Evolutionary dynamics of the severe acute respiratory syndrome coronavirus 2 genomes

作     者：Zhaohui Qian Pei Li Xiaolu Tang Jian Lu Zhaohui Qian;Pei Li;Xiaolu Tang;Jian Lu

作者机构：Institute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100176China NHC Key Laboratory of Systems Biology of PathogensInstitute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100871China State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100176China State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China 

出 版 物：《Medical Review》 (医学评论（英文）)

年 卷 期：2022年第2卷第1期

页      面：3-22页

学科分类：1001[医学-基础医学(可授医学、理学学位)] 100103[医学-病原生物学] 10[医学] 

基　　金：National Key Research and Development Projects of theMinistry of Science and Technology of China,Grant Nos.2021YFC0863300,2020YFA0707600,2020YFC0847000,2021YFC2301300 Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences,Grant No.2021-12M-1-038. 

主　　题：molecular evolution population genetics severe acute respiratory syndrome coronavirus 2 variant virus. 

摘      要：The coronavirus disease 2019(COVID-19)pandemic has caused immense losses in human lives and the global economy and posed significant challenges for global public health.As severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the causative agent of COVID-19,has evolved,thousands of single nucleotide variants(SNVs)have been identified across the viral genome.The roles of individual SNVs in the zoonotic origin,evolution,and transmission of SARS-CoV-2 have become the focus of many studies.This review summarizes recent comparative genomic analyses of SARS-CoV-2 and related coronaviruses(SC2r-CoVs)found in non-human animals,including delineation of SARS-CoV-2 lineages based on characteristic SNVs.We also discuss the current understanding of receptor-binding domain(RBD)evolution and characteristic mutations in variants of concern(VOCs)of SARS-CoV-2,as well as possible co-evolution between RBD and its receptor,angiotensin-converting enzyme 2(ACE2).We propose that the interplay between SARS-CoV-2 and host RNA editing mechanisms might have partially resulted in the bias in nucleotide changes during SARS-CoV-2 evolution.Finally,we outline some current challenges,including difficulty in deciphering the complicated relationship between viral pathogenicity and infectivity of different variants,and monitoring transmission of SARS-CoV-2 between humans and animals as the pandemic progresses.