Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission

Xintian Xu; Ping Chen; Jingfang Wang; Jiannan Feng; Hui Zhou; Xuan Li; Wu Zhong; Pei Hao

doi:10.1007/s11427-020-1637-5

SCIENCE CHINA Life Sciences

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SCIENCE CHINA Life Sciences, Volume 63 , Issue 3 : 457-460(2020) https://doi.org/10.1007/s11427-020-1637-5

Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission

Xintian Xu ^1,†, Ping Chen ^2,5,†, Jingfang Wang ^3,†, Jiannan Feng ⁴, Hui Zhou ², Xuan Li ^2,*, Wu Zhong ^4,*, Pei Hao ^1,5,*

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Affiliations：

1. Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai 200031, China;

2. Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China;

3. Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China;

4. National Engineering Research Center for the Emergence Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China;

5. The Joint Program in Infection and Immunity: a. Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China; b. Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China

† Contributed equally to this work
* Corresponding authors (Pei Hao, email: phao@ips.ac.cn; Wu Zhong, email: zhongwu@bmi.ac.cn; Xuan Li, email: lixuan@sippe.ac.cn)

ReceivedJan 16, 2020
AcceptedJan 20, 2020
PublishedJan 21, 2020

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Abstract

There is no abstract available for this article.

Acknowledgment

This work was supported in part by grants from the National Science and Technology Major Projects for “Major New Drugs Innovation and Development” (directed by Dr. Song Li) (2018ZX09711003) of China, the National Key R&D Program (2018YFC0310600) of China, the National Natural Science Foundation of China (31771412), and Special Fund for strategic bio-resources from Chinese Academy of Sciences (ZSYS-014). We also acknowledge the National Institute for Viral Disease Control and Prevention, China CDC; Wuhan Institute of Virology, Chinese Academy of Sciences; Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College; and Wuhan Jinyintan Hospital for their efforts in research and collecting the data and genome sequencing sharing. In addition, we acknowledge GISAID (https://www.gisaid.org/) for facilitating open data sharing.

Interest statement

The author(s) declare that they have no conflict of interest.

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SUPPORTING INFORMATION

Figure S1 Sequence similarity analysis among six Wuhan CoV genomes and between Wuhan CoV and the human-infecting coronaviruses, SARS-CoV and MERS-CoV.

Table S1 Acknowledgement to the authors, originating and submitting laboratories of the sequences from GISAID

The supporting information is available online at http://life.scichina.com and https://link.springer.com. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.

References

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[10] Shu, Y., and McCauley, J. (2017). GISAID: Global initiative on sharing all influenza data—from vision to reality. EuroSurveillance 22, PMCID: PMC5388101. Google Scholar

[11] WHO. (2020). Pneumonia of unknown cause in China. https://www.who.int/csr/don/05-january-2020-pneumonia-of-unkown-cause-china/en/. Google Scholar

[12] Zhang, Y.Z. (2020). Initial genome release of novel coronavirus. http://virological.org/t/initial-genome-release-of-novel-coronavirus/319?from=groupmessage. Google Scholar

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Figure 1
Evolutionary analysis of the coronaviruses and modeling of the Wuhan CoV S-protein interacting with human ACE2. A, Phylogenetic tree of coronaviruses based on full-length genome sequences. The tree was constructed with the Maximum-likelihood method using RAxML with GTRGAMMA as the nucleotide substitution model and 1,000 bootstrap replicates. Only bootstraps ≥50% values are shown as filled circles. The host for each coronavirus is marked with corresponding silhouette. Known human-infecting betacoronaviruses are indicated with a red star. B, Amino acid sequence alignment of the RBD domain of coronavirus S-protein. Residues 442, 472, 479, 487, and 491 (numbered based on SARS-CoV S-protein sequence) are important residues for interaction with human ACE2 molecule. C, Structural modeling of the Wuhan CoV (WH-human_1 as representative) S-protein complexed with human ACE2 molecule. Middle panel: The model of the Wuhan CoV S-protein (brown ribbon) is superimposed with the structural template of the SARS CoV S-protein (light blue ribbon). The protein backbone structure of human ACE2 is represented in magenta ribbon. Left panel: The region is shown for hydrogen bonding interactions between Arg426 in S-protein and Gln325/Glu329 in ACE2. The relevant residues are presented in ball and stick representations. Right panel: The region is shown for hydrogen bonding interactions between Tyr436 in S-protein and Asp38/Gln42 in ACE2.

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Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission

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