Emergence and evolution of HoBi-like pestivirus clades a and c in sheep from central China

HoBi-like pestivirus (HoBiPeV), also known as Pestivirus brazilense, is a new species of the genus Pestivirus that can cause a variety of clinical signs in cattle and small ruminants. Sheep has been shown to be susceptible to HoBiPeV in China. However, the epidemiology of HoBiPeV in sheep has been limited documented. Hence, the aim of this study was to determine the occurrence and genetic variability of HoBiPeV in sheep in central China. From 2020 to 2024, a total of 596 blood samples, 56 lung samples, and 56 intestine samples were collected from sheep. To investigate the occurrence and genetic variability of HoBiPeV in sheep, these samples were analyzed by serology, PCR, virus isolation and genome sequencing, identification, and analysis. 17 blood samples, four lung samples, and five intestine samples were positive for pestiviruses, including six that were positive for BVDV-1 and 20 that were positive for HoBiPeV. Then six HoBiPeV strains were isolated and sequenced. Phylogenetic relationships showed that three strains belonged to HoBiPeV clade a and three to HoBiPeV clade c. Bayesian molecular clock analysis indicated that HoBiPeV most likely originated in Brazil, with a tMRCA of 1979 CE (95% credibility interval, 1956–1992 CE), the rate of evolution of HoBiPeVs was estimated to be 2.59 × 10− 3 (95% HPD 1.40 × 10− 3-3.64 × 10− 3) for the genome. Selection pressure analysis showed modest selection pressure, and six HoBiPeV migration routes were observed. In addition, 39% (198/503) of serum samples from sheep were positive for antibodies against bovine pestiviruses (BVDV-1, BVDV-2 or HoBiPeV) by VN test. This work enhances our understanding of the epidemiology and genetic heterogeneity among HoBiPeV strains in China, highlighting that sheep, as an alternative host, play a role in the evolution of the virus, and at least two clades of HoBiPeV have been endemic in China. Greater prevention and control measures should be implemented against HoBiPeV infection.