Complete Genome Sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04)

Bi, Shengli; Qin, E’de; Xu, Zuyuan; Li, Wei; Wang, Jing; Hu, Yongwu; Liu, Yong; Duan, Shumin; Hu, Jianfei; Han, Yujun; Xu, Jing; Li, Yan; Yi, Yao; Zhou, Yongdong; Lin, Wei; Wen, Jie; Xu, Hong; Li, Ruan; Zhang, Zizhang; Sun, Haiyan; Zhu, Jingui; Yu, Man; Fan, Baochang; Wu, Qingfa; Lin, Wei; Tang, Lin; Yang, Bao’an; Li, Guoqing; Peng, Wenming; Li, Wenjie; Jiang, Tao; Deng, Yajun; Liu, Bohua; Shi, Jianping; Deng, Yongqiang; Wei, Wei; Liu, Hong; Tong, Zongzhong; Zhang, Feng; Zhang, Yu; Wang, Cui’e; Li, Yuquan; Ye, Jia; Gan, Yonghua; Ji, Jia; Li, Xiaoyu; Tian, Xiangjun; Lu, Fushuang; Tan, Gang; Yang, Ruifu; Liu, Bin; Liu, Siqi; Li, Songgang; Wang, Jun; Wang, Jian; Cao, Wuchun; Yu, Jun; Dong, Xiaoping; Yang, Huanming

We summarized the non-synonymous substitutions according to their subregions defined by a combination of structural and/or functional properties in the corresponding ORFs (Table 6 ). Data were classified according to the computationally predictable changes of physiochemical features and/or the secondary structure they would make in the corresponding subregions. For example, the predicted alterations by the substitutions of the M protein would lead to an increased pI (isoelectric point) of the N-terminal exterior region, decreased or increased hydrophobicity in the TM (transmembrane) domains, and decreased hydrophilicity in the C-terminal interior region, respectively. These predictable changes should suggest that the virus might benefit from these substitutions with remarkable changes that may be advantageous for the virus to defend the host immune system or drift to a new status ready for coming back. No single base insertion or deletion has been found so far in all the sequences published to this date; it states clearly the fidelity of the viral replication machinery.