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

An extra sequence segment of 29-nt (GD-Ins29) in length was unambiguously identified within the overlapped region of BGI-PUP5 and BGI-PUP6. This sequence was confirmed with 60 high-quality sequencing reads from 35 clones of the site-specific amplicon-library constructed with RT-PCR products from this genomic region. Among them, 25 clones were sequenced from both ends. No other sequence variations were found in the sequences from this particular amplicon-library, even though minor variants are occasionally seen in other amplicon-libraries from different sequences due to minor variations from viral populations and, to a much less extent, RT-PCR generated aberrant products. We have also identified another SARS-CoV isolate that harbors the same sequence segment from a SARS patient in Guangdong Province. These results strongly suggest that we have found a novel yet minor genotype of SARS-CoV, but not encountered a sequence anomaly.