Abstract: Atypical porcine pestivirus (APPV) is a pathogen that causes congenital tremors in newborn piglets. To investigate the epidemical and phylogenetic characterization of APPV in China, 285 serum samples collected from 93 pig farms distributed among 22 provinces, during 2015-2017, were detected for APPV, and the sequences of E2 gene were further analyzed in this study. Meanwhile, the full-genomic sequencing and phylogenetic analysis on an APPV strain from a piglet with congenital tremors were also carried out. The results showed that APPV-positive rate of the tested samples was 25.26% (72/285, 95% CI=20.3% to 30.7%), with a prevalence of 38.71% (36/93, 95% CI=59.7% to 94.8%) at farm level, and the positive rate has increased year by year from 2015 to 2017. The nucleic acid homology of thirty-five APPV E2 gene sequences obtained from the positive samples is 83.4%-100.0% and the similarity of deduced amino acids was 90.5%-100.0%. Phylogenetic analysis of the E2 gene showed that they were highly diverse, and all listed strains could be divided into four subgroups. Most of the Chinese strains belong to subgroup 1, which are closely related to 000515 from the United States; and few sequenced strains are clustered into subgroup 2, together with European strains Bavaria S5/9 and NL1 Farm1, as well as ISDVDL2014016573 from the United States; six obtained sequences belong to subgroup 3; and all the strains in subgroup 4 are from Guangdong province; and the subgroups 3 and 4 are all composed of the Chinese strains. Whole-genomic sequence alignment shows that the identity of CHheb1701 with other referenced strains is 81.3% to 98.6%. The phylogenetic analysis indicates that all APPV strains could be divided into two main branches. The CHheb1701 is clustered into the branch containing all previous strains from the countries out of China and it is closed to Chinese virus GX04/2017 and the US strain 000515, which are clustered into the same subbranch. Meanwhile, another branch is composed of Chinese strains only from Guangdong province. The results above indicate that APPV is widely distributed in China, with wide variations, and the strains in China might be introduced from different resources. This study provides valuable information for further prevention and research of APPV.

Key words: atypical porcine pestivirus, E2 gene, phylogenetic analysis