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Two-step fitness selection for intra-host variations in SARS-CoV-2.
Li, Jiarui; Du, Pengcheng; Yang, Lijiang; Zhang, Ju; Song, Chuan; Chen, Danying; Song, Yangzi; Ding, Nan; Hua, Mingxi; Han, Kai; Song, Rui; Xie, Wen; Chen, Zhihai; Wang, Xianbo; Liu, Jingyuan; Xu, Yanli; Gao, Guiju; Wang, Qi; Pu, Lin; Di, Lin; Li, Jie; Yue, Jinglin; Han, Junyan; Zhao, Xuesen; Yan, Yonghong; Yu, Fengting; Wu, Angela R; Zhang, Fujie; Gao, Yi Qin; Huang, Yanyi; Wang, Jianbin; Zeng, Hui; Chen, Chen.
  • Li J; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Du P; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Yang L; Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China.
  • Zhang J; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Song C; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Chen D; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Song Y; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Ding N; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Hua M; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Han K; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Song R; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
  • Xie W; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
  • Chen Z; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
  • Wang X; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
  • Liu J; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
  • Xu Y; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
  • Gao G; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
  • Wang Q; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
  • Pu L; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
  • Di L; Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenz
  • Li J; School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China.
  • Yue J; Peking University Ditan Teaching Hospital, Beijing 100015, China.
  • Han J; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Zhao X; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Yan Y; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China.
  • Yu F; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
  • Wu AR; Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, P.R. China; Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong SAR, P.R. China.
  • Zhang F; Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China. Electronic address: treatment@chinaaids.cn.
  • Gao YQ; Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; Institute of Systems and P
  • Huang Y; Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; School of Life Sciences, P
  • Wang J; School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Chinese Institute for Brain Research, Beijing 102206, China. Electronic address: jianbinwang@tsinghua.edu.cn.
  • Zeng H; Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China. Electronic address: zenghui@ccmu.edu.cn.
  • Chen C; Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China. Electronic address: chenchen1@ccmu.edu.cn.
Cell Rep ; 38(2): 110205, 2022 01 11.
Article in English | MEDLINE | ID: covidwho-1588142
ABSTRACT
Spontaneous mutations introduce uncertainty into coronavirus disease 2019 (COVID-19) control procedures and vaccine development. Here, we perform a spatiotemporal analysis on intra-host single-nucleotide variants (iSNVs) in 402 clinical samples from 170 affected individuals, which reveals an increase in genetic diversity over time after symptom onset in individuals. Nonsynonymous mutations are overrepresented in the pool of iSNVs but underrepresented at the single-nucleotide polymorphism (SNP) level, suggesting a two-step fitness selection process a large number of nonsynonymous substitutions are generated in the host (positive selection), and these substitutions tend to be unfixed as SNPs in the population (negative selection). Dynamic iSNV changes in subpopulations with different gender, age, illness severity, and viral shedding time displayed a varied fitness selection process among populations. Our study highlights that iSNVs provide a mutational pool shaping the rapid global evolution of the virus.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Host-Pathogen Interactions / SARS-CoV-2 / COVID-19 Type of study: Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Adolescent / Adult / Aged / Child / Child, preschool / Female / Humans / Infant / Male / Middle aged Language: English Journal: Cell Rep Year: 2022 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Host-Pathogen Interactions / SARS-CoV-2 / COVID-19 Type of study: Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Adolescent / Adult / Aged / Child / Child, preschool / Female / Humans / Infant / Male / Middle aged Language: English Journal: Cell Rep Year: 2022 Document Type: Article