Genomic Characteristics of SARS-CoV, MERS-CoV and 2019-nCoV
LI Tong, YU Xing, CHEN Meng-xiang, LV Yuan*, ZHA Wen-ting*
Medical College of Hunan Normal University, Key Laboratory of Molecular Epidemiology of Hunan Province, School of Medicine, Hunan Normal University, Changsha 410081, China
Genomic Characteristics of SARS-CoV, MERS-CoV and 2019-nCoV
LI Tong, YU Xing, CHEN Meng-xiang, LV Yuan*, ZHA Wen-ting*
Medical College of Hunan Normal University, Key Laboratory of Molecular Epidemiology of Hunan Province, School of Medicine, Hunan Normal University, Changsha 410081, China
摘要In December 2019, Wuhan, the capital of Hubei Province in China, reported a series of unexplained cases of pneumonia, which has been confirmed to be an acute infectious respiratory disease caused by Novel Corona Virus 2019 (2019-nCoV) infection. The World Health Organization (WHO) named this pneumonia Corona Virus Disease 2019(COVID-19). The 21st century had witnessed the spread of two previously unrecognized coronaviruses around the world with high pathogenicity before, namely severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) respectively. At present, 2019-nCoV 's genome has been sequenced by researchers all over the world represented by China. Based on the systematic review and analysis of the genomic sequence characteristics of three highly pathogenic coronaviruses, this paper expounds the basic characteristics of the genomes of SARS-CoV, MERS-CoV and 2019-nCoV,which all belong to β-coronaviruses, the functionally important ORFs, ORF1a, ORF1b and major structural proteins including the spike (S), membrane (M) and envelop (E) and nucleiccapsid (N) proteins have no significant difference with each other. However, as the majority of genetic variations being seen at the N-terminal part of S protein, 2019-nCoV aligned best with the bat SARS-like virus bat-SL-CoVZX45. And Structure analysis of the spike (S) protein of 2019-nCoV showed that it's S protein only binds weakly to the Angiotensin Converting Enzyme2 (ACE2) receptor on human cells whereas the human SARS-Cov exhibits high affinity to the ACE receptor and MERS-Cov does not need ACE2 to infect human cells, its receptor on human cells is DPP4. In the future, we hope to provide new ideas for the prevention and treatment of coronavirus by strengthening the research of coronavirus S protein and ACE2 receptor, and continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by a genetic mutation.
Abstract：In December 2019, Wuhan, the capital of Hubei Province in China, reported a series of unexplained cases of pneumonia, which has been confirmed to be an acute infectious respiratory disease caused by Novel Corona Virus 2019 (2019-nCoV) infection. The World Health Organization (WHO) named this pneumonia Corona Virus Disease 2019(COVID-19). The 21st century had witnessed the spread of two previously unrecognized coronaviruses around the world with high pathogenicity before, namely severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) respectively. At present, 2019-nCoV 's genome has been sequenced by researchers all over the world represented by China. Based on the systematic review and analysis of the genomic sequence characteristics of three highly pathogenic coronaviruses, this paper expounds the basic characteristics of the genomes of SARS-CoV, MERS-CoV and 2019-nCoV,which all belong to β-coronaviruses, the functionally important ORFs, ORF1a, ORF1b and major structural proteins including the spike (S), membrane (M) and envelop (E) and nucleiccapsid (N) proteins have no significant difference with each other. However, as the majority of genetic variations being seen at the N-terminal part of S protein, 2019-nCoV aligned best with the bat SARS-like virus bat-SL-CoVZX45. And Structure analysis of the spike (S) protein of 2019-nCoV showed that it's S protein only binds weakly to the Angiotensin Converting Enzyme2 (ACE2) receptor on human cells whereas the human SARS-Cov exhibits high affinity to the ACE receptor and MERS-Cov does not need ACE2 to infect human cells, its receptor on human cells is DPP4. In the future, we hope to provide new ideas for the prevention and treatment of coronavirus by strengthening the research of coronavirus S protein and ACE2 receptor, and continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by a genetic mutation.
