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

Virions were prepared from Vero-E6 cell culture. Aliquots of the RT-PCR products from the viral RNA were sequenced directly and the remaining was cloned into a plasmid vector (amplicon-library). Multiple clones from each amplicon-library were subsequently sequenced from both directions to confirm the results from those directly acquired from PCR products. High-quality sequences were assembled by using a sequence assembly package, Phred-Phrap-Consed (10). The consensus sequences from different amplicon-derived clones are accounted and minor variations among different clones are ignored for the consensus assembly. A total number of 75 amplicons and 2,718 sequencing reads were generated (1,538,993 bp of raw data), equivalent to approximately 52-fold coverage of the viral genome. A complete sequence of 29.757 Kb with an overall error rate of 0.0016% was obtained. The sequence of Isolate GD01 is available in GenBank (Accession No. AY278489).