Molecular evolution analysis and geographic investigation of severe acute respiratory syndrome coronavirus-like virus in palm civets at an animal market and on farms.
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.
Kan
Biao
B
State Key Laboratory for Infectious Disease Prevention and Control (China CDC), Chinese Center for Disease Control and Prevention, P.O. Box 5, Changping, Beijing 102206, People's Republic of China.
Wang
Ming
M
Jing
Huaiqi
H
Xu
Huifang
H
Jiang
Xiugao
X
Yan
Meiying
M
Liang
Weili
W
Zheng
Han
H
Wan
Kanglin
K
Liu
Qiyong
Q
Cui
Buyun
B
Xu
Yanmei
Y
Zhang
Enmin
E
Wang
Hongxia
H
Ye
Jingrong
J
Li
Guichang
G
Li
Machao
M
Cui
Zhigang
Z
Qi
Xiaobao
X
Chen
Kai
K
Du
Lin
L
Gao
Kai
K
Zhao
Yu-Teng
YT
Zou
Xiao-Zhong
XZ
Feng
Yue-Ju
YJ
Gao
Yu-Fan
YF
Hai
Rong
R
Yu
Dongzhen
D
Guan
Yi
Y
Xu
Jianguo
J
D000595:Amino Acid Sequence; D000818:Animals; D000829:Animals, Domestic / Q000821:virology; D002681:China / Q000453:epidemiology; D004196:Disease Outbreaks; D004197:Disease Reservoirs; D019143:Evolution, Molecular; D014644:Genetic Variation; D006801:Humans; D008562:Membrane Glycoproteins / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D046031:Raccoon Dogs / Q000821:virology; D045473:Severe acute respiratory syndrome-related coronavirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D017386:Sequence Homology, Amino Acid; D045169:Severe Acute Respiratory Syndrome / Q000453:epidemiology / Q000635:transmission / Q000821:virology; D064370:Spike Glycoprotein, Coronavirus; D014759:Viral Envelope Proteins / Q000235:genetics; D045949:Viverridae / Q000821:virology*
D008562:Membrane Glycoproteins; D064370:Spike Glycoprotein, Coronavirus; D014759:Viral Envelope Proteins; C578557:spike glycoprotein, SARS-CoV