Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes

作     者：Yali Hou Shilei Zhao Qi Liu Xiaolong Zhang Tong Sha Yankai Su Wenming Zhao Yiming Bao Yongbiao Xue Hua Chen Yali Hou;Shilei Zhao;Qi Liu;Xiaolong Zhang;Tong Sha;Yankai Su;Wenming Zhao;Yiming Bao;Yongbiao Xue;Hua Chen

作者机构：Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of SciencesBeijing 100049China Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming 650223China 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2022年第20卷第6期

页      面：1214-1223页

核心收录：

学科分类：1007[医学-药学(可授医学、理学学位)] 100705[医学-微生物与生化药学] 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：supported by the National Key R&D Program of China(Grant Nos.2021YFC0863400,2021YFC2301305,2020YFC0847000,2018YFC1406902,and 2018YFC0910402) the Key Program of Chinese Academy of Sciences(Grant No.KJZD-SW-L14) the National Natural Science Foundation of China(Grant Nos.31571370,91731302,and 91631106) the Shanghai Municipal Science and Technology Major Project,China(Grant No.2017SHZDZX01) the Strategic Priority Research Program of the Chinese Academy of Sciences,China(Grant Nos.XDPB17 and XDB38040200) 

主　　题：COVID-19 SARS-CoV-2 Viral evolution Natural selection Darwinian selection 

摘      要：SARS-CoV-2 is a new RNA virus affecting humans and spreads extensively throughout the world since its first outbreak in December,*** the transmissibility and pathogenicity of SARS-CoV-2 in humans after zoonotic transfer are actively evolving,and driven by adaptation to the new host and environments is still under *** the evolutionary mechanism underlying epidemiological and pathological characteristics of COVID-19 is essential for predicting the epidemic trend,and providing guidance for disease control and *** novel strategies for identifying natural selection using within-species polymorphisms and 3,674,076 SARSCoV-2 genome sequences of 169 countries as of December 30,2021,we demonstrate with population genetic evidence that during the course of SARS-CoV-2 pandemic in humans,1)SARS-CoV-2 genomes are overall conserved under purifying selection,especially for the 14 genes related to viral RNA replication,transcription,and assembly;2)ongoing positive selection is actively driving the evolution of 6 genes(e.g.,S,ORF3a,and N)that play critical roles in molecular processes involving pathogen–host interactions,including viral invasion into and egress from host cells,and viral inhibition and evasion of host immune response,possibly leading to high transmissibility and mild symptom in SARS-CoV-2 *** to an established haplotype phylogenetic relationship of 138 viral clusters,a spatial and temporal landscape of 556 critical mutations is constructed based on their divergence among viral haplotype clusters or repeatedly increase in frequency within at least 2 clusters,of which multiple mutations potentially conferring alterations in viral transmissibility,pathogenicity,and virulence of SARS-CoV-2 are highlighted,warranting attention.