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

it introduces another minor allele c at Locus 9,835. Even if we exclude either BJ01 or BJ03, the two isolates from a single patient, the haplotype still stands out; it has differentiated the group from all other isolates (T/c-C-T/g-C/t-A/g-C/t-A-T/c-C-T/c) identified so far. This BJ Group-specific haplotype represents the first population of SARS-CoV responsible for the acute outbreak in the metropolitan area of Beijing. T T T T T T T T T T T 9,835 T T T T The H-U Group (from Hong Kong to USA) has a different haplotype, T/c-C-T/g-T/c-G/a-C-A-T/c-C-T/c. The major allele T within the group at Locus 17,827 that is shared by CUHK-W1 and CUHK-Su10, together with the major allele G at Locus 19,045 shared by CUHK-W1 and Urbani (named after Dr. Carlo Urbani who was the first WHO officer to identify the outbreak of this new disease in an American businessman who had been admitted to a hospital in Hanoi), establishes the internal association within the H-U Group. The fact that the H-U Group overlaps with the BJ Group by Isolate CUHK-W1 (c-Cg-T-G-C-A-c-C-c) suggests a possible link or path of transmission between the BJ and H-U Groups. The H-U Group appears to be a mosaic genotype of the BJ and other groups. The result suggests the existence of an intermediate state in the transmission path connecting China to the outside. In addition to the haplotype, T-C-T-C-A-T-A-T-C-T, identical to the H-T Group (from Hong Kong to Toronto) as well as Isolates ZJ01 (Zhejiang) and TW1 (Taiwan), the SP Group (Singapore) possesses a monolocus marker T, as opposed to C for all others at Locus 19,065, thus establishing the internal phylogenetic relationship within the group and differentiating it from all others. GD01 shares an almost identical haplotype with the BJ Group at the defined loci, except for the minor allele c at Locus 9,835, which distances itself from the BJ Group but links it to all the other groups.