COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas.

Xianwen Ren, Wen Wen, Xiaoying Fan, Wenhong Hou, Bin Su, Pengfei Cai, Jiesheng Li, Yang Liu, Fei Tang, Fan Zhang, Yu Yang, Jiangping He, Wenji Ma, Jingjing He, Pingping Wang, Qiqi Cao, Fangjin Chen, Yuqing Chen, Xuelian Cheng, Guohong Deng, Xilong Deng, Wenyu Ding, Yingmei Feng, Rui Gan, Chuang Guo, Weiqiang Guo, Shuai He, Chen Jiang, Juanran Liang, Yi-Min Li, Jun Lin, Yun Ling, Haofei Liu, Jianwei Liu, Nianping Liu, Shu-Qiang Liu, Meng Luo, Qiang Ma, Qibing Song, Wujianan Sun, GaoXiang Wang, Feng Wang, Ying Wang, Xiaofeng Wen, Qian Wu, Gang Xu, Xiaowei Xie, Xinxin Xiong, Xudong Xing, Hao Xu, Chonghai Yin, Dongdong Yu, Kezhuo Yu, Jin Yuan, Biao Zhang, Peipei Zhang, Tong Zhang, Jincun Zhao, Peidong Zhao, Jianfeng Zhou, Wei Zhou, Sujuan Zhong, Xiaosong Zhong, Shuye Zhang, Lin Zhu, Ping Zhu, Bin Zou, Jiahua Zou, Zengtao Zuo, Fan Bai, Xi Huang, Penghui Zhou, Qinghua Jiang, Zhiwei Huang, Jin-Xin Bei, Lai Wei, Xiu-Wu Bian, Xindong Liu, Tao Cheng, Xiangpan Li, Pingsen Zhao, Fu-Sheng Wang, Hongyang Wang, Bing Su, Zheng Zhang, Kun Qu, Xiaoqun Wang, Jiekai Chen, Ronghua Jin, Zemin Zhang
Author Information
  1. Xianwen Ren: Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China.
  2. Wen Wen: National Center for Liver Cancer, Second Military Medical University, Shanghai 200003, China; Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200003, China; Ministry of Education (MOE) Key Laboratory on Signaling Regulation and Targeting Therapy of Liver Cancer, Second Military Medical University, Shanghai 200003, China.
  3. Xiaoying Fan: Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  4. Wenhong Hou: Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
  5. Bin Su: Beijing Youan Hospital, Capital Medical University, Beijing 100069, China.
  6. Pengfei Cai: Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China.
  7. Jiesheng Li: Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China.
  8. Yang Liu: Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, China.
  9. Fei Tang: Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China.
  10. Fan Zhang: Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China.
  11. Yu Yang: Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China.
  12. Jiangping He: Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.
  13. Wenji Ma: State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  14. Jingjing He: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
  15. Pingping Wang: Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, China.
  16. Qiqi Cao: National Center for Liver Cancer, Second Military Medical University, Shanghai 200003, China; Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200003, China; Ministry of Education (MOE) Key Laboratory on Signaling Regulation and Targeting Therapy of Liver Cancer, Second Military Medical University, Shanghai 200003, China.
  17. Fangjin Chen: Center for Quantitative Biology, Peking University, Beijing 100871, China.
  18. Yuqing Chen: Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China.
  19. Xuelian Cheng: State Key Laboratory of Experimental Hematology and National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine and Department of Stem Cell & Regenerative Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
  20. Guohong Deng: Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing 400038, China.
  21. Xilong Deng: Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510060, China.
  22. Wenyu Ding: State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China.
  23. Yingmei Feng: Beijing Youan Hospital, Capital Medical University, Beijing 100069, China.
  24. Rui Gan: Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China.
  25. Chuang Guo: Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China.
  26. Weiqiang Guo: Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China.
  27. Shuai He: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
  28. Chen Jiang: Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China.
  29. Juanran Liang: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China.
  30. Yi-Min Li: State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China.
  31. Jun Lin: Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China.
  32. Yun Ling: Department of Infectious Disease, Shanghai Public Health Clinical Center, Shanghai 201052, China.
  33. Haofei Liu: Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing 400038, China.
  34. Jianwei Liu: Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.
  35. Nianping Liu: Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China.
  36. Shu-Qiang Liu: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
  37. Meng Luo: Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, China.
  38. Qiang Ma: State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  39. Qibing Song: Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China.
  40. Wujianan Sun: Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China.
  41. GaoXiang Wang: Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
  42. Feng Wang: Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
  43. Ying Wang: Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
  44. Xiaofeng Wen: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China.
  45. Qian Wu: State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China.
  46. Gang Xu: Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, China.
  47. Xiaowei Xie: State Key Laboratory of Experimental Hematology and National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine and Department of Stem Cell & Regenerative Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
  48. Xinxin Xiong: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
  49. Xudong Xing: Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China.
  50. Hao Xu: Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China.
  51. Chonghai Yin: State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  52. Dongdong Yu: Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China.
  53. Kezhuo Yu: Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China.
  54. Jin Yuan: Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, China.
