Virus recovery and full-length sequence analysis of atypical bovine pestivirus Th/04_KhonKaen

Phylogenetic analysis of recently identified "atypical" bovine pestiviruses, performed based on different gene regions, has revealed unclear relationships with other established species, therefore, their phylogenetic position could not be determined so far. In this study, the atypical pestivirus Th/04_KhonKaen was recovered from serum of a naturally infected calf and the complete genome sequence was determined and analysed, as means to define its position. The viral genome is 12,337 nucleotides (nt) long, and comprises a 5'-UTR of 383 nt, a 3'-UTR of 254 nt and an open reading frame of 11,700 nt, without duplication of viral sequences or insertions of cellular sequences. The phylogenetic analyses of the full-length sequence, performed by Neighbor-joining, Maximum likelihood, and the Bayesian approach, unanimously placed Th/04_KhonKaen in a single lineage, distinct from the established pestivirus species, and close to bovine viral diarrhea virus types 1 and 2. Furthermore, Th/04_KhonKaen and two previously reported atypical pestiviruses D32/00_'HoBi' and CH-KaHo/cont formed a well-supported monophyletic clade in trees based on the complete N(pro) and E2 gene regions. The finding provides conclusive classification of the Th/04_KhonKaen virus and confirms the standing of the "atypical" bovine pestiviruses as a novel pestivirus species.