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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Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study

Matthew Cotten, Simon Watson, Paul Kellam … (2013)

Summary Background Since June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has, worldwide, caused 104 infections in people including 49 deaths, with 82 cases and 41 deaths reported from Saudi Arabia. In addition to confirming diagnosis, we generated the MERS-CoV genomic sequences obtained directly from patient samples to provide important information on MERS-CoV transmission, evolution, and origin. Methods Full genome deep sequencing was done on nucleic acid extracted directly from PCR-confirmed clinical samples. Viral genomes were obtained from 21 MERS cases of which 13 had 100%, four 85–95%, and four 30–50% genome coverage. Phylogenetic analysis of the 21 sequences, combined with nine published MERS-CoV genomes, was done. Findings Three distinct MERS-CoV genotypes were identified in Riyadh. Phylogeographic analyses suggest the MERS-CoV zoonotic reservoir is geographically disperse. Selection analysis of the MERS-CoV genomes reveals the expected accumulation of genetic diversity including changes in the S protein. The genetic diversity in the Al-Hasa cluster suggests that the hospital outbreak might have had more than one virus introduction. Interpretation We present the largest number of MERS-CoV genomes (21) described so far. MERS-CoV full genome sequences provide greater detail in tracking transmission. Multiple introductions of MERS-CoV are identified and suggest lower R0 values. Transmission within Saudi Arabia is consistent with either movement of an animal reservoir, animal products, or movement of infected people. Further definition of the exposures responsible for the sporadic introductions of MERS-CoV into human populations is urgently needed. Funding Saudi Arabian Ministry of Health, Wellcome Trust, European Community, and National Institute of Health Research University College London Hospitals Biomedical Research Centre.

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Mystery virus found in Wuhan resembles bat viruses but not SARS, Chinese scientist says

Dennis Normile (2020)

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GISAID: Global initiative on sharing all influenza data—from vision to reality

Y Shu, J. MCCAULEY (2017)

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Author and article information

Contributors

Xuan Li: lixuan@sippe.ac.cn

Wu Zhong: zhongwu@bmi.ac.cn

Pei Hao: phao@ips.ac.cn

Journal

Journal ID (nlm-ta): Sci China Life Sci

Journal ID (iso-abbrev): Sci China Life Sci

Title: Science China. Life Sciences

Publisher: Science China Press (Beijing )

ISSN (Print): 1674-7305

ISSN (Electronic): 1869-1889

Publication date (Electronic): 21 January 2020

Publication date (Print): 2020

Volume: 63

Issue: 3

Pages: 457-460

Affiliations

[1 ]GRID grid.9227.e, ISNI 0000000119573309, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, , Chinese Academy of Sciences, ; Shanghai, 200031 China

[2 ]GRID grid.9227.e, ISNI 0000000119573309, Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, , Chinese Academy of Sciences, ; Shanghai, 200032 China

[3 ]GRID grid.16821.3c, ISNI 0000 0004 0368 8293, Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, , Shanghai Jiao Tong University, ; Shanghai, 200240 China

[4 ]GRID grid.410740.6, ISNI 0000 0004 1803 4911, National Engineering Research Center for the Emergence Drugs, , Beijing Institute of Pharmacology and Toxicology, ; Beijing, 100850 China

[5 ]GRID grid.410737.6, ISNI 0000 0000 8653 1072, The Joint Program in Infection and Immunity: Guangzhou Women and Children’s Medical Center, , Guangzhou Medical University, ; Guangzhou, 510623 China

[6 ]GRID grid.9227.e, ISNI 0000000119573309, The Joint Program in Infection and Immunity: Institute Pasteur of Shanghai, , Chinese Academy of Sciences, ; Shanghai, 200031 China

Article

Publisher ID: 1637

DOI: 10.1007/s11427-020-1637-5

PMC ID: 7089049

PubMed ID: 32009228

SO-VID: 6511c6e8-48b2-4d33-8c79-380670d771c8

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This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

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Date received : 16 January 2020

Date accepted : 20 January 2020

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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Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study

Mystery virus found in Wuhan resembles bat viruses but not SARS, Chinese scientist says

GISAID: Global initiative on sharing all influenza data—from vision to reality

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