  55. Biao Zhang: State Key Laboratory of Experimental Hematology and National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine and Department of Stem Cell & Regenerative Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
  56. Peipei Zhang: Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing 400038, China; Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), and Department of Pathology, the First Hospital Affiliated to USTC, Hefei, Anhui 230036, China; Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
  57. Tong Zhang: Beijing Youan Hospital, Capital Medical University, Beijing 100069, China.
  58. Jincun Zhao: State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China.
  59. Peidong Zhao: Analytical Biosciences Beijing Limited, Beijing 100084, China.
  60. Jianfeng Zhou: Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
  61. Wei Zhou: Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.
  62. Sujuan Zhong: State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China.
  63. Xiaosong Zhong: Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China.
  64. Shuye Zhang: Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai 201508, China.
  65. Lin Zhu: Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China.
  66. Ping Zhu: State Key Laboratory of Experimental Hematology and National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine and Department of Stem Cell & Regenerative Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
  67. Bin Zou: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China.
  68. Jiahua Zou: Cancer Center, Huanggang Hospital of Traditional Chinese Medicine, Huanggang 438000, China.
  69. Zengtao Zuo: State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  70. Fan Bai: Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China.
  71. Xi Huang: Center for Infection and Immunity, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong 519000, China.
  72. Penghui Zhou: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China. Electronic address: zhouph@sysucc.org.cn.
  73. Qinghua Jiang: Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, China. Electronic address: qhjiang@hit.edu.cn.
  74. Zhiwei Huang: Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China. Electronic address: huangzhiwei2009@gmail.com.
  75. Jin-Xin Bei: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China. Electronic address: beijx@sysucc.org.cn.
  76. Lai Wei: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China. Electronic address: weilai@gzzoc.com.
  77. Xiu-Wu Bian: Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing 400038, China; Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), and Department of Pathology, the First Hospital Affiliated to USTC, Hefei, Anhui 230036, China. Electronic address: bianxiuwu@263.net.
  78. Xindong Liu: Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing 400038, China; Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), and Department of Pathology, the First Hospital Affiliated to USTC, Hefei, Anhui 230036, China. Electronic address: xindongliu@hotmail.com.
  79. Tao Cheng: State Key Laboratory of Experimental Hematology and National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine and Department of Stem Cell & Regenerative Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China. Electronic address: chengtao@ihcams.ac.cn.
  80. Xiangpan Li: Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China. Electronic address: rm001227@whu.edu.cn.
  81. Pingsen Zhao: Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Laboratory for Diagnosis of Clinical Microbiology and Infection, Medical Research Center, Shantou University Medical College, Shaoguan 512025, China. Electronic address: zhaopingsen01@163.com.
  82. Fu-Sheng Wang: Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China. Electronic address: fswang302@163.com.
  83. Hongyang Wang: National Center for Liver Cancer, Second Military Medical University, Shanghai 200003, China; Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200003, China; Ministry of Education (MOE) Key Laboratory on Signaling Regulation and Targeting Therapy of Liver Cancer, Second Military Medical University, Shanghai 200003, China. Electronic address: hywangk@vip.sina.com.
  84. Bing Su: Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China. Electronic address: bingsu@sjtu.edu.cn.
  85. Zheng Zhang: Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, China. Electronic address: zhangzheng1975@aliyun.com.
  86. Kun Qu: Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China. Electronic address: qukun@ustc.edu.cn.
  87. Xiaoqun Wang: Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: xiaoqunwang@ibp.ac.cn.
  88. Jiekai Chen: Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China. Electronic address: chen_jiekai@gibh.ac.cn.
  89. Ronghua Jin: Beijing Youan Hospital, Capital Medical University, Beijing 100069, China. Electronic address: ronghuajin_youan@126.com.
  90. Zemin Zhang: Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China. Electronic address: zemin@pku.edu.cn.

Abstract

A dysfunctional immune response in coronavirus disease 2019 (COVID-19) patients is a recurrent theme impacting symptoms and mortality, yet a detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 196 COVID-19 patients and controls and created a comprehensive immune landscape with 1.46 million cells. The large dataset enabled us to identify that different peripheral immune subtype changes are associated with distinct clinical features, including age, sex, severity, and disease stages of COVID-19. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was found in diverse epithelial and immune cell types, accompanied by dramatic transcriptomic changes within virus-positive cells. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis of and developing effective therapeutic strategies for COVID-19.

Keywords

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MeSH Term

Adolescent
Adult
Aged
Aged, 80 and over
COVID-19
Child
China
Cohort Studies
Cytokines
Female
Humans
Male
Megakaryocytes
Middle Aged
Monocytes
RNA, Viral
SARS-CoV-2
Single-Cell Analysis
Transcriptome
Young Adult

Chemicals

Cytokines
RNA, Viral