Abstract
Border disease virus (BDV), a member of the Pestivirus genus within the Flaviviridae family, is known to inflict significant economic losses on livestock farms due to its association with reproductive disorders and persistent infections in sheep and goats. However, comprehensive epidemiological investigations of BDV in China are scarce. This study examined BDV infection in sheep from Hulunbuir, Inner Mongolia, northeastern China, utilizing metagenomic sequencing and polymerase chain reaction (PCR) assay. Among the 96 serum samples analyzed, only one tested positive for BDV nucleotide sequence, yielding a prevalence rate of 1.0%. A total of 11,985 nt long genome sequences was amplified, which showed nucleotide identities ranging from 76.6% to 87.2% and amino acid identities ranging from 85.2% to 93.2% with other BDV strains worldwide. Phylogenetic analysis unequivocally placed the viral strain within genotype BDV-3, showing a close genetic affinity with strain JSLS12-01 identified in Jiangsu province, China. Furthermore, selection pressure analyses suggested that purifying selection predominantly influenced the evolutionary dynamics of BDV genomes. This study marks the inaugural detection of BDV in sheep within Inner Mongolia, northeastern China, thereby enhancing our understanding of the extensive genetic diversity and geographical distribution of BDV strains across the country. These findings hold relevance for the livestock industry and disease surveillance efforts, offering valuable insights into the prevalence and genetic characteristics of BDV in this region.