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

The genome landscape of this isolate is not greatly different from others reported by our group and other laboratories. Twelve ORFs (open reading frames), including 6 CDSs (coding sequences) and 6 PUPs (postulated uncharacterized proteins) were predicted in the viral genome (Table 2; Figure 1). We annotated two new PUPs, BGI-PUP5 (so named to avoid possible ambiguity in nomenclature) and BGI-PUP6, located between the previously reported PUP4 and the N protein. These PUPs overlap in a 35-nt region (position 27,843 and 27,879, in reference to nucleotide position in the complete sequence of BJ01). Both PUPs share the same consensus leader sequence (5′-agUCUAAAAGAAC-3′) that is immediately followed by the predicted start codon of BGI-PUP5, and approximately 95-nt away from that of BGI-PUP6. The expression, actual existence of protein products, and possible function of the PUPs, such as that of BGI-PUP6, remain to be elucidated experimentally.