Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns.
Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns.
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DOI：
10.1016/j.ygeno.2021.05.008
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发表时间：
2021-07
期刊：
影响因子：
4.4
通讯作者：
Roy S
中科院分区：
文献类型：
--
作者：
Das JK;Roy S
当前的COVID-19大流行引起了科学界对研究严重急性呼吸系统综合征冠状病毒2（SARS-CoV-2）进化起源的关注。本研究对7种人类冠状病毒（HCoV）的蛋白质编码序列进行了全面的定量分析，以破译核苷酸序列变异和密码子使用模式。了解病毒的生存能力、它们对宿主的适应以及它们的进化是至关重要的。目前的分析显示，相对二核苷酸（比值比），GC和CT对的第一个和最后两个密码子的位置，分别高丰度，以及低丰度的CG对的密码子的最后两个位置，这可能与病毒的进化。7种冠状病毒密码子第3位GC含量差异显著。具有高RSCU值的密码子主要来自脂肪族和羟基氨基酸基团，并且具有低RSCU值的密码子属于脂肪族、环状、带正电荷和含硫氨基酸基团。为了阐明7种冠状病毒的进化过程，根据密码子的RSCU得分构建了系统发育树（树状图）。严重和轻度类别冠状病毒位于不同的分支。与其他冠状病毒的比较系统发育研究表明，SARS-CoV-2与穿山甲（Manis javanica，Pangolin-CoV）和猫（Felis卡图斯，SARS（r）-CoV）分离的CoV接近。对有效密码子数（ENC）使用偏倚的进一步分析显示，与SARS-CoV-2相比，SARS-CoV和MERS-CoV的偏倚相对较高。针对GC 3的ENC图表明，突变偏倚可能在决定候选病毒之间的密码子使用变异中起作用。对一些人类宿主寄生虫（来自不同王国）（包括CoV）的密码子适应性研究显示了不同的适应性模式。与MERS CoV相比，SARS-CoV-2和SARS-CoV表现出相对较低但相似的密码子适应性。
The prevailing COVID-19 pandemic has drawn the attention of the scientific community to study the evolutionary origin of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). This study is a comprehensive quantitative analysis of the protein-coding sequences of seven human coronaviruses (HCoVs) to decipher the nucleotide sequence variability and codon usage patterns. It is essential to understand the survival ability of the viruses, their adaptation to hosts, and their evolution. The current analysis revealed a high abundance of the relative dinucleotide (odds ratio), GC and CT pairs in the first and last two codon positions, respectively, as well as a low abundance of the CG pair in the last two positions of the codon, which might be related to the evolution of the viruses. A remarkable level of variability of GC content in the third position of the codon among the seven coronaviruses was observed. Codons with high RSCU values are primarily from the aliphatic and hydroxyl amino acid groups, and codons with low RSCU values belong to the aliphatic, cyclic, positively charged, and sulfur-containing amino acid groups. In order to elucidate the evolutionary processes of the seven coronaviruses, a phylogenetic tree (dendrogram) was constructed based on the RSCU scores of the codons. The severe and mild categories CoVs were positioned in different clades. A comparative phylogenetic study with other coronaviruses depicted that SARS-CoV-2 is close to the CoV isolated from pangolins (Manis javanica, Pangolin-CoV) and cats (Felis catus, SARS(r)-CoV). Further analysis of the effective number of codon (ENC) usage bias showed a relatively higher bias for SARS-CoV and MERS-CoV compared to SARS-CoV-2. The ENC plot against GC3 suggested that the mutational bias might have a role in determining the codon usage variation among candidate viruses. A codon adaptability study on a few human host parasites (from different kingdoms), including CoVs, showed a diverse adaptability pattern. SARS-CoV-2 and SARS-CoV exhibit relatively lower but similar codon adaptability compared to MERS-CoV.
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