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Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China

Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Yi Hu, Zhi-Gang Song, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei, Ming-Li Yuan, Yu-Ling Zhang, Fa-Hui Dai, Yi Liu, Qi-Min Wang, Jiao-Jiao Zheng, Lin Xu, Edward C. Holmes, Yong-Zhen Zhang
doi: https://doi.org/10.1101/2020.01.24.919183
Fan Wu
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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Su Zhao
2Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
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Bin Yu
3Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
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Yan-Mei Chen
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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Wen Wang
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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Yi Hu
2Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
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Zhi-Gang Song
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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Zhao-Wu Tao
2Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
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Jun-Hua Tian
3Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
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Yuan-Yuan Pei
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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Ming-Li Yuan
2Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
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Yu-Ling Zhang
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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Fa-Hui Dai
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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Yi Liu
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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Qi-Min Wang
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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Jiao-Jiao Zheng
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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Lin Xu
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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Edward C. Holmes
4Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
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Yong-Zhen Zhang
1Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China
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  • For correspondence: zhangyongzhen@shphc.org.cn
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Abstract

Emerging and re-emerging infectious diseases, such as SARS, MERS, Zika and highly pathogenic influenza present a major threat to public health1–3. Despite intense research effort, how, when and where novel diseases appear are still the source of considerable uncertainly. A severe respiratory disease was recently reported in the city of Wuhan, Hubei province, China. At the time of writing, at least 62 suspected cases have been reported since the first patient was hospitalized on December 12nd 2019. Epidemiological investigation by the local Center for Disease Control and Prevention (CDC) suggested that the outbreak was associated with a sea food market in Wuhan. We studied seven patients who were workers at the market, and collected bronchoalveolar lavage fluid (BALF) from one patient who exhibited a severe respiratory syndrome including fever, dizziness and cough, and who was admitted to Wuhan Central Hospital on December 26th 2019. Next generation metagenomic RNA sequencing4 identified a novel RNA virus from the family Coronaviridae designed WH-Human-1 coronavirus (WHCV).

Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that WHCV was most closely related (89.1% nucleotide similarity similarity) to a group of Severe Acute Respiratory Syndrome (SARS)-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) previously sampled from bats in China and that have a history of genomic recombination. This outbreak highlights the ongoing capacity of viral spill-over from animals to cause severe disease in humans.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 02, 2020.
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Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China
Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Yi Hu, Zhi-Gang Song, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei, Ming-Li Yuan, Yu-Ling Zhang, Fa-Hui Dai, Yi Liu, Qi-Min Wang, Jiao-Jiao Zheng, Lin Xu, Edward C. Holmes, Yong-Zhen Zhang
bioRxiv 2020.01.24.919183; doi: https://doi.org/10.1101/2020.01.24.919183
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Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China
Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Yi Hu, Zhi-Gang Song, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei, Ming-Li Yuan, Yu-Ling Zhang, Fa-Hui Dai, Yi Liu, Qi-Min Wang, Jiao-Jiao Zheng, Lin Xu, Edward C. Holmes, Yong-Zhen Zhang
bioRxiv 2020.01.24.919183; doi: https://doi.org/10.1101/2020.01.24.919183

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