Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site
ABSTRACTThe mutations in the SARS-CoV-2 virus genome during COVID-19 dissemination are unclear. In 788 COVID-19 patients from Zhejiang province, we observed decreased rate of severe/critical cases compared with patients in Wuhan. For mechanisms exploration, we isolated one strain of SARS-CoV-2 (ZJ01...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2020-01-01
|
| Series: | Emerging Microbes and Infections |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/22221751.2020.1781551 |
| _version_ | 1827320771191504896 |
|---|---|
| author | Xi Jin Kangli Xu Penglei Jiang Jiangshan Lian Shaorui Hao Hangping Yao Hongyu Jia Yimin Zhang Lin Zheng Nuoheng Zheng Dong Chen Jinmei Yao Jianhua Hu Jianguo Gao Liang Wen Jian Shen Yue Ren Guodong Yu Xiaoyan Wang Yingfeng Lu Xiaopeng Yu Liang Yu Dairong Xiang Nanping Wu Xiangyun Lu Linfang Cheng Fumin Liu Haibo Wu Changzhong Jin Xiaofeng Yang Pengxu Qian Yunqing Qiu Jifang Sheng Tingbo Liang Lanjuan Li Yida Yang |
| author_facet | Xi Jin Kangli Xu Penglei Jiang Jiangshan Lian Shaorui Hao Hangping Yao Hongyu Jia Yimin Zhang Lin Zheng Nuoheng Zheng Dong Chen Jinmei Yao Jianhua Hu Jianguo Gao Liang Wen Jian Shen Yue Ren Guodong Yu Xiaoyan Wang Yingfeng Lu Xiaopeng Yu Liang Yu Dairong Xiang Nanping Wu Xiangyun Lu Linfang Cheng Fumin Liu Haibo Wu Changzhong Jin Xiaofeng Yang Pengxu Qian Yunqing Qiu Jifang Sheng Tingbo Liang Lanjuan Li Yida Yang |
| author_sort | Xi Jin |
| collection | DOAJ |
| description | ABSTRACTThe mutations in the SARS-CoV-2 virus genome during COVID-19 dissemination are unclear. In 788 COVID-19 patients from Zhejiang province, we observed decreased rate of severe/critical cases compared with patients in Wuhan. For mechanisms exploration, we isolated one strain of SARS-CoV-2 (ZJ01) from a mild COVID-19 patient. Thirty-five specific gene mutations were identified. Phylogenetic and relative synonymous codon usage analysis suggested that ZJ01 may be a potential evolutionary branch of SARS-CoV-2. We classified 54 global virus strains based on the base (C or T) at positions 8824 and 28247 while ZJ01 has T at both sites. The prediction of the Furin cleavage site (FCS) and sequence alignment indicated that the FCS may be an important site of coronavirus evolution. ZJ01 mutations identified near the FCS (F1-2) caused changes in the structure and electrostatic distribution of the S surface protein, further affecting the binding capacity of Furin. Single-cell sequencing and ACE2-Furin co-expression results confirmed that the Furin expression was especially higher in glands, liver, kidneys, and colon. The evolutionary pattern of SARS-CoV-2 towards FCS formation may result in its clinical symptom becoming closer to HKU-1 and OC43 caused mild flu-like symptoms, further showing its potential in differentiating into mild COVID-19 subtypes. |
| first_indexed | 2024-03-07T17:24:02Z |
| format | Article |
| id | doaj.art-7126e1b96b604860b779a1b8962631ba |
| institution | Directory Open Access Journal |
| issn | 2222-1751 |
| language | English |
| last_indexed | 2024-04-25T00:51:43Z |
| publishDate | 2020-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Emerging Microbes and Infections |
| spelling | doaj.art-7126e1b96b604860b779a1b8962631ba2024-03-11T16:04:23ZengTaylor & Francis GroupEmerging Microbes and Infections2222-17512020-01-01911474148810.1080/22221751.2020.1781551Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage siteXi Jin0Kangli Xu1Penglei Jiang2Jiangshan Lian3Shaorui Hao4Hangping Yao5Hongyu Jia6Yimin Zhang7Lin Zheng8Nuoheng Zheng9Dong Chen10Jinmei Yao11Jianhua Hu12Jianguo Gao13Liang Wen14Jian Shen15Yue Ren16Guodong Yu17Xiaoyan Wang18Yingfeng Lu19Xiaopeng Yu20Liang Yu21Dairong Xiang22Nanping Wu23Xiangyun Lu24Linfang Cheng25Fumin Liu26Haibo Wu27Changzhong Jin28Xiaofeng Yang29Pengxu Qian30Yunqing Qiu31Jifang Sheng32Tingbo Liang33Lanjuan Li34Yida Yang35Department of Gastroenterology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaEmergency and Trauma Center, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaCenter of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Institute of Hematology, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaDepartment of Colorectal Surgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaLaboratory Department, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaDepartment of Gastroenterology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaDepartment of Neurosurgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaDepartment of Neurosurgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaDepartment of Gastroenterology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaDepartment of Neurosurgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaCenter of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Institute of Hematology, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaDepartment of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaABSTRACTThe mutations in the SARS-CoV-2 virus genome during COVID-19 dissemination are unclear. In 788 COVID-19 