Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 (COVID-19) which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In this study, we performed a genome-wide analysis on the codon usage bias (CUB) of 13 SARS-CoV-2 isolates from different geo-locations (countries) in an attempt to characterize it, unravel the main force shaping its pattern, and understand its adaptation to Homo sapiens. Overall results revealed that, SARS-CoV-2 codon usage is slightly biased similarly to other RNA viruses. Nucleotide and dinucleotide compositions displayed a bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Eight common putative preferred codons were identified, and all of them were A/U-ended (U-ended: 7, A-ended: 1). In addition, natural selection was found to be the main force structuring the codon usage pattern of SARS-CoV-2. However, mutation pressure and other factors such as compositional constraints and hydrophobicity had an undeniable contribution. Two adaptation indices were utilized and indicated that SARS-CoV-2 is moderately adapted to Homo sapiens compared to other human viruses. The outcome of this study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 and may aid in vaccine design strategies.

中文翻译：

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深入了解不同地理位置的13种严重急性呼吸系统综合症冠状病毒2（SARS-CoV-2）的密码子使用偏见

严重急性呼吸系统综合症冠状病毒2（SARS-CoV-2）是冠状病毒病2019（COVID-19）的病原体，是一种传播于世界各地的传染病，并被世界卫生组织（WHO）宣布为大流行病。在这项研究中，我们对来自不同地理位置（国家/地区）的13个SARS-CoV-2分离株的密码子使用偏倚（CUB）进行了全基因组分析，以试图对其特征进行描述，揭示形成其模式的主要力量，并了解其对智人的适应性。总体结果显示，SARS-CoV-2密码子的使用与其他RNA病毒类似，略有偏向。核苷酸和二核苷酸组成分别在所有密码子位置和CpU末端密码子偏好性上显示出对A / U含量的偏向。确定了八个常用推定的首选密码子，并且它们都是A / U端的（U端：7，A端：1）。此外，发现自然选择是构建SARS-CoV-2密码子使用方式的主要力量。但是，突变压力和其他因素（例如组成限制和疏水性）具有不可否认的作用。利用了两个适应指数，表明与其他人类病毒相比，SARS-CoV-2对人的适应性中等。这项研究的结果可能有助于了解与SARS-CoV-2进化有关的潜在因素，并可能有助于疫苗设计策略。突变压力和其他因素（例如组成限制和疏水性）具有不可否认的作用。利用了两个适应指数，表明与其他人类病毒相比，SARS-CoV-2对人的适应性中等。这项研究的结果可能有助于了解与SARS-CoV-2进化有关的潜在因素，并可能有助于疫苗设计策略。突变压力和其他因素（例如组成限制和疏水性）具有不可否认的作用。利用了两个适应指数，表明与其他人类病毒相比，SARS-CoV-2对人的适应性中等。这项研究的结果可能有助于了解与SARS-CoV-2进化有关的潜在因素，并可能有助于疫苗设计策略。