Identification of two phylogenetic lineages of equine hepacivirus and high prevalence in Brazil.

Non-primate hepacivirus (NPHV), as described in horses, is the virus most genetically related to hepatitis C virus (HCV). Although detected worldwide, limited data on genomic variability and distribution of NPHV are available in Latin America. The aim of this study was to investigate the genetic diversity and prevalence of equine NPHV in Brazil. Thirteen percent of 202 equines from three Brazilian states were positive for NPHV genome by reverse transcriptase PCR. Nucleotide sequences of the partial NS5B genome presented the greatest diversity described to date (25.6%), which is comparable to the upper limit of diversity for HCV subtype classification for the same region. Phylogenetic analysis revealed that Brazilian NPHV sequences along with isolates worldwide form two strongly supported clades (pp = 1.0) suggesting the existence of two distinct lineages.