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

We report a complete genomic sequence of rare isolates (minor genotype) of the SARS-CoV from SARS patients in Guangdong, China, where the first few cases emerged. The most striking discovery from the isolate is an extra 29-nucleotide sequence located at the nucleotide positions between 27,863 and 27,864 (referred to the complete sequence of BJ01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream of the N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29, suggests a significant genetic event and differentiates it from the previously reported genotype, the dominant form among all sequenced SARS-CoV isolates. A 17-nt segment of this extra sequence is identical to a segment of the same size in two human mRNA sequences that may interfere with viral genome replication and transcription in the cytosol of the infected cells. It provides a new avenue for the exploration of the virus-host interaction in viral evolution, host pathogenesis, and vaccine development.