Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)

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.

猪非典型瘟病毒（Atypical porcine pestivirus, APPV）已被确定为仔猪A-II型先天性震颤（congenital tremor type A-II, CT A-II）的主要病原体，该病毒正威胁着全球猪群的健康。然而，目前对APPV的演化过程仍知之甚少。本研究通过系统发育分析发现，APPV可分为三个系统发育群（I、II、III）：系统发育群I和II包含源自中国的病毒毒株，而系统发育群III则涵盖来自欧洲、北美及亚洲的毒株，且初步推测系统发育群I和II起源于中国。随后的组成特性分析显示，APPV基因组中核苷酸A以及以A结尾的密码子使用频率较高。有趣的是，偏好密码子分析结果表明，AGA[精氨酸（Arg）]与AGG[精氨酸（Arg）]的使用频率显著偏高；二核苷酸CC的使用频率偏高，而二核苷酸CG的使用频率则偏低。此外，研究发现APPV较弱的密码子使用偏好性主要由选择压力而非突变压力所主导。密码子适应指数（CAI）、相对密码子退化解指数（RCDI）以及相似性指数（SiD）分析结果显示，相较于系统发育群I，系统发育群II和III的密码子使用模式与猪的更为相似，这提示系统发育群II和III可能更适配猪宿主。综上，本研究通过系统发育分析与密码子使用模式分析，为APPV的演化研究提供了新的视角。