12 novel atypical porcine pestivirus genomes from neonatal piglets with congenital tremors: A newly emerging branch and high prevalence in China

Abstract Atypical porcine pestivirus (APPV), a newly discovered member of the genus Pestivirus , is considered to be associated with congenital tremors (CT) in piglets. From June 2016 to January 2018, 440 serum and tissue samples from CT-affected piglets in Anhui, Guangdong and Guangxi provinces were collected to detect APPV. The results showed a high level of 63.4% preference for APPV in 27 swine farms and complicated co-infection cases between APPV and other 12 swine viruses. Meanwhile, 12 novel APPV genomes were screened and identified. Results showed that complete genomes, N pro and NS5A genes of these novel 12 APPV sequences revealed 80.5%–99.8%, 78%–100% and 76.9%–99.8% nucleotide identities, respectively. Phylogenetic analyses based on sequences of full-length genomes, N pro and NS5A genes of APPV indicated three well-defined clades including a newly emerging branch in China. This study provides novel epidemiological information of APPV in China.