Department of Mathematics, Statistics, and Computer Science, The University of Illinois at Chicago, Chicago, IL 60607-7045, USA.
Department of Mathematical Sciences, Tsinghua University, Beijing 100084, China.
J Theor Biol. 2021 Dec 7;530:110885. doi: 10.1016/j.jtbi.2021.110885. Epub 2021 Aug 31.
The world faces a great unforeseen challenge through the COVID-19 pandemic caused by coronavirus SARS-CoV-2. The virus genome structure and evolution are positioned front and center for further understanding insights on vaccine development, monitoring of transmission trajectories, and prevention of zoonotic infections of new coronaviruses. Of particular interest are genomic elements Inverse Repeats (IRs), which maintain genome stability, regulate gene expressions, and are the targets of mutations. However, little research attention is given to the IR content analysis in the SARS-CoV-2 genome. In this study, we propose a geometric analysis method and using the method to investigate the distributions of IRs in SARS-CoV-2 and its related coronavirus genomes. The method represents each genomic IR sequence pair as a single point and constructs the geometric shape of the genome using the IRs. Thus, the IR shape can be considered as the signature of the genome. The genomes of different coronaviruses are then compared using the constructed IR shapes. The results demonstrate that SARS-CoV-2 genome, specifically, has an abundance of IRs, and the IRs in coronavirus genomes show an increase during evolution events.
世界正面临着由冠状病毒 SARS-CoV-2 引起的 COVID-19 大流行这一前所未有的挑战。病毒基因组结构和进化处于进一步了解疫苗开发、监测传播轨迹和预防新的冠状病毒人畜共患感染的前沿。特别有趣的是基因组元件反向重复（IR），它维持基因组稳定性、调节基因表达，并且是突变的目标。然而，人们对 SARS-CoV-2 基因组中的 IR 含量分析关注甚少。在这项研究中，我们提出了一种几何分析方法，并使用该方法研究了 SARS-CoV-2 及其相关冠状病毒基因组中 IR 的分布。该方法将每个基因组 IR 序列对表示为一个点，并使用 IR 构建基因组的几何形状。因此，IR 形状可以被视为基因组的特征。然后使用构建的 IR 形状比较不同冠状病毒的基因组。结果表明，SARS-CoV-2 基因组具有丰富的 IR，并且冠状病毒基因组中的 IR 在进化事件中呈增加趋势。
