A Genome Sequence of Novel SARS-CoV Isolates: the Genotype, GD-Ins29, Leads to a Hypothesis of Viral Transmission in South China

Qin, E’de; He, Xionglei; Tian, Wei; Liu, Yong; Li, Wei; Wen, Jie; Wang, Jingqiang; Fan, Baochang; Wu, Qingfa; Chang, Guohui; Cao, Wuchun; Xu, Zuyuan; Yang, Ruifu; Wang, Jing; Yu, Man; Li, Yan; Xu, Jing; Si, Bingyin; Hu, Yongwu; Peng, Wenming; Tang, Lin; Jiang, Tao; Shi, Jianping; Ji, Jia; Zhang, Yu; Ye, Jia; Wang, Cui’e; Han, Yujun; Zhou, Jun; Deng, Yajun; Li, Xiaoyu; Hu, Jianfei; Wang, Caiping; Yan, Chunxia; Zhang, Qingrun; Bao, Jingyue; Li, Guoqing; Chen, Weijun; Fang, Lin; Li, Changfeng; Lei, Meng; Li, Dawei; Tong, Wei; Tian, Xiangjun; Wang, Jin; Zhang, Bo; Zhang, Haiqing; Zhang, Yilin; Zhao, Hui; Zhang, Xiaowei; Li, Shuangli; Cheng, Xiaojie; Zhang, Xiuqing; Liu, Bin; Zeng, Changqing; Li, Songgang; Tan, Xuehai; Liu, Siqi; Dong, Wei; Wang, Jun; Wong, Gane Ka-Shu; Yu, Jun; Wang, Jian; Zhu, Qingyu; Yang, Huanming

The SARS-CoV has nearly identical genome organization, especially its gene order, with other members in Coronaviridae found in humans and other animals. The sequences of the SARS-CoV genome from various isolates are also almost identical with only a few dozen nucleotide substitutions per genome compared with each other. Therefore, we are strongly in favor of the hypothesis that the SARS-CoV may have originated from non-human animals, no matter it is virulent or latent to its host, in unknown reservoirs of the wild and recently moved onto humans through a less frequently established contacting route. It is of great importance that such non-human hosts should be promptly identified in order to prevent further evasion into human and other animal populations. The discovery of the GD-Ins29 genotype is very useful in differentiating the origin of SARS-CoV. The fact that we have only identified a couple of isolates in Guangdong Province supports the scenario that GD-Ins29 is the original form transmitted from non-human host to human ones and later turned into a new genotype after deletion of a DNA segment that may hinders its efficiency of propagation. Therefore, we predict two likely outcomes when surveying the animal reservoirs. First, the non-human reservoir of SARS-CoV may harbor genome sequences close to GD-Ins29, not the deleted form or the major genotype found most widespread among its human hosts. Second, both variants of the major and the minor genotypes could be found in the same animal reservoir owing to multiple transmissions of the virus back and forth between its human and non-human hosts.