Surveying the global virome: identification and characterization of HCV-related animal hepaciviruses

Abstract

Recent advances in sequencing technologies have greatly enhanced our abilities to identify novel microbial sequences. Thus, our understanding of the global virome and the virome of specific host species in particular is rapidly expanding. Identification of animal viruses is important for understanding animal disease, the origin and evolution of human viruses, as well as zoonotic reservoirs for emerging infections. Although the human hepacivirus, hepatitis C virus (HCV), was identified 25years ago, its origin has remained elusive. In 2011, the first HCV homolog was reported in dogs but subsequent studies showed the virus to be widely distributed in horses. This indicated a wider hepacivirus host range and paved the way for identification of rodent, bat and non-human primate hepaciviruses. The equine non-primate hepacivirus (NPHV) remains the closest relative of HCV and is so far the best characterized. Identification and characterization of novel hepaciviruses may in addition lead to development of tractable animal models to study HCV persistence, immune responses and pathogenesis. This could be particular important, given the current shortage of immunocompetent models for robust HCV infection. Much remains to be learned on the novel hepaciviruses, including their association with disease, and thereby how relevant they will become as HCV model systems and for studies of animal disease. This review discusses how virome analysis led to identification of novel hepaci- and pegiviruses, their genetic relationship and characterization and the potential use of animal hepaciviruses as models to study hepaciviral infection, immunity and pathogenesis. This article forms part of a symposium in Antiviral Research on "Hepatitis C: Next steps toward global eradication."

Figure 1

Phylogenetic analysis of the NS3 (helicase) region of hepaciviruses. Amino acid sequences were aligned with MUSCLE 3.8 (Edgar, 2004), and the trees constructed using maximum likelihood methods as implemented in the MEGA 6 software package (Tamura et al., 2013). Optimum maximum likelihood models for NS3 alignments were determined and used for phylogenetic reconstruction. Phylogenetic analysis used the Le-Gascuel model with gamma (γ) distribution (5 rates) and invariant sites (LG+γ+I). Bootstrap re-sampling was used to determine robustness of grouping. Hepacivirus sequences are annotated using their GenBank accession numbers, except for the unpublished hepacivirus sequences found in deer mice, Peromyscus leucopus (labeled as RHV-PL-XXX.). Mammalian phylogeny is merely a representative drawing of published data (Meredith et al., 2011).