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Journal of Virology, September 2005, p. 11892-11900, Vol. 79, No. 18
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.18.11892-11900.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Molecular Evolution Analysis and Geographic Investigation of Severe Acute Respiratory Syndrome Coronavirus-Like Virus in Palm Civets at an Animal Market and on Farms{ddagger}

Biao Kan,1,2,{dagger} Ming Wang,3,{dagger} Huaiqi Jing,1,2,{dagger} Huifang Xu,3,{dagger} Xiugao Jiang,2 Meiying Yan,1,2 Weili Liang,1,2 Han Zheng,1,2 Kanglin Wan,1,2 Qiyong Liu,2 Buyun Cui,2 Yanmei Xu,1,2 Enmin Zhang,1,2 Hongxia Wang,1,2 Jingrong Ye,1,2 Guichang Li,2 Machao Li,2 Zhigang Cui,1,2 Xiaobao Qi,1,2 Kai Chen,1,2 Lin Du,3 Kai Gao,3 Yu-teng Zhao,3 Xiao-zhong Zou,3 Yue-Ju Feng,3 Yu-Fan Gao,3 Rong Hai,1,2 Dongzhen Yu,1,2 Yi Guan,4 and Jianguo Xu1,2*

State Key Laboratory for Infectious Disease Prevention and Control (China CDC),1 National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, P.O. Box 5, Changping, Beijing 102206, People's Republic of China,2 Guangzhou Center for Disease Control and Prevention, 23 Third Zhongshan Road, Guangzhou, Guangdong 510080, People's Republic of China,3 Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China4

Received 5 March 2005/ Accepted 11 June 2005

Massive numbers of palm civets were culled to remove sources for the reemergence of severe acute respiratory syndrome (SARS) in Guangdong Province, China, in January 2004, following SARS coronavirus detection in market animals. The virus was identified in all 91 palm civets and 15 raccoon dogs of animal market origin sampled prior to culling, but not in 1,107 palm civets later sampled at 25 farms, spread over 12 provinces, which were claimed to be the source of traded animals. Twenty-seven novel signature variation residues (SNVs) were identified on the spike gene and were analyzed for their phylogenetic relationships, based on 17 sequences obtained from animals in our study and from other published studies. Analysis indicated that the virus in palm civets at the live-animal market had evolved to infect humans. The evolutionary starting point was a prototype group consisting of three viral sequences of animal origin. Initially, seven SNV sites caused six amino acid changes, at positions 147, 228, 240, 479, 821, and 1080 of the spike protein, to generate low-pathogenicity viruses. One of these was linked to the first SARS patient in the 2003-2004 period. A further 14 SNVs caused 11 amino acid residue changes, at positions 360, 462, 472, 480, 487, 609, 613, 665, 743, 765, and 1163. The resulting high-pathogenicity groups were responsible for infections during the so-called early-phase epidemic of 2003. Finally, the remaining six SNVs caused four amino acid changes, at positions 227, 244, 344, and 778, which resulted in the group of viruses responsible for the global epidemic.

* Corresponding author. Mailing address: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, P.O. Box 5, Changping, Beijing 102206, People's Republic of China. Phone: 8610-61739579. Fax: 8610-61730233. E-mail: xujg{at}public.bta.net.cn.

{ddagger} Supplemental material for this article may be found at http://jvi.asm.org/.

{dagger} These authors contributed equally to this work.

Journal of Virology, September 2005, p. 11892-11900, Vol. 79, No. 18
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.18.11892-11900.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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