Evidence map›Paper›PMID 33657410›Full record

ArticleCell2021

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 and 80 more

Erratum issuedAbstract read
In one paragraph

Article in Cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 513 papers, 3 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
513citing papers in PubMed, 3 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

513 citing papers in PubMed, 3 syntheses or guidelines pooled it.

  1. Single-cell RNA sequencing offers novel perspectives in viral infection research.Frontiers in cellular and infection microbiology · 2026
    Pooled it
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  3. Pooled it
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  7. Article
  8. Monocytes in pneumonia: Functional plasticity and innate memory (Review).International journal of molecular medicine · 2026
    Review
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  18. Extra gene coding capacity of SARS-CoV-2 provides a virus engineering platform for in vitro and in vivo applications.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  19. Article
  20. Article

453 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

90 authors.

Xianwen RenBiomedical 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.
Wen WenNational 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.
Xiaoying FanBioland 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.
Wenhong HouInstitute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
Bin SuBeijing Youan Hospital, Capital Medical University, Beijing 100069, China.
Pengfei CaiDepartment 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.
Jiesheng LiBiomedical 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.
Yang LiuInstitute 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.
Fei TangBiomedical 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.
Fan ZhangCenter for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China.
Yu YangBiomedical 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.
Jiangping HeBioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.
Wenji MaState 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.
Jingjing HeState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
Pingping WangCenter for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, China.
Qiqi CaoNational 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.
Fangjin ChenCenter for Quantitative Biology, Peking University, Beijing 100871, China.
Yuqing ChenBiomedical 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.
Xuelian ChengState 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.
Guohong DengDepartment of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing 400038, China.
Xilong DengGuangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510060, China.
Wenyu DingState 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.
Yingmei FengBeijing Youan Hospital, Capital Medical University, Beijing 100069, China.
Rui GanCenter for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China.
Chuang GuoDepartment 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.
Weiqiang GuoYuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China.
Shuai HeState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
Chen JiangDepartment 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.
Juanran LiangState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China.
Yi-Min LiState 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.
Jun LinDepartment 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.
Yun LingDepartment of Infectious Disease, Shanghai Public Health Clinical Center, Shanghai 201052, China.
Haofei LiuInstitute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing 400038, China.
Jianwei LiuBioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.
Nianping LiuDepartment 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.
Shu-Qiang LiuState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
Meng LuoCenter for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, China.
Qiang MaState 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.
Qibing SongCancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China.
Wujianan SunDepartment 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.
GaoXiang WangDepartment of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
Feng WangShanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
Ying WangShanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
Xiaofeng WenState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China.
Qian WuState Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China.
Gang XuInstitute 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.
Xiaowei XieState 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.
Xinxin XiongState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
Xudong XingDepartment of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China.
Hao XuDepartment 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.
Chonghai YinState 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.
Dongdong YuCancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China.
Kezhuo YuBiomedical 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.
Jin YuanInstitute 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.
Biao ZhangState 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.
Peipei ZhangInstitute 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.
Tong ZhangBeijing Youan Hospital, Capital Medical University, Beijing 100069, China.
Jincun ZhaoState 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.
Peidong ZhaoAnalytical Biosciences Beijing Limited, Beijing 100084, China.
Jianfeng ZhouDepartment of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
Wei ZhouBioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.
Sujuan ZhongState Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China.
Xiaosong ZhongBeijing Shijitan Hospital, Capital Medical University, Beijing 100038, China.
Shuye ZhangShanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai 201508, China.
Lin ZhuDepartment 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.
Ping ZhuState 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.
Bin ZouState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China.
Jiahua ZouCancer Center, Huanggang Hospital of Traditional Chinese Medicine, Huanggang 438000, China.
Zengtao ZuoState 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.
Fan BaiBiomedical 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.
Xi HuangCenter for Infection and Immunity, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong 519000, China.
Penghui ZhouState 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.
Qinghua JiangCenter for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, China. Electronic address: qhjiang@hit.edu.cn.
Zhiwei HuangCenter for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China. Electronic address: huangzhiwei2009@gmail.com.
Jin-Xin BeiState 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.
Lai WeiState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China. Electronic address: weilai@gzzoc.com.
Xiu-Wu BianInstitute 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.
Xindong LiuInstitute 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.
Tao ChengState 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.
Xiangpan LiCancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China. Electronic address: rm001227@whu.edu.cn.
Pingsen ZhaoDepartment 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.
Fu-Sheng WangDepartment 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.
Hongyang WangNational 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.
Bing SuShanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China. Electronic address: bingsu@sjtu.edu.cn.
Zheng ZhangInstitute 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.
Kun QuDepartment 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.
Xiaoqun WangBioland 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.
Jiekai ChenBioland 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.
Ronghua JinBeijing Youan Hospital, Capital Medical University, Beijing 100069, China. Electronic address: ronghuajin_youan@126.com.
Zemin ZhangBiomedical 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.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

RNA, ViralAdolescentAdultAgedAged, 80 and overChildChinaCohort StudiesCOVID-19CytokinesFemaleHumansMaleMegakaryocytesMiddle AgedMonocytesCytokinesRNA, ViralB cell receptor sequencingcell-cell interactionCOVID-19cytokine stormhost cell rangeligand-receptor interactionSARS-CoV-2single-cell RNA-seqsingle-cell transcriptomicsT cell receptor sequencing

Identifiers

PMID33657410
PMCPMC7857060

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