基金资助:grant sponsor: Construct Program of the Key Discipline in Hunan Province, Science and Technology Plan Project of Changsha; grant number: kq2001025, 2020-2021; grant sponsor: the National Natural Science Foundation of China; grant number: 811773530; grant sponsor: the National Natural Science Foundation of Hunan Province; grant number: 2020JJ405; grant sponsor: Educational Department Project of Hunan Province; grant number: JG2018B041
[1] Zu ZY, Jiang MD, Xu PP, et al.Coronavirus Disease 2019 (COVID-19): a perspective from China[J]. Radiology, 2020:200490. [2] Niu M, Wang RL, Wang ZX, et al.Rapid establishment of traditional Chinese medicine prevention and treatment of 2019-nCoV based on clinical experience and molecular docking[J]. China Journal of Chinese Materia Medica, 2020, 45(6):1213-1218. [3] Yu H, Wang XC, Li J, et al.Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China[J]. Chinese Journal of Preventive Medicine, 2020, 54:E026. [4] Lu R, Zhao X, Li J, ,et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding[J]. Lancet, 2020, 395(10224):565-574. [5] Zhang SM, Liao Y, Neo TL, et al.Identification and application of self-binding zipper-like sequences in SARS-CoV spike protein[J]. International Journal of Biochemistry & Cell Biology, 2018, 101:103-112. [6] Wang YX, Ma JR, Wang SQ, et al.Utilizing integrating network pharmacological approaches to investigate the potential mechanism of Ma Xing Shi Gan Decoction in treating COVID-19[J]. European Review for Medical and Pharmacological Sciences, 2020, 24(6):3360-3384. [7] Lee S, Jo SD, Son K, et al.Genetic characteristics of coronaviruses from Korean bats in 2016[J]. Microbial Ecology, 2018, 75(1):174-182. [8] Wu JT, Leung K, Leung GM.Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study[J]. Lancet, 2020, 395(10225):689-697. [9] Yin C.Genotyping coronavirus SARS-CoV-2: methods and implications[J]. Genomics, 2020, 112(5):3588-3596. [10] Khailany RA, Safdar M, Ozaslan M.Genomic characterization of a novel SARS-CoV-2[J]. Gene Reports, 2020, 19:100682. [11] Yue Y, Nabar NR, Shi C-S, et al.SARS-Coronavirus open reading frame-3a drives multimodal necrotic cell death[J]. Cell Death & Disease, 2018, 9(9):504. [12] Xie Q, Cao Y, Su J, et al.Genomic sequencing and analysis of the first imported Middle East Respiratory Syndrome Coronavirus (MERS CoV) in China[J]. Science China-Life Sciences, 2015, 58(8):818-820. [13] Lee JY, Bae S, Myoung J.Middle East respiratory syndrome coronavirus-encoded accessory proteins impair MDA5-and TBK1-mediated activation of NF-kappa B[J]. Journal of Microbiology and Biotechnology, 2019, 29(8):1316-1323. [14] Liu X, Chen Y, Tang W, et al.Single-cell transcriptome analysis of the novel coronavirus (SARS-CoV-2) associated gene ACE2 expression in normal and non-obstructive azoospermia (NOA) human male testes[J]. Science China Life Sciences, 2020, 63:1006-1015. [15] Chu DKW, Hui KPY, Perera RAPM, et al.MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity[J]. Virus Evolution, 2019, 5: S16. [16] Cotten M, Watson SJ, Zumla AI, et al.Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus[J]. Mbio, 2014, 5(1): e01062-13. [17] Kandeel M, Ibrahim A, Fayez M, et al.From SARS and MERS CoVs to SARS-CoV-2: moving toward more biased codon usage in viral structural and nonstructural genes[J]. Journal of Medical Virology, 2020, 92(6):660-666. [18] Alnazawi M, Altaher A, Kandeel M.Comparative genomic analysis MERS CoV isolated from humans and camels with special reference to virus encoded helicase[J]. Biological & Pharmaceutical Bulletin, 2017, 40(8):1289-1298. [19] Tian X, Li C, Huang A, et al: Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody[J]. Emerging Microbes & Infections, 2020, 9(1):382-385. [20] Ou X, Liu Y, Lei X, et al.Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV[J]. Nature Communications, 2020, 11(1). DOI: 10.1038/s41467-020-15562-9. [21] Chan KA, Bernal AB, Vickers MH, et al.Early life exposure to undernutrition induces ER stress, apoptosis, and reduced vascularization in ovaries of adult rat offspring[J]. Biology of Reproduction ,2015, 92(4):1-14. [22] Xu H, Zhong L, Deng J, et al.High expression of ACE2 receptor of 2019-nCoV on the epithelial cells of oral mucosa[J]. International Journal of Oral Science, 2020, 12(1):77-81. [23] Benvenuto D, Giovanetti M, Ciccozzi A, et al.The 2019-new coronavirus epidemic: Evidence for virus evolution[J]. Journal of Medical Virology, 2020, 92(4):455-459. [24] Nguyen TM, Zhang Y, Pandolfi PP.Virus against virus: a potential treatment for 2019-nCov (SARS-CoV-2) and other RNA viruses[J]. Cell Research, 2020, 30(3):189-190. [25] Paraskevis D, Kostaki EG, Magiorkinis G, et al.Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event[J]. Infection Genetics and Evolution, 2020, 79:104212. [26] Yang CW, Chen MF.Composition of human-specific slow codons and slow di-codons in SARS-CoV and 2019-nCoV are lower than other coronaviruses suggesting a faster protein synthesis rate of SARS-CoV and 2019-nCoV[J]. Journal of Microbiology, Immunology, and Infection, 2020, 53(3):419-420. [27] Cao YH, Liu XL, Xiong LJ, et al.Imaging and clinical features of patients with 2019 novel coronavirus SARS-CoV-2: a systematic review and meta-analysis[J]. Journal of Medical Virology, 2020, 92(3). DOI: 10.1002/jmv.25822.
