Abstract
ABSTRACT Atypical porcine pestivirus (APPV) has been identified as the main causative agent for congenital tremor (CT) type A-II in piglets, which is threatening the health of the global swine herd. However, the evolution of APPV remains largely unknown. In this study, phylogenetic analysis showed that APPV could be divided into three phylogroups (I, II, and III). Phylogroups I and II included viral strains from China, while phylogroup III contained strains from Europe, North America, and Asia. Phylogroups I and II are tentatively thought to be of Chinese origin. Next, compositional property analysis revealed that a high frequency of nucleotide A and A-end codons was used in the APPV genome. Intriguingly, the analysis of preferred codons revealed that the AGA[Arg] and AGG[Arg] were overrepresented. Dinucleotide CC was found to be overrepresented, and dinucleotide CG was underrepresented. Furthermore, it was found that the weak codon usage bias of APPV was mainly dominated by selection pressures versus mutational forces. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses showed that the codon usage patterns of phylogroup II and III were more similar to the one of a pig than phylogroup I, suggesting that phylogroup II and III may be more adaptive to pigs. Overall, this study provides insights into APPV evolution through phylogeny and codon usage pattern analysis.
Highlights
As an emerging novel swine virus, atypical porcine pesti virus (APPV) is a member of the genus Pestivirus within the family Flaviviridae [1]
The virus genome contains an open reading frame (ORF) encoding a polyprotein consisted of 3635 amino acids that were putatively processed into four structural pro teins (C, Erns, E1, and E2) and eight non-structural proteins (Npro, P7, NS2, NS3, NS4A, NS4B, NS5A, and NS5B) [1]
After removing the recombinant APPV coding DNA sequences (CDSs), the remaining 53 sequences were used for further analysis (Supplementary Table 1)
Summary
As an emerging novel swine virus, atypical porcine pesti virus (APPV) is a member of the genus Pestivirus within the family Flaviviridae [1]. APPV has been classified as Pestivirus K by the International Committee on Taxonomy of Viruses (ICTV) [2]. It is regarded as the main causative agent for congenital tremor (CT) type A-II in piglets [3]. APPV is highly variable in the virus genome among diverse strains, which undoubtedly poses several challenges for the development of diagnostic tests and vaccines, as well as virus research [4,6]. The origin and evolution of APPV remain largely unclear, though a preliminary phylogeny exists including a number of APPV clusters with high variability
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