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SARS-CoV-2引起的持续COVID-19大流行的4个月内，从全球不同地区的感染者中分离出的ORF1ab病毒中已检测到250个以上的核苷酸突变。这些观察结果提出了一个明显的问题，即突变压力的发生率和方向，以便进一步设计疫苗和治疗药物。在这项研究中，我们通过使用第一个分离株（武汉菌株）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的转变。同义的C到U过渡的比率显着高于非同义的过渡的比率，表明在氨基酸取代上存在负选择。此外，已经在49种冠状病毒物种中研究了核苷酸使用偏倚的趋势。在所有研究的冠状病毒的ORF1ab中，在四个简并位点上核苷酸的使用偏向尿嘧啶的强烈偏见：在ORF1a和ORF1b中，这都归功于程序化核糖体移码，在不同物种中效率为14 – 45％ 。在ORF1a中比在ORF1b中观察到更大的突变U压力，这可能是因为ORF1a的翻译频率比ORF1b更频繁。甚至在不是从基因组RNA加链翻译而来的ORF中也存在突变U压力，但这种偏向性比ORF1ab中的弱。与其他核苷酸突变不同，由胞嘧啶脱氨引起的突变U压力（大多发生在RNA加链复制和翻译过程中）无法通过冠状病毒的校对机制进行校正。