patients from Zhejiang province, we observed decreased rate of severe/critical cases compared with patients in Wuhan. For mechanisms exploration, we isolated one strain of SARS-CoV-2 (ZJ01) from a mild COVID-19 patient. Thirty-five specific gene mutations were identified. Phylogenetic and relative synonymous codon usage analysis suggested that ZJ01 may be a potential evolutionary branch of SARS-CoV-2. We classified 54 global virus strains based on the base (C or T) at positions 8824 and 28247 while ZJ01 has T at both sites. The prediction of the Furin cleavage site (FCS) and sequence alignment indicated that the FCS may be an important site of coronavirus evolution. ZJ01 mutations identified near the FCS (F1-2) caused changes in the structure and electrostatic distribution of the S surface protein, further affecting the binding capacity of Furin. Single-cell sequencing and ACE2-Furin co-expression results confirmed that the Furin expression was especially higher in glands, liver, kidneys, and colon. The evolutionary pattern of SARS-CoV-2 towards FCS formation may result in its clinical symptom becoming closer to HKU-1 and OC43 caused mild flu-like symptoms, further showing its potential in differentiating into mild COVID-19 subtypes.https://www.tandfonline.com/doi/10.1080/22221751.2020.1781551SARS-CoV-2COVID-19FurinACE2 |
| spellingShingle | Xi Jin Kangli Xu Penglei Jiang Jiangshan Lian Shaorui Hao Hangping Yao Hongyu Jia Yimin Zhang Lin Zheng Nuoheng Zheng Dong Chen Jinmei Yao Jianhua Hu Jianguo Gao Liang Wen Jian Shen Yue Ren Guodong Yu Xiaoyan Wang Yingfeng Lu Xiaopeng Yu Liang Yu Dairong Xiang Nanping Wu Xiangyun Lu Linfang Cheng Fumin Liu Haibo Wu Changzhong Jin Xiaofeng Yang Pengxu Qian Yunqing Qiu Jifang Sheng Tingbo Liang Lanjuan Li Yida Yang Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site Emerging Microbes and Infections SARS-CoV-2 COVID-19 Furin ACE2 |
| title | Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site |
| title_full | Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site |
| title_fullStr | Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site |
| title_full_unstemmed | Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site |
| title_short | Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site |
| title_sort | virus strain from a mild covid 19 patient in hangzhou represents a new trend in sars cov 2 evolution potentially related to furin cleavage site |
| topic | SARS-CoV-2 COVID-19 Furin ACE2 |
| url | https://www.tandfonline.com/doi/10.1080/22221751.2020.1781551 |
| work_keys_str_mv | AT xijin virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT kanglixu virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT pengleijiang virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT jiangshanlian virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT shaoruihao virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT hangpingyao virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT hongyujia virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT yiminzhang virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT linzheng virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT nuohengzheng virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT dongchen virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT jinmeiyao virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT jianhuahu virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT jianguogao virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT liangwen virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT jianshen virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT yueren virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT guodongyu virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT xiaoyanwang virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT yingfenglu virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT xiaopengyu virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT liangyu virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT dairongxiang virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT nanpingwu virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT xiangyunlu virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT linfangcheng virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT fuminliu virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT haibowu virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT changzhongjin virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT xiaofengyang virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT pengxuqian virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT yunqingqiu virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT jifangsheng virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT tingboliang virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT lanjuanli virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite AT yidayang virusstrainfromamildcovid19patientinhangzhourepresentsanewtrendinsarscov2evolutionpotentiallyrelatedtofurincleavagesite |