). ORF3 encodes a precursor polyprotein (pp3) that undergoes post-translation processing to generate envelope glycoproteins (gp116 and gp64) and an N-terminal triple-membrane-spanning fragment of unknown function (p25). The ribosomal frameshift site (RFS) allows read-through translation of polyprotein pp1ab from ORF1a and ORF1b. Known (▼) and likely (▽) sites of proteolytic cleavage of expressed polyproteins pp1a and pp1ab are indicated together with the two signal peptidase type 1 cleavage sites in pp3 (↓).
Figure 3 Unrooted phylogenetic tree of representatives of each of the six okavirus genotypes based on a 781 nucleotide region of the ORF1b gene [see Wijegoonawardane et al. (2008) for strain details and expanded phylogenetic analyses]. The sequences were aligned using Clustal W, phylogenetic inference was determined by the neighbor-joining method and the tree was constructed using Treeview software. Bootstrap values obtained for a 1000 replicate analyses were 1000 at each genotype branching node. Branch lengths are proportional to phylogenetic distance and the bar represents a sequence divergence of 1.0%.