Reconstruction of the most recent common ancestor sequences of SARS-Cov S gene and detection of adaptive evolution in the spike protein

Chinese Science Bulletin

Volumn 49, Issue 12, 2004, Pages 1311-1313

  Zhang, Yuan ^a   Zheng, Nan ^b,c   Hao, Pei ^d,e   Zhong, Yang ^f  

^a INSTITUTE OF BOTANY   (China)

^b BEIJING NORMAL UNIVERSITY   (China)

^c NATIONAL INSTITUTE FOR VIRAL DISEASE CONTROL AND PREVENTION   (China)

^d Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^e SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^f FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

SARS CORONAVIRUS;

EID: 18444400345     PISSN: 10016538     EISSN: 18619541     Source Type: Journal    
DOI: 10.1360/04wc0153     Document Type: Article

References (25)

1. Peiris, J., Lai, S., Poon, L. et al., Coronavirus as a possible cause of severe acute respiratory syndrome, Lancet, 2003, 361(9366): 1319-1325.
2. Lu, Y., Chen, Y. H., Spike protein homology between the SARS-associated virus and murine hepatitis virus implies existence of a putative receptor-binding region, Chi. Sci. Bull., 2003, 48(11): 1115-1117.
3. Yu, X. J., Luo, C., Lin, J. C. et al., Putative hAPN receptor binding sites in SARS_CoV spike protein, Acta Pharmaco. Sin., 2003, 24(6): 481-488.
4. Ksiazek, T. G., Erdman, D., Goldsmith, C. S. et al., A novel coronavirus associated with severe acute respiratory syndrome, N. Engl. J. Med., 2003, 348(20): 1953-1966.
5. Drosten, C., Gunther, S., Preiser, W. et al., Identification of a novel coronavirus in patients with severe acute respiratory syndrome, N. Engl. J. Med., 2003, 348(20): 1967-1976.
6. Kuiken, T., Fouchier, R. A., Schutten, M. et al., Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome, Lancet, 2003, 362(9380): 263-270.
7. Rota, P. A., Oberste, M. S., Monroe, S. S. et al., Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science, 2003, 300(5624): 1394-1399.
8. Marra, M. A., Jones, S. J. M., Astell, C. R. et al., The genome sequence of the SARS-associated coronavirus, Science, 2003, 300(5624): 1399-1404.
9. Snijder, E. J., Bredenbeek, P. J., Dobbe, J. C. et al., Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage, J. Mol. Biol., 2003, 331(5): 991-1004.
10. Thiel, V., Ivanov, K. A., Putics, A. et al., Mechanisms and enzymes involved in SARS coronavirus genome expression, J. Gen. Virol., 2003, 84: 2305-2315.
11. Knipe, D. M., Howley, P. M., Fields Virology, Philadelphia, PA: Lippincott Williams & Wilkins Publishers, 2001.
12. Guan, Y., Zheng, B. J., He, Y. Q. et al., Isolation and characterization of viruses related to the SARS coronavirus from animals in Southern China, Science, 2003, 302(5643): 276-278.
13. Thompson, J. D., Higgins, D. G., Gibson, T. J., CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucle. Acid. Res., 1994, 22(22): 4673-4680.
14. Saitou, N., Nei, M., The neighbor-joining method: A new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 1987, 4(4): 406-425.
15. Kumar, S., Tamura, K., Jakobsen, I. B. et al., MEGA2: molecular evolutionary genetics analysis software, Bioinformatics, 2001, 17(12): 1244-1245.
16. Kimura, M., The Neutral Theory of Molecular Evolution, Cambridge (UK): Cambridge University Press, 1983.
17. The Chinese SARS Molecular Epidemiology Consortium, Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China, Science, 2004, 303(5664): 1666-1669.
18. Li, W., Moore, M. J., Vasilieva, N. et al., Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus, Nature, 2003, 426(6965): 450-454.
19. Wong, S. K., Li, W., Moore, M. J. et al., A 193-amino acid fragment of the SARS coronavirus S protein efficiently binds angiotensin-converting enzyme 2, J. Biol. Chem., 2004, 279(5): 3197-3201.
20. Sui, J., Li, W., Murakami, A. et al., Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association, Proc. Natl. Acad. Sci. U S A, 2004, 101(8): 2536-2541.
21. Goldman, N., Yang, A., A codon-based model of nucleotide substitution for protein-coding DNA sequences, Mol. Biol. Evol., 1994, 11(5): 725-736.
22. Yang, Z., Kumar, S., Nei, M., A new method of inference of ancestral nucleotide and amino acid sequences, Genetics, 1995, 141(4): 1641-1650.
23. Yang, Z., PAML: A program package for phylogenetic analysis by maximum likelihood, Comput. Appl. Biosci., 1997, 13: 555-556.
24. McClellan, D. A., McCracken, K. G., Estimating the influence of selection on the variable amino acid sites of the cytochrome B protein functional domains, Mol. Biol. Evol., 2001, 18(6): 917-925.
25. Woolley, S., Johnson, J., Smith, M. J. et al., TreeSAAP: selection on amino acid properties using phylogenetic trees, Bioinformatics, 2003, 19(5): 671-672