Characterization of a canine homolog of hepatitis C virus

Abstract

An estimated 3% of the world's population is chronically infected with hepatitis C virus (HCV). Although HCV was discovered more than 20 y ago, its origin remains obscure largely because no closely related animal virus homolog has been identified; furthermore, efforts to understand HCV pathogenesis have been hampered by the absence of animal models other than chimpanzees for human disease. Here we report the identification in domestic dogs of a nonprimate hepacivirus. Comparative phylogenetic analysis of the canine hepacivirus (CHV) confirmed it to be the most genetically similar animal virus homolog of HCV. Bayesian Markov chains Monte Carlo and associated time to most recent common ancestor analyses suggest a mean recent divergence time of CHV and HCV clades within the past 500-1,000 y, well after the domestication of canines. The discovery of CHV may provide new insights into the origin and evolution of HCV and a tractable model system with which to probe the pathogenesis, prevention, and treatment of diseases caused by hepacivirus infection.

Fig. 1.

In situ hybridization of CHV RNA in canine liver. (A) Uninfected liver. (B and C) Infected liver. Top, Middle, and Bottom represent fluorescent, bright-field, and superimposed images, respectively (bright red dots indicate probe bound to CHV genomic RNA; blue is hematoxylin counterstain).

Fig. 2.

Structural and functional map of the CHV genome. (A) Structural protein cleavage is mediated by cellular signal peptidase (black triangle); NS2–NS3 cleavage is mediated by the NS2–NS3 autoprotease (white triangle); and cleavage of other nonstructural proteins is mediated by NS3–NS4A protease complex (gray triangles). (B) Amino acid sequence divergence scan of CHV polyprotein, HCV genotypes, and GBV-B. (C) Amino acid sequence of different viruses adjacent to predicted protease cleavage sites (10 aa on each side are shown). (D) Reported functional role of different proteins in the virus life cycle.

Fig. 3.

Sequence and secondary structure of CHV 5′ UTR. Bases conserved among different hepaciviruses are shown with different colored circles. The miR-122 binding sites and different internal ribosome entry site stems are labeled according to previously reported hepacivirus 5′ UTR structures (34).

Fig. 4.

Phylogenetic analysis of conserved regions in the helicase (motifs I–VI) (A) and RdRp (B) genes of CHV aligned with representative members of the Hepacivirus, Pegivirus (GBV viruses A, C, and D), Pestivirus, and Flavivirus genera. Translated amino acid sequences were aligned with the program ClustalW. Trees were constructed by neighbor joining of pairwise amino acid distances with the program MEGA5 (according to the distance scale provided). Bootstrap resampling was used to determine robustness of branches; values of ≥70% (from 1,000 replicates) are shown. Regions compared corresponded to positions 3697–4477 (helicase domain of NS3) and 7705–8550 (RdRp in NS5B; numbered according to the AF011751 HCV genotype 1a reference sequence). A listing of virus abbreviations and original accession numbers for each sequence are provided in Table S2.