从同源多聚核苷酸重复序列推测SARS-CoV-2的进化趋势
Evolutionary trend of SARS-CoV-2 inferred by the homopolymeric nucleotide repeats
摘要：
严重急性呼吸系统综合征冠状病毒2（SARS-CoV-2）是目前全球COVID-19大流行的病原体，已造成数百万人死亡。了解冠状病毒的人畜共患进化可能为开发有效疫苗，监测传播趋势和预防新的人畜共患感染提供见解。同源多聚核苷酸重复序列（homopolymericnucleotiderepeats，HP）是最简单的串联重复序列，是真核生物基因组中普遍存在的特征。然而，HP在冠状病毒基因组进化中的分布和作用研究得很少。在这项研究中，我们描述了蝙蝠和人类冠状病毒和SARS-CoV-2变异体基因组中的HP分布和趋势。结果表明，SARS-CoV-2基因组中HP含量丰富，且在进化过程中HP含量增加。特别是在人类宿主中，冠状病毒的HP poly-（A/T）和poly-（C/G）的差异随着进化而增加。HP poly-（A/T）和poly-（C/G）的差异与宿主适应性和病毒毒力水平有关。因此，我们建议HP差异可以作为冠状病毒人畜共患进化水平的定量度量。特别地，HP差异测量推断SARS-CoV-2 Omicron变体具有HP poly-（A/T）和poly-（C/G）的高度差异，表明对人类宿主的高度适应。
英文摘要：
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current global COVID-19 pandemic, in which millions of lives have been lost. Understanding the zoonotic evolution of the coronavirus may provide insights for developing effective vaccines, monitoring the transmission trends, and preventing new zoonotic infections. Homopolymeric nucleotide repeats (HP), the most simple tandem repeats, are a ubiquitous feature of eukaryotic genomes. Yet the HP distributions and roles in coronavirus genome evolution are poorly investigated. In this study, we characterize the HP distributions and trends in the genomes of bat and human coronaviruses and SARS-CoV-2 variants. The results show that the SARS-CoV-2 genome is abundant in HPs, and has augmented HP contents during evolution. Especially, the disparity of HP poly-(A/T) and ploy-(C/G) of coronaviruses increases during the evolution in human hosts. The disparity of HP poly-(A/T) and ploy-(C/G) is correlated to host adaptation and the virulence level of the coronaviruses. Therefore, we propose that the HP disparity can be a quantitative measure for the zoonotic evolution levels of coronaviruses. Peculiarly, the HP disparity measure infers that SARS-CoV-2 Omicron variants have a high disparity of HP poly-(A/T) and ploy-(C/G), suggesting a high adaption to the human hosts.
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