Virus strain of a mild COVID-19 patient in Hangzhou representing a new trend in SARS-CoV-2 evolution related to Furin cleavage site

Xi, Jin; Xu, Kangli; Jiang, Penglei; Lian, Jiangshan; Hao, Shaorui; Jia, Hongyu; Yao, Hangping; Zhang, Yimin; Zheng, Ruoheng; Chen, Dong; Yao, Jinmei; Hu, Jianhua; Gao, Jianguo; Shen, Jian; Wen, Liang; Ren, Yue; Yu, Guodong; Wang, Xiaoyan; Lu, Yingfeng; Yu, Xiaopeng; Yu, Liang; Xiang, Dairong; Zheng, Lin; Wu, Nanping; Lu, Xiangyun; Cheng, Linfang; Liu, Fumin; Wu, Haibo; Jin, Changzhong; Yang, Xiaofeng; Qian, Pengxu; Qiu, Yunqing; Sheng, Jifang; Liang, Tingbo; Li, Lanjuan; Yang, Yida

We found, in our 788 confirmed COVID-19 patients, the decreased rate of severe/critical type, increased liver/kidney damage and prolonged period of nuclear acid positivity during virus dissemination, when compared with Wuhan. To investigate the underlining mechanism, we isolated one strain of SARS- CoV-2 (ZJ01) in mild COVID-19 patient and found the existence of 35 specific gene mutation by gene alignment. Further phylogenetic analysis and RSCU heat map results suggested that ZJ01 may be a potential evolutionary branch of SARS-CoV-2. We classified 54 strains of viruses worldwide (C/T type) based on the base (C or T) at positions 8824 and 28247. ZJ01 were both T at these two sites, becoming the only TT type currently identified in the world. The prediction of Furin cleavage site (FCS) and the sequence alignment of virus family indicated that FCS may be an important site of coronavirus evolution. ZJ01 had mutations near FCS (F1-2), which caused changes in the structure and the electrostatic distribution of the S protein surface, further affecting the binding capacity of Furin. Single cell sequencing and ACE2-Furin co-expression results confirmed that Furin level was higher in the whole body, especially in glands, liver, kidney and colon while FCS may help SARS-CoV-2 infect these organs. The evolutionary pattern of SARS-CoV-2 towards FCS formation may result in its clinical symptom becoming closer to HKU-1 and OC43 (the source of FCS sequence-PRRA) caused influenza, further showing potential in differentiating into mild COVID-19 subtypes.