title: Genetic drift of human coronavirus OC43 spike gene during adaptive evolution.
abstract: Coronaviruses (CoVs) continuously threaten human health. However, to date, the evolutionary mechanisms that govern CoV strain persistence in human populations have not been fully understood. In this study, we characterized the evolution of the major antigen-spike (S) gene in the most prevalent human coronavirus (HCoV) OC43 using phylogenetic and phylodynamic analysis. Among the five known HCoV-OC43 genotypes (A to E), higher substitution rates and dN/dS values as well as more positive selection sites were detected in the S gene of genotype D, corresponding to the most dominant HCoV epidemic in recent years. Further analysis showed that the majority of substitutions were located in the S1 subunit. Among them, seven positive selection sites were chronologically traced in the temporal evolution routes of genotype D, and six were located around the critical sugar binding region in the N-terminal domain (NTD) of S protein, an important sugar binding domain of CoV. These findings suggest that the genetic drift of the S gene may play an important role in genotype persistence in human populations, providing insights into the mechanisms of HCoV-OC43 adaptive evolution.
authors.affiliation: 1] MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) &Peking Union Medical College, P. R. China, Beijing 100730, P. R. China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, P.R. China.
authors.forename: Lili
authors.initials: L
authors.lastname: Ren
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) &Peking Union Medical College, P. R. China, Beijing 100730, P. R. China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) &Peking Union Medical College, P. R. China, Beijing 100730, P. R. China.
authors.forename: Jianguo
authors.initials: J
authors.lastname: Li
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) &Peking Union Medical College, P. R. China, Beijing 100730, P. R. China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) &Peking Union Medical College, P. R. China, Beijing 100730, P. R. China.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) &Peking Union Medical College, P. R. China, Beijing 100730, P. R. China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) &Peking Union Medical College, P. R. China, Beijing 100730, P. R. China.
authors.forename: Lan
authors.initials: L
authors.lastname: Chen
authors.affiliation: Fondation Mérieux, Lyon, 69007, France.
authors.forename: Gláucia
authors.initials: G
authors.lastname: Paranhos-Baccalà
authors.affiliation: 1] MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) &Peking Union Medical College, P. R. China, Beijing 100730, P. R. China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, P.R. China.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Wang
mesh_terms: D028962:Coronavirus OC43, Human / Q000235:genetics*; D019143:Evolution, Molecular; D005814:Genes, Viral; D040961:Genetic Drift; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D012641:Selection, Genetic