FIG 3.

Genome characteristics of SFV, sequencing coverage, and comparisons of the SFV genome and genes to those of representatives of the Flavivirus genus. (A) Genome characteristics of SFV, which is composed of typical flaviviral proteins organized in two open reading frames, unlike classical flaviviruses. (B) Sliding-window analysis showing pairwise distances of SFV amino acids from those of other flaviviruses. Protein sequences from the two SFV ORFs are concatenated for analysis. HCV, hepatitis C virus; YFV, yellow fever virus; DV, dengue virus. Intergenus divergence (SFV-HCV) was compared with intragenus/interspecies divergence (DV-YFV, SFV-YFV, and SFV-DV) and intergenotype divergence (between DV genotypes). Pairwise distance is shown along the y axis. (C) Continuous high sequence coverage used to construct the SFV genome, with the 5′ and 3′ NCR further confirmed by RACE and Sanger sequencing. (D) Pairwise identities (expressed as percentages) of SFV proteins with those of representatives of the Flavivirus genus.