School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
Int J Biol Macromol. 2022 Apr 15;204:356-363. doi: 10.1016/j.ijbiomac.2022.02.034. Epub 2022 Feb 8.
Infections caused by SARS-CoV-2 have brought great harm to human health. After transmission for over two years, SARS-CoV-2 has diverged greatly and formed dozens of different lineages. Understanding the trend of its genome evolution could help foresee difficulties in controlling transmission of the virus. In this study, we conducted an extensive monthly survey and in-depth analysis on variations of nucleotide, amino acid and codon numbers in 311,260 virus samples collected till January 2022. The results demonstrate that the evolution of SARS-CoV-2 is toward increasing U-content and reducing genome-size. C, G and A to U mutations have all contributed to this U-content increase. Mutations of C, G and A at codon position 1, 2 or 3 have no significant difference in most SARS-CoV-2 lineages. Current viruses are more cryptic and more efficient in replication, and are thus less virulent yet more infectious. Delta and Omicron variants have high mutability over other lineages, bringing new threat to human health. This trend of genome evolution may provide a clue for tracing the origin of SARS-CoV-2, because ancestral viruses should have lower U-content and probably bigger genome-size.
新冠病毒（SARS-CoV-2）感染给人类健康带来了巨大危害。在传播两年多后，SARS-CoV-2 发生了巨大的变异，形成了数十种不同的谱系。了解其基因组进化的趋势有助于预测病毒传播控制的困难。在这项研究中，我们对截至 2022 年 1 月收集的 311260 个病毒样本的核苷酸、氨基酸和密码子数量变异进行了广泛的月度调查和深入分析。结果表明，SARS-CoV-2 的进化方向是增加 U 含量和减少基因组大小。C、G 和 A 到 U 的突变都促成了 U 含量的增加。在大多数 SARS-CoV-2 谱系中，密码子位置 1、2 或 3 处的 C、G 和 A 的突变没有显著差异。目前的病毒在复制过程中更加隐匿和高效，因此毒力降低但传染性增强。德尔塔和奥密克戎变体相对于其他谱系具有更高的突变率，给人类健康带来新的威胁。这种基因组进化的趋势可能为追溯 SARS-CoV-2 的起源提供线索，因为原始病毒应该具有较低的 U 含量和可能更大的基因组大小。
