Comprehensive analysis of codon usage pattern of porcine deltacoronavirus and its host adaptability
Comprehensive analysis of codon usage pattern of porcine deltacoronavirus and its host adaptability
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猪三角洲冠状病毒密码子使用模式及其宿主适应性综合分析
DOI：
10.1111/tbed.14588
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Bin Li
中科院分区：
文献类型：
--
作者：
Qi Peng;Xue Zhang;Jizong Li;Wenlong He;Baochao Fan;Yanxiu Ni;Maojun Liu;Bin Li
猪三角冠状病毒（PDCoV）是一种新发现的猪肠道冠状病毒，可感染多种细胞。在海地，最近报告了患有急性无分化性发热的儿童感染PDCoV。考虑到PDCoV在种间传播的巨大潜力，我们对54株具有代表性的带穗(S)基因的PDCoV菌株的密码子使用模式和宿主适应谱进行了综合分析。对PDCoV S基因的系统发育分析表明，PDCoV菌株可分为5个基因群。我们发现，在S基因中存在一定的密码子使用偏差，同义密码子常以U或a结尾，热图分析显示，所有PDCoV毒株的密码子使用趋势相似。dN/dS比小于1的PDCoV S基因为负选择基因。中性分析表明，自然选择是形成PDCoV S基因密码子使用偏好的主导力量。出乎意料的是，宿主适应分析显示PDCoV对智人和鸡的适应水平高于对猪的适应水平。与美国家系相比，中国早期家系和泰国家系的PDCoV菌株对宿主的适应性较差，这表明进化过程对PDCoV的适应能力起重要作用。本研究的这些发现增加了我们对PDCoV的进化、适应性和种间传播的理解。
The porcine deltacoronavirus (PDCoV) is a newly discovered pig enteric coronavirus that can infect cells from various species. In Haiti, PDCoV infections in children with acute undifferentiated febrile fever were recently reported. Considering the great potential of inter-species transmission of PDCoV, we performed a comprehensive analysis of codon usage patterns and host adaptation profiles of 54 representative PDCoV strains with the spike (S) gene. Phylogenetic analysis of the PDCoV S gene indicates that the PDCoV strains can be divided into five genogroups. We found a certain codon usage bias existed in the S gene, in which the synonymous codons are often ended with U or A. Heat map analysis revealed that all the PDCoV strains shared a similar codon usage trend. The PDCoV S gene with a dN/dS ratio lower than 1 reveals a negative selection on the PDCoV S gene. Neutrality analysis showed that natural selection is the dominant force in shaping the codon usage bias of the PDCoV S gene. Unexpectedly, host adaptation analysis reveals a higher adaptation level of PDCoV to Homo sapiens and Gallus gallus than to Sus scrofa. Compared to the USA lineage, the PDCoV strains in the Early China lineage and Thailand lineage were less adapted to their hosts, which indicates that the evolutionary process plays an important role in the adaptation ability of PDCoV. These findings of this study add to our understanding of PDCoV's evolution, adaptability, and inter-species transmission.