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Background: Atypical porcine pestivirus (APPV) was identified and associated with congenital tremor (CT) type A-II in new born piglets and has been reported in many countries around the world since 2015. In China, the first APPV infection in swine herds was reported in Guangdong province in 2016.To investigate the genetic characteristics of APPV from Guangxi province seated in Southern China, the full-length sequences of APPV strains were amplified and analyzed.Results: Tissue samples from neonatal piglets with CT from Guangxi province were detected by reverse transcription-polymerase chain reaction (RT-PCR). APPV positive samples were amplified, cloned and sequenced, and the complete genomic sequences of five APPV strains were obtained.Sequence analysis revealed that all six APPV strains from Guangxi province, including five strains from this study and one from other researchers, shared 83.3%-97.5% nucleotide identity of complete genome and 91.7%-99.1% amino acid identity of open reading frame (ORF) with one another, and shared 77.7%-97.7% nucleotide identity of complete genome and 90.6%-99.3% amino acid identity of ORF with other reference strains available in Genbank. Phylogenetic analysis indicated that the APPV strains from Guangxi province belonged to four different subgroups in the phylogenetic tree based on the complete genomic sequences, and similar topology was observed in the phylogenetic trees based on N pro , E rns and E2 gene sequences, respectively. No sign of recombination was observed for strains from Guangxi province by using Recombination Detection Program 4 (RDP4) and Simplot analysis. Evolution analysis performed on the complete genome of 58 APPV strains available in Genbank showed that APPV strains from America, Europe and Asia during 2006-2019 evolved at a mean rate of 1.37×10 -4 substitutions/site/year, and the most recent common ancestor ( tMRCA ) of them was estimated as 1700.5 years ago.Conclusions: The findings of this study indicated that there existed a high degree of genetic diversity of APPV from Guangxi province, Southern China, which provided important information on the epidemiological features and evolutionary relationships of APPV.

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