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Originally published in Science Express on 29 January 2004
Science 12 March 2004:
Vol. 303. no. 5664, pp. 1666 - 1669
DOI: 10.1126/science.1092002
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Reports

Molecular Evolution of the SARS Coronavirus During the Course of the SARS Epidemic in China

The Chinese SARS Molecular Epidemiology Consortium*

Sixty-one SARS coronavirus genomic sequences derived from the early, middle, and late phases of the severe acute respiratory syndrome (SARS) epidemic were analyzed together with two viral sequences from palm civets. Genotypes characteristic of each phase were discovered, and the earliest genotypes were similar to the animal SARS-like coronaviruses. Major deletions were observed in the Orf8 region of the genome, both at the start and the end of the epidemic. The neutral mutation rate of the viral genome was constant but the amino acid substitution rate of the coding sequences slowed during the course of the epidemic. The spike protein showed the strongest initial responses to positive selection pressures, followed by subsequent purifying selection and eventual stabilization.

1Guangdong Center for Disease Control and Prevention, 176 Xingangxi Road, Guangzhou 510300, Guangdong, China. 2Second Affiliated Hospital of Sun Yat-Sen University, 107 Yanjiang West Road, Guangzhou 510120, Guangdong, China. 3Institute of Zoology, Chinese Academy of Sciences, 19 Zhongguancun Road, Haidian, Beijing 100080, China. 4Guangzhou Center for Disease Control and Prevention, 23 Third Zhongshan Road, Guangzhou 510080, Guangdong, China. 5Guangzhou Institute of Respiratory Disease, 151 Yanjiang West Road, Guangzhou 510120, Guangdong, China. 6Department of Infectious Diseases and Molecular Immunology, Nanfang Hospital, First Medical University of PLA, Guangzhou 510515, Guangdong, China. 7Wuhan Institute of Virology, Chinese Academy of Sciences, 44 Xiaohongshan, Wuhan 430071, Hubei, China. 8State Key Laboratory for Medical Genomics/Pôc6;le Sino-Français de Recherche en Sciences du Vivant et Génomique, Ruijin Hospital Affiliated to Shanghai Second Medical University, 197 Rui Jin Road II, Shanghai 200025, China. 9Chinese National Human Genome Center at Shanghai, 250 Bi Bo Road, Zhang Jiang High Tech Park, Shanghai 201203, China. 10School of Pharmacy, Shanghai Jiaotong University, 1954 Huashan Road, Shanghai 200030, China. 11Bioinformation Center/Institute of Plant Physiology and Ecology/Health Science Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China. 12Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235, China. 13Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA. 14School of Life Sciences, Fudan University, Shanghai 200433, China. 15Department of Chemical Pathology, 16Department of Microbiology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region, China.


* Epidemiology group: Jian-Feng He,1{dagger} Guo-Wen Peng,1 Jun Min,2 De-Wen Yu,1 Wen-Jia Liang,1 Shu-Yi Zhang,3 Rui-Heng Xu1{ddagger} Virology group: Huan-Ying Zheng,1{dagger} Xin-Wei Wu,4{dagger} Jun Xu,5 Zhan-Hui Wang,6 Ling Fang,1 Xin Zhang,1 Hui Li,1 Xin-Ge Yan,1 Jia-Hai Lu,1 Zhi-Hong Hu,7 Ji-Cheng Huang,1 Zhuo-Yue Wan,1{ddagger} Jin-Lin Hou,6{ddagger} Jin-Yan Lin1{ddagger} Molecular biology group: Huai-Dong Song,8{dagger} Sheng-Yue Wang,9{dagger} Xiang-Jun Zhou,10{dagger} Guo-Wei Zhang,8 Bo-Wei Gu,8 Hua-Jun Zheng,9 Xiang-Lin Zhang,9 Mei He,10 Kui Zheng,1 BoFei Wang,9 Gang Fu,9 Xiao-Ning Wang,6 Sai-Juan Chen,8 Zhu Chen8,9{ddagger} Data analysis group: Pei Hao,11,12{dagger} Hua Tang,13{dagger} Shuang-Xi Ren,9{dagger} Yang Zhong,12,14{dagger} Zong-Ming Guo,12 Qi Liu,11 You-Gang Miao,11 Xiang-Yin Kong,11 Wei-Zhong He,12 Yi-Xue Li,11,12 Chung-I Wu,13{ddagger} Guo-Ping Zhao9,11{ddagger}§ Chinese University of Hong Kong group: Rossa W. K. Chiu,15{dagger} Stephen S. C. Chim,15 Yu-kwan Tong,15 Paul K. S. Chan,16 John S. Tam,16 Y. M. Dennis Lo15{ddagger}

{dagger}These authors contributed equally to this work.

{ddagger}Corresponding authors for each group. §Corresponding author for overall work. E-mail: gpzhao{at}sibs.ac.cn

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