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

In the GD-Ins29 sequence, the 29-nt segment is located in-frame after the second nucleotide of Codon 35 in BGI-PUP5 (position 27,863) and the first nucleotide of Codon 7 of BGI-PUP6. The resulted hypothetical protein is predicted to have 122 amino acids. Without affecting the coding frame, the 29-nt sequence theoretically could be spliced out in two different ways since there is uncertainty whether the uridine is at the beginning or at the end of the extra sequence, 5′- UCCUACUGGUUACCAACCUGAAUGGAAUA-3′ or 5′-CCUACUGGUUACCAACCUGAAUGGAAUAU-3′. No obvious sequence signatures were found within and around the sequence except several short stretches of simple repetitive sequences of 6 to 8 nucleotides in unit length. The actual mechanism, as to how such sequence was deleted, is yet to be revealed.