Serology enabled discovery of genetically diverse hepaciviruses in a new host

Genetic and biological characterization of new hepaciviruses infecting animals contributes to our understanding of the ultimate origins of hepatitis C virus (HCV) infections in humans and dramatically enhances our ability to study its pathogenesis using tractable animal models. Animal homologs of HCV include a recently discovered canine hepacivirus (CHV) and GBV-B, both viruses with largely undetermined natural host ranges. Here we used a versatile serology based approach to determine the natural host of the only known non-primate hepacivirus, CHV which is also the closest phylogenetic relative of HCV. Recombinant protein expressed from the helicase domain of CHV NS3 was used as antigen in LIPS assay to screen several non-primate animal species. Samples of 36 from 103 horses were immunoreactive and viral genomic RNA was present in 8 of the 36 seropositive animals and none of the seronegatives. Complete genome sequences of these 8 genetically diverse non-primate hepaciviruses (NPHV) showed 14% (range 6.4% - 17.2%) nucleotide sequence divergence, with most changes occurring at synonymous sites. RNA secondary structure prediction of the 383 base 5' untranslated region of NPHV was refined and extended through mapping of polymorphic sites to unpaired regions or (semi-)covariant pairings. Similar approaches were adopted to delineate extensive RNA secondary structures in the coding region of the genome, predicted to form 27 regularly spaced thermodynamically stable stem-loops. Together, these findings suggest a promising new non-primate animal model and provide a database that will aid creation of functional NPHV cDNA clones and other novel tools for hepacivirus studies.