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

137 sequence variations (142 if counted independently by each ORF) were defined by comparing the sequences of the BJ Group with other isolates, including 3 (GD01, ZJ01, and TW1) identified in China, and 10 others elsewhere (Figure 2 , Table 4 ). Out of the total, 42 were contributed by the BJ Group alone, amounting to nearly 30% of the grand total. These variations were confirmed among over a dozen high-quality sequence reads from re-sequencing of the RT-PCR products directly and clones from the corresponding amplicon-derived libraries. Although possible sequence variations acquired during the limited generations in the host body and viral culture as well as sequencing errors arisen from the RT-PCR and amplification/cloning could not be easily excluded, the likelihood that all BJ isolates mutate in a similar way is rather slim since the sequencing was done in a systematic way with overlapping segments and high quality. The quality of complete genome sequences from other contributors was assessed by manually checking the submitted sequence traces when publicly available. In the substitutions identified from the BJ group, 76% are categorized as non-synonymous, slightly higher than the average (70%, 100/142) calculated from all 17 isolates. As a benchmark, we have summarized a few commonly used parameters for viral evolution studies together with those of two other RNA viruses, the HIV-1 and influenza ( Table 5 ). The SARS-CoV in many ways is quite different from these two viruses, except that their genomes are all RNA in nature. In particular, the HIV lives with the host for a long time so the constant escape from the host immune system is of essence for its survival until it overwhelms the system (6). The influenza virus that has an 85-year recorded history of infecting humans causes recurrent annual epidemics until a novel virus rises to stir up major worldwide pandemics (7). Our results did not lead to any strong conclusions due to insufficient data points compared to both HIV and influenza but it is quite necessary to compare the SARS-CoV data with those of the two prevalent viruses from time to time. Aside from mutation rate calculations, a popular test for selection on a particular protein is the ratio of Ka/Ks (8) . Generally, most non-synonymous SNPs (single nucleotide polymorphisms) are believed to be deleterious and rapidly removed from the given population of viruses by selection, leaving Ka/Ks less than one. Conversely, Ka/Ks greater than one is a strong indicator of positive selection. Although we have seen a high ratio in the case of PUP2, the indication of such a number from an uncharacterized putative transcript remains to be elucidated. At the present time, limited by the amount of experimental data, the ratio of Ka/Ks in the SARS-CoV data is higher than that of most genes in HIV and influenza viruses, in which selection and adaptation are both playing significant roles in changing the rate of non-synonymous substitutions, especially for the structural proteins that are the targets of the host immune systems.