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

Instead, we have inspected these substitutions individually to the nucleotide positions in a context of a codon. It is not surprising to find that the threenucleotide positions within a codon have a similar frequency to be mutated when insufficient evolutionary processes are yet to be experienced by the newly emerged virus. Among all the 139 substitutions (including 2 counted in 2 ORFs), 45 are at the first nucleotide position, 47 are at the second one, and 47 are at the third one. It implies that the selective pressure has yet to work on these mutations that were most likely generated in the initial viral population due to replication errors of the viral machinery. Many interesting non-synonymous substitutions were found among the group. A common A/C transversion (Locus 26,031, C in both BJ01 and BJ03, A in all other isolates, including two of the BJ Group, BJ02 and *S and N-Sys stand for synonymous and non-synonymous substitutions, respectively. †A single substitution at the same position in a region overlapping with two ORFs was counted as 2. The total number is 137 when such a substitution event was counted only once so the total number of substitutions contributed by the BJ Group is reduced to 40. BJ04), leading to a Gln (CAA)-to-Pro (CCA) change, was noticed in the BJ Group specific variations. Since it resides in the PUP2 coding sequence, the functional significance of such a mutation is yet to be revealed experimentally in the future. A G/A transition (Locus 25,280, A in BJ03 and BJ02, G in all others) leading to Gly/Pro (from polar to non-polar) was also identified. These changes are not as drastic in terms of biochemical characteristics in the amino acid composition as the one found within the BJ01/BJ03 patient, indicating there might be possible selection on the latter cases. BJ04 has all the alleles at the loci mentioned above, the same as all the other isolates, assuring its relationship with isolates outside the BJ Group. GD01 shares the same alleles at three loci with either BJ01 or BJ02, which are different from all the others, suggesting that these mutations are early replication errors before the viral invasion into Beijing, providing a link between the BJ Group and the GD Group in Guangdong where the first major epidemics of SARS occurred. The sequence variation between BJ01 and BJ03 was expected to reflect the replication error rates, emerging from both replication cycles and in different tissues inside a single host. The sequence variation between BJ01/03 and BJ02 would reflect the replication errors between the first and the second round of the infection among the hosts, as well as the selective pressure from the host or possible advantages taken by the viruses. Somewhat to our surprises, we have noticed a "square-root rule" of the non-synonymous substitutions among the member isolates in the BJ Group ( Figure 3 ). There are approximately 15 to 16 non-synonymous substitutions in the first round of the transmission (15 between BJ01 and BJ03, 16 between BJ01 and BJ02, 16 between BJ01 and BJ04); it approximately equals to 4 2 or 2 4 . In the second round of the infection, there are 25 to 26 non-synonymous substitutions (25 between BJ02 and BJ04, 25 between BJ02 and BJ03, 25 between BJ03 and BJ04); it is close to 5 2 , or to 2 5 when both non-synonymous and synonymous substitutions are accounted. Such a "square-root rule" implies that the mutations occur freely without any constraints from patients to patients, perhap