猪肠道α冠状病毒密码子使用模式分析及其与宿主的适应性。

Analysis of codon usage patterns of porcine enteric alphacoronavirus and its host adaptability.

机构信息

National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.

出版信息

Virology. 2023 Oct;587:109879. doi: 10.1016/j.virol.2023.109879. Epub 2023 Sep 1.

DOI:10.1016/j.virol.2023.109879

PMID:37677987

Abstract

Porcine enteric alphacoronavirus (PEAV) is a newly emerging swine enteropathogen that poses a threat to the swine industry. To understand the PEAV genome evolution, we performed a comprehensive analysis of the codon usage patterns in fifty-nine PEAV strains currently available. Phylogenetic analysis showed that PEAV can be divided into six lineages. Effective number of codons analysis demonstrated that the PEAV genome exhibits a low codon usage bias (CUB). Nucleotide composition analysis indicated that the PEAV genome has the most abundant nucleotide U content, with GC content (39.37% ± 0.08%) much lower than AU content (60.63% ± 0.08%). Neutrality and effective number of codons plot analyses suggested that natural selection rather than mutation pressure dominates the CUB of PEAV. Host adaptation analysis revealed that PEAV fits the codon usage pattern of non-human primates, humans and mice better than that of pigs. Our data enriches information on PEAV evolution, host adaptability, and cross-species transmission.

摘要

猪肠道α冠状病毒（PEAV）是一种新出现的猪肠道病原体，对养猪业构成威胁。为了了解 PEAV 基因组的进化，我们对目前 59 株 PEAV 株的密码子使用模式进行了全面分析。系统发育分析表明，PEAV 可分为六个谱系。有效密码子数分析表明，PEAV 基因组表现出低的密码子使用偏性（CUB）。核苷酸组成分析表明，PEAV 基因组含有最丰富的核苷酸 U，GC 含量（39.37%±0.08%）远低于 AU 含量（60.63%±0.08%）。中性和有效密码子数图分析表明，自然选择而不是突变压力主导着 PEAV 的 CUB。宿主适应性分析表明，PEAV 比猪更适合非人类灵长类动物、人类和小鼠的密码子使用模式。我们的数据丰富了 PEAV 进化、宿主适应性和跨物种传播的信息。