Genome Characterization and Phylogenetic Analysis of Bovine Hepacivirus in Inner Mongolia, Northeastern China

Objective: Bovine hepacivirus (BovHepV) is a new member of the genus Hepacivirus in the family Flaviviridae, which has been detected in cattle in more than seven countries. The purpose of this study was to identify and genetically characterize BovHepV in cattle in Inner Mongolia, northeastern (NE) China. Methods: A total of 116 serum samples from cattle were collected from HulunBuir in Inner Mongolia from April to May, 2021, and were divided into three pools for metagenomic sequencing. The samples were verified with semi-nested RT-PCR with primers based on the BovHepV sequences obtained from metagenomic sequencing. The complete genomes of BovHepV were amplified, and were used for genome characterization and phylogenetic analysis. Results: BovHepV was detected in two pools through metagenomic sequencing. Five BovHepV positive samples were identified in Yakeshi of HulunBuir, thus indicating a prevalence of 8.8% (5/57). Two 8840 nucleotide long BovHepV strains YKS01/02 were amplified from the positive samples and showed 79.3%–91.9% nucleotide sequence identity with the discovered BovHepV strains. Phylogenetic analysis classified the YKS01/02 strains into BovHepV subtype G group. Conclusion: This study reports the first identification of BovHepV in cattle in northeastern China, and expands the known geographical distribution and genetic diversity of BovHepV in the country.