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Morais IJ, Polveiro RC, Souza GM, Bortolin DI, Sassaki FT, Lima ATM. The global population of SARS-CoV-2 is composed of six major subtypes. Sci Rep 2020; 10:18289. [PMID: 33106569 PMCID: PMC7588421 DOI: 10.1038/s41598-020-74050-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022] Open
Abstract
The World Health Organization characterized COVID-19 as a pandemic in March 2020, the second pandemic of the twenty-first century. Expanding virus populations, such as that of SARS-CoV-2, accumulate a number of narrowly shared polymorphisms, imposing a confounding effect on traditional clustering methods. In this context, approaches that reduce the complexity of the sequence space occupied by the SARS-CoV-2 population are necessary for robust clustering. Here, we propose subdividing the global SARS-CoV-2 population into six well-defined subtypes and 10 poorly represented genotypes named tentative subtypes by focusing on the widely shared polymorphisms in nonstructural (nsp3, nsp4, nsp6, nsp12, nsp13 and nsp14) cistrons and structural (spike and nucleocapsid) and accessory (ORF8) genes. The six subtypes and the additional genotypes showed amino acid replacements that might have phenotypic implications. Notably, three mutations (one of them in the Spike protein) were responsible for the geographical segregation of subtypes. We hypothesize that the virus subtypes detected in this study are records of the early stages of SARS-CoV-2 diversification that were randomly sampled to compose the virus populations around the world. The genetic structure determined for the SARS-CoV-2 population provides substantial guidelines for maximizing the effectiveness of trials for testing candidate vaccines or drugs.
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Affiliation(s)
- Ivair José Morais
- Departamento de Fitopatologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Richard Costa Polveiro
- Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Gabriel Medeiros Souza
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, MG, 38410-337, Brazil
| | - Daniel Inserra Bortolin
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, MG, 38410-337, Brazil
| | - Flávio Tetsuo Sassaki
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Monte Carmelo, MG, 38500-000, Brazil
| | - Alison Talis Martins Lima
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, MG, 38410-337, Brazil.
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Wang ZG, Zheng ZH, Shang L, Li LJ, Cong LM, Feng MG, Luo Y, Cheng SY, Zhang YJ, Ru MG, Wang ZX, Bao QY. Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV. FEBS Lett 2005; 579:4928-36. [PMID: 16112670 PMCID: PMC7118731 DOI: 10.1016/j.febslet.2005.07.075] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 07/15/2005] [Indexed: 01/19/2023]
Abstract
In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. One hundred and seventy-four of these sites existed in two or more SARS-CoV genome sequences. According to the sequence polymorphism, all SARS-CoVs can be divided into three groups: (I) group 1, animal-origin viruses (such as SARS-CoV SZ1, SZ3, SZ13 and SZ16); (II) group 2, all viruses with clinical origin during first epidemic; and (III) group 3, SARS-CoV GD03T0013. According to 10 special loci, group 2 again can be divided into genotypes C and T, which can be further divided into sub-genotypes C1-C4 and T1-T4. Positive Darwinian selections were identified between any pair of these three groups. Genotype C gives neutral selection. Genotype T, however, shows negative selection. By comparing the death rates of SARS patients in the different regions, it was found that the death rate caused by the viruses of the genotype C was lower than that of the genotype T. SARS-CoVs might originate from an unknown ancestor.
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Affiliation(s)
- Zhi-Gang Wang
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Zhi-Hua Zheng
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Lei Shang
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
| | - Lan-Juan Li
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Li-Ming Cong
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Ming-Guang Feng
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
| | - Yun Luo
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Su-Yun Cheng
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Yan-Jun Zhang
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Miao-Gui Ru
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Zan-Xin Wang
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Qi-Yu Bao
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
- Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China
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Zeng R, Yang RF, Shi MD, Jiang MR, Xie YH, Ruan HQ, Jiang XS, Shi L, Zhou H, Zhang L, Wu XD, Lin Y, Ji YY, Xiong L, Jin Y, Dai EH, Wang XY, Si BY, Wang J, Wang HX, Wang CE, Gan YH, Li YC, Cao JT, Zuo JP, Shan SF, Xie E, Chen SH, Jiang ZQ, Zhang X, Wang Y, Pei G, Sun B, Wu JR. Characterization of the 3a protein of SARS-associated coronavirus in infected vero E6 cells and SARS patients. J Mol Biol 2004; 341:271-9. [PMID: 15312778 PMCID: PMC7127270 DOI: 10.1016/j.jmb.2004.06.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 05/31/2004] [Accepted: 06/08/2004] [Indexed: 01/25/2023]
Abstract
Proteomics was used to identify a protein encoded by ORF 3a in a SARS-associated coronavirus (SARS-CoV). Immuno-blotting revealed that interchain disulfide bonds might be formed between this protein and the spike protein. ELISA indicated that sera from SARS patients have significant positive reactions with synthesized peptides derived from the 3a protein. These results are concordant with that of a spike protein-derived peptide. A tendency exists for co-mutation between the 3a protein and the spike protein of SARS-CoV isolates, suggesting that the function of the 3a protein correlates with the spike protein. Taken together, the 3a protein might be tightly correlated to the spike protein in the SARS-CoV functions. The 3a protein may serve as a new clinical marker or drug target for SARS treatment.
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Affiliation(s)
- Rong Zeng
- Research Center for Proteome Analysis, Key Lab of Proteomics, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
- Corresponding authors
| | - Rui-Fu Yang
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Mu-De Shi
- Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Man-Rong Jiang
- Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - You-Hua Xie
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Hong-Qiang Ruan
- Research Center for Proteome Analysis, Key Lab of Proteomics, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Xiao-Sheng Jiang
- Research Center for Proteome Analysis, Key Lab of Proteomics, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Lv Shi
- Research Center for Proteome Analysis, Key Lab of Proteomics, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Hu Zhou
- Research Center for Proteome Analysis, Key Lab of Proteomics, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Lei Zhang
- Research Center for Proteome Analysis, Key Lab of Proteomics, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Xiao-Dong Wu
- Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Ying Lin
- Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Yong-Yong Ji
- Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Lei Xiong
- Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Yan Jin
- Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Er-Hei Dai
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Xiao-Yi Wang
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Bin-Ying Si
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Jin Wang
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Hong-Xia Wang
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Cui-E Wang
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yong-Hua Gan
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yu-Chuan Li
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Ju-Tian Cao
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Jiang-Ping Zuo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Shanghai 201203, China
| | - Shi-Fang Shan
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - En Xie
- Shanghai Laboratorial Animal Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Jiu-Tin Town, Shanghai 201615, China
| | - Song-Hua Chen
- Cell Bank of Type Culture Collection Committee, Cell Resources Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Zhi-Qin Jiang
- Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Xi Zhang
- Shanghai Center for Disease Control and Prevention, 1360 Zhong-Shang Road, Shanghai 200336, China
| | - Yuan Wang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Gang Pei
- Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Bing Sun
- Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
- Corresponding author.
| | - Jia-Rui Wu
- Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
- Corresponding author.
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