A Genome Sequence of Novel SARS-CoV Isolates: the Genotype, GD-Ins29, Leads to a Hypothesis of Viral Transmission in South China

Qin, E’de; He, Xionglei; Tian, Wei; Liu, Yong; Li, Wei; Wen, Jie; Wang, Jingqiang; Fan, Baochang; Wu, Qingfa; Chang, Guohui; Cao, Wuchun; Xu, Zuyuan; Yang, Ruifu; Wang, Jing; Yu, Man; Li, Yan; Xu, Jing; Si, Bingyin; Hu, Yongwu; Peng, Wenming; Tang, Lin; Jiang, Tao; Shi, Jianping; Ji, Jia; Zhang, Yu; Ye, Jia; Wang, Cui’e; Han, Yujun; Zhou, Jun; Deng, Yajun; Li, Xiaoyu; Hu, Jianfei; Wang, Caiping; Yan, Chunxia; Zhang, Qingrun; Bao, Jingyue; Li, Guoqing; Chen, Weijun; Fang, Lin; Li, Changfeng; Lei, Meng; Li, Dawei; Tong, Wei; Tian, Xiangjun; Wang, Jin; Zhang, Bo; Zhang, Haiqing; Zhang, Yilin; Zhao, Hui; Zhang, Xiaowei; Li, Shuangli; Cheng, Xiaojie; Zhang, Xiuqing; Liu, Bin; Zeng, Changqing; Li, Songgang; Tan, Xuehai; Liu, Siqi; Dong, Wei; Wang, Jun; Wong, Gane Ka-Shu; Yu, Jun; Wang, Jian; Zhu, Qingyu; Yang, Huanming

Severe Acute Respiratory Syndrome (SARS) has infected thousands of people and cost hundreds of deaths globally since it first emerged in Guangdong, China, in November 2002 (ref. 1; http://www.who.int/csr/sars/en/). Sixteen complete or partial genome sequences of SARS-CoV isolates have been available since March 14 this year (ref. 2., 3., 4., 5.; http://www.ncbi.nlm.nih.gov/; Table 1). In the process of surveying all available genomic sequences of the SARS-CoV, we have obtained the complete genomic sequence of an isolate, named Isolate GZ01 originally. The sequence contains an extra 29-nucleotide segment in the vicinity of the viral structural proteins, M (the membrane protein) and N (the nucleocapsid protein). We have renamed the isolate as GD-Ins29 to indicate the origin, length, and the type of mutation. We believe that this novel genotype represents one of the early variants of the SARS-CoV. The absence of the 29-nt fragment may help the virus to escape the likely interference from locally homologous RNA molecules of host origin and to become more prevalent in human hosts. This sequence also holds unusually high number of variations among all the sequenced SARS-CoV isolates, suggesting a more distant relationship from other sequences SARS-CoV genomes published thus far.