Khrustalev Vladislav Victorovich, Giri Rajanish, Khrustaleva Tatyana Aleksandrovna, Kapuganti Shivani Krishna, Stojarov Aleksander Nicolaevich, Poboinev Victor Vitoldovich
Department of General Chemistry, Belarusian State Medical University, Minsk, Belarus.
School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India.
Front Microbiol. 2020 Sep 22;11:559165. doi: 10.3389/fmicb.2020.559165. eCollection 2020.
Within 4 months of the ongoing COVID-19 pandemic caused by SARS-CoV-2, more than 250 nucleotide mutations have been detected in ORF1ab of the virus isolated from infected persons from different parts of the globe. These observations open up an obvious question about the rate and direction of mutational pressure for further vaccine and therapeutics designing. In this study, we did a comparative analysis of ORF1a and ORF1b by using the first isolate (Wuhan strain) as the parent sequence. We observed that most of the nucleotide mutations are C to U transitions. The rate of synonymous C to U transitions is significantly higher than the rate of non-synonymous ones, indicating negative selection on amino acid substitutions. Further, trends in nucleotide usage bias have been investigated in 49 coronaviruses species. A strong bias in nucleotide usage in fourfold degenerate sites toward uracil residues is seen in ORF1ab of all the studied coronaviruses: both in the ORF1a and in the ORF1b translated thanks to the programmed ribosomal frameshifting that has an efficiency of 14 - 45% in different species. A more substantial mutational U-pressure is observed in ORF1a than in ORF1b perhaps because ORF1a is translated more frequently than ORF1b. Mutational U-pressure is there even in ORFs that are not translated from genomic RNA plus strands, but the bias is weaker than in ORF1ab. Unlike other nucleotide mutations, mutational U-pressure caused by cytosine deamination, mostly occurring during the RNA plus strand replication and also translation, cannot be corrected by the proof-reading machinery of coronaviruses. The knowledge generated on the mutational U-pressure that becomes stronger during translation of viral RNA plus strands has implications for vaccine and nucleoside analog development for treating COVID-19 and other coronavirus infections.
在由严重急性呼吸综合征冠状病毒2（SARS-CoV-2）引发的持续新冠疫情的4个月内，从全球不同地区感染个体分离出的病毒的开放阅读框1ab（ORF1ab）中检测到了250多个核苷酸突变。这些观察结果引发了一个关于突变压力的速率和方向的明显问题，这对于进一步设计疫苗和治疗方法至关重要。在本研究中，我们以首个分离株（武汉毒株）作为亲本序列，对ORF1a和ORF1b进行了比较分析。我们观察到，大多数核苷酸突变是从C到U的转换。同义C到U转换的速率显著高于非同义转换的速率，这表明对氨基酸替换存在负选择。此外，我们还研究了49种冠状病毒物种中核苷酸使用偏好的趋势。在所有研究的冠状病毒的ORF1ab中，四倍简并位点的核苷酸使用对尿嘧啶残基存在强烈偏好：在ORF1a和通过程序性核糖体移码翻译的ORF1b中均如此，程序性核糖体移码在不同物种中的效率为14% - 45%。与ORF1b相比，在ORF1a中观察到了更显著的突变U压力，这可能是因为ORF1a的翻译频率高于ORF1b。即使在不从基因组RNA正链翻译的开放阅读框中也存在突变U压力，但这种偏好比在ORF1ab中弱。与其他核苷酸突变不同，由胞嘧啶脱氨导致的突变U压力主要发生在RNA正链复制和翻译过程中，无法被冠状病毒的校对机制纠正。关于在病毒RNA正链翻译过程中变得更强的突变U压力所产生的知识，对于开发治疗新冠病毒和其他冠状病毒感染的疫苗及核苷类似物具有重要意义。
