Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study

Li Li Ren; Ye Ming Wang; Zhi Qiang WU; Zi Chun Xiang; Li Guo; Teng XU; Yong Zhong Jiang; Yan Xiong; Yong Jun LI; Hui LI; Guo Hui Fan; Xiao Ying GU; Yan Xiao; Hong Gao; Jiu Yang XU; Fan Yang; Xin Ming Wang; Chao WU; Lan Chen; Yi Wei Liu; Bo Liu; Jian Yang; Jie Dong; Li LI; Chao Lin Huang; Jian Ping Zhao; Yi HU; Zhen Shun Cheng; Lin Lin Liu; Zhao Hui Qian; Chuan Qin; Qi Jin; Bin Cao; Jian Wei Wang

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Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study

Author: Li Li REN ¹ ; Ye Ming WANG ^{2
,

3} ; Zhi Qiang WU ⁴ ; Zi Chun XIANG ¹ ; Li GUO ¹ ; Teng XU ⁵ ; Yong Zhong JIANG ⁶ ; Yan XIONG ⁷ ; Yong Jun LI ⁵ ; Hui LI ⁸ ; Guo Hui FAN ⁹ ; Xiao Ying GU ⁹ ; Yan XIAO ¹ ; Hong GAO ¹⁰ ; Jiu Yang XU ¹¹ ; Fan YANG ⁴ ; Xin Ming WANG ¹ ; Chao WU ¹ ; Lan CHEN ¹ ; Yi Wei LIU ¹ ; Bo LIU ⁴ ; Jian YANG ⁴ ; Jie DONG ⁴ ; Li LI ⁴ ; Chao Lin HUANG ¹² ; Jian Ping ZHAO ¹³ ; Yi HU ¹⁴ ; Zhen Shun CHENG ¹⁵ ; Lin Lin LIU ⁵ ; Zhao Hui QIAN ⁴ ; Chuan QIN ¹⁰ ; Qi JIN ⁴ ; Bin CAO ^{2
,

3} ; Jian Wei WANG ¹
Author Information

1. NHC 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, Beijing 100730, China
2. Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing 100029, China
3. Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100029, China
4. NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, China
5. Vision Medicals Co., Ltd, Guangzhou, Guangdong 510000, China
6. Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei 430079, China
7. Wuhan Center for Disease Control and Prevention, Wuhan, Hubei 430022, China
8. Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
9. Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing 100029, China
10. Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
11. Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing, 100084, China
12. Jin Yin-tan Hospital, Wuhan, Hubei 430022, China
13. Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei 430030, China
14. Department of Pulmonary and Critical Care Medicine, Central Hospital of Wuhan, Wuhan, Hubei 430014, China
15. Department of Respiratory medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
Publication Type:Journal Article
Keywords: Bat-origin; Coronavirus; Zoonotic transmission; Pneumonia; Etiology; Next-generation sequencing
From: Chinese Medical Journal 2020;133(0):E001-E001
CountryChina
Language:English
Abstract: Background: Human infections with zoonotic coronaviruses (CoVs), including severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV, have raised great public health concern globally. Here, we report a novel bat-origin CoV causing severe and fatal pneumonia in humans. Methods: We collected clinical data and bronchoalveolar lavage (BAL) specimens from five patients with severe pneumonia from Jin Yin-tan Hospital, Wuhan, Hubei province, China. Nucleic acids of the BAL were extracted and subjected to next-generation sequencing. Virus isolation was carried out, and maximum-likelihood phylogenetic trees were constructed. Results: Five patients hospitalized from December 18 to December 29, 2019 presented with fever, cough, and dyspnea accompanied by complications of acute respiratory distress syndrome. Chest radiography revealed diffuse opacities and consolidation. One of these patients died. Sequence results revealed the presence of a previously unknown β-CoV strain in all five patients, with 99.8–99.9% nucleotide identities among the isolates. These isolates showed 79.0% nucleotide identity with the sequence of SARS-CoV (GenBank NC_004718) and 51.8% identity with the sequence of MERS-CoV (GenBank NC_019843). The virus is phylogenetically closest to a bat SARS-like CoV (SL-ZC45, GenBank MG772933) with 87.6–87.7% nucleotide identity, but is in a separate clade. Moreover, these viruses have a single intact open reading frame gene 8, as a further indicator of bat-origin CoVs. However, the amino acid sequence of the tentative receptor-binding domain resembles that of SARS-CoV, indicating that these viruses might use the same receptor. Conclusion: A novel bat-borne CoV was identified that is associated with severe and fatal respiratory disease in humans.