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

The sequences of the four complete genomes have a size range of 29,725-29,745 nucleotides (nt). The difference is primarily due to the extension of the 5 -end sequence, which has no significant changes in the overall genome structure and gene size. In the genomes of these isolates, the predicted number of ORFs (open reading frames) remains as 13, in contrast to the genome of Isolate GD01, where a 29-nt insertion was discovered. Sequence evidence from another SARS-CoV isolate collected in Guangdong has confirmed this significant finding (BGI unpublished data). Referring to the BJ01 genome annotation, we have previously reported that, in the GD01 genome, two additional BGI-PUPs (BGI-Postulated Uncharacterized Proteins), BGI-PUP5 (nt positions 27,763-27,882) and BGI-PUP6 (nt positions 27,848-28,102), were predicted in the largest (478 nt) intergenic region between the ORFs for BGI-PUP4 and the N protein (nucleoprotein); PUP5 was previously so named in BJ01 and now renamed as BGI-PUP7. Putative leader sequences were determined in these genomes, based on alignments of the leader sequence at the 5 -end of the genome (5 -UCUCUAAACGAACUUUAAAAUCUG) to the sequences upstream of each ORF. The organization and general features of viral proteins, including the R (replicase) protein and the structural proteins (the spike or S, envelope or E, membrane or M, and N proteins), among all the isolates are nearly identical except the 29-nt insertion in the GD isolates and the limited number of nucleotide substitutions.