A Novel Subtype of Bovine Hepacivirus Identified in Ticks Reveals the Genetic Diversity and Evolution of Bovine Hepacivirus

Jian-Wei Shao,Quan Liu,Yao-Xian Yuan,Ji-Ming Chen,Jun Ma,Luan-Ying Guo

doi:10.3390/v13112206

Abstract

Hepaciviruses represent a group of viruses that pose a significant threat to the health of humans and animals. New members of the genus Hepacivirus in the family Flaviviridae have recently been identified in a wide variety of host species worldwide. Similar to the Hepatitis C virus (HCV), bovine hepacivirus (BovHepV) is hepatotropic and causes acute or persistent infections in cattle. BovHepVs are distributed worldwide and classified into two genotypes with seven subtypes in genotype 1. In this study, three BovHepV strains were identified in the samples of ticks sucking blood on cattle in the Guangdong province of China, through unbiased high-throughput sequencing. Genetic analysis revealed the polyprotein-coding gene of these viral sequences herein shared 67.7–84.8% nt identity and 76.1–95.6% aa identity with other BovHepVs identified worldwide. As per the demarcation criteria adopted for the genotyping and subtyping of HCV, these three BovHepV strains belonged to a novel subtype within the genotype 1. Additionally, purifying selection was the dominant evolutionary pressure acting on the genomes of BovHepV, and genetic recombination was not common among BovHepVs. These results expand the knowledge about the genetic diversity and evolution of BovHepV distributed globally, and also indicate genetically divergent BovHepV strains were co-circulating in cattle populations in China.

Highlights

The genus Hepacivirus, belonging to the family Flaviviridae, comprises a genetically diverse group of human and animal pathogens
We identified bovine hepacivirus (BovHepV) from the 30 original RNA samples using RT-PCR
Using the complete genome sequence of BovHepV/GDZJ02 as the reference sequence, 224 reads were remapped to this reference sequence and provided 92.1% genome coverage (8115 nt/8808 nt) with 99.7% pairwise identity at a mean depth of 3.8×, and the percentage virus reads of the total number of nonribosomal reads is 0.0038% (224 reads/5,883,446 reads) (Figure 1)

Summary

Introduction

The genus Hepacivirus, belonging to the family Flaviviridae, comprises a genetically diverse group of human and animal pathogens. The genome of hepaciviruses is an unsegmented, single-stranded, and positive-sense RNA molecule about 10 kb in length, which contains a 5 untranslated region (UTR) and a 3 UTR, and a single long open reading frame (ORF) encoding a single polyprotein. This polyprotein is further cleaved by cellular and viral proteases into three structural proteins (Core, E1, and E2) and seven nonstructural proteins (p7, NS2, NS3, NS4A, NS4B, NS5A, and NS5B) [1,2]. A novel HCV-like, provisionally named as Hepacivirus P, was identified in long-tailed ground squirrels in China [21]

Methods

Results

Conclusion