1
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Li W, Xu Z, Niu T, Xie Y, Zhao Z, Li D, He Q, Sun W, Shi K, Guo W, Chang Z, Liu K, Fan Z, Qi J, Gao GF. Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins. EMBO J 2024; 43:1484-1498. [PMID: 38467833 PMCID: PMC11021471 DOI: 10.1038/s44318-024-00062-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Abstract
Since SARS-CoV-2 Omicron variant emerged, it is constantly evolving into multiple sub-variants, including BF.7, BQ.1, BQ.1.1, XBB, XBB.1.5 and the recently emerged BA.2.86 and JN.1. Receptor binding and immune evasion are recognized as two major drivers for evolution of the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein. However, the underlying mechanism of interplay between two factors remains incompletely understood. Herein, we determined the structures of human ACE2 complexed with BF.7, BQ.1, BQ.1.1, XBB and XBB.1.5 RBDs. Based on the ACE2/RBD structures of these sub-variants and a comparison with the known complex structures, we found that R346T substitution in the RBD enhanced ACE2 binding upon an interaction with the residue R493, but not Q493, via a mechanism involving long-range conformation changes. Furthermore, we found that R493Q and F486V exert a balanced impact, through which immune evasion capability was somewhat compromised to achieve an optimal receptor binding. We propose a "two-steps-forward and one-step-backward" model to describe such a compromise between receptor binding affinity and immune evasion during RBD evolution of Omicron sub-variants.
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Affiliation(s)
- Weiwei Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Tianhui Niu
- Air Force Medical University, Air Force Medical center, PLA, Beijing, China
| | - Yufeng Xie
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Zhennan Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Dedong Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Qingwen He
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wenqiao Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Kaiyuan Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wenjing Guo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Chang
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Zheng Fan
- Institutional Core Facility, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
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2
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Shi K, Li L, Luo C, Xu Z, Huang B, Ma S, Liu K, Yu G, Gao GF. Structural basis of increased binding affinities of spikes from SARS-CoV-2 Omicron variants to rabbit and hare ACE2s reveals the expanding host tendency. mBio 2024; 15:e0298823. [PMID: 38112468 PMCID: PMC10870819 DOI: 10.1128/mbio.02988-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
The potential host range of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been expanding alongside its evolution during the pandemic, with rabbits and hares being considered important potential hosts, supported by a report of rabbit sero-prevalence in nature. We measured the binding affinities of rabbit and hare angiotensin-converting enzyme 2 (ACE2) with receptor-binding domains (RBDs) from SARS-CoV, SARS-CoV-2, and its variants and found that rabbit and hare ACE2s had broad variant tropism, with significantly enhanced affinities to Omicron BA.4/5 and its subsequent-emerged sub-variants (>10 fold). The structures of rabbit ACE2 complexed with either SARS-CoV-2 prototype (PT) or Omicron BA.4/5 spike (S) proteins were determined, thereby unveiling the importance of rabbit ACE2 Q34 in RBD-interaction and elucidating the molecular basis of the enhanced binding with Omicron BA.4/5 RBD. These results address the highly enhanced risk of rabbits infecting SARS-CoV-2 Omicron sub-variants and the importance of constant surveillance.IMPORTANCEThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has swept the globe and caused immense health and economic damage. SARS-CoV-2 has demonstrated a broad host range, indicating a high risk of interspecies transmission and adaptive mutation. Therefore, constant monitoring for potential hosts is of immense importance. In this study, we found that Omicron BA.4/5 and subsequent-emerged sub-variants exhibited enhanced binding to both rabbit and hare angiotensin-converting enzyme 2 (ACE2), and we elucidated the structural mechanism of their recognition. From the structure, we found that Q34, a unique residue of rabbit ACE2 compared to other ACE2 orthologs, plays an important role in ACE2 recognition. These results address the probability of rabbits/hares being potential hosts of SARS-CoV-2 and broaden our knowledge regarding the molecular mechanism of SARS-CoV-2 interspecies transmission.
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Affiliation(s)
- Kaiyuan Shi
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chunliang Luo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Baihan Huang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Sufang Ma
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guanghui Yu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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3
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Liu W, Huang Z, Xiao J, Wu Y, Xia N, Yuan Q. Evolution of the SARS-CoV-2 Omicron Variants: Genetic Impact on Viral Fitness. Viruses 2024; 16:184. [PMID: 38399960 PMCID: PMC10893260 DOI: 10.3390/v16020184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Over the last three years, the pandemic of COVID-19 has had a significant impact on people's lives and the global economy. The incessant emergence of variant strains has compounded the challenges associated with the management of COVID-19. As the predominant variant from late 2021 to the present, Omicron and its sublineages, through continuous evolution, have demonstrated iterative viral fitness. The comprehensive elucidation of the biological implications that catalyzed this evolution remains incomplete. In accordance with extant research evidence, we provide a comprehensive review of subvariants of Omicron, delineating alterations in immune evasion, cellular infectivity, and the cross-species transmission potential. This review seeks to clarify the underpinnings of biology within the evolution of SARS-CoV-2, thereby providing a foundation for strategic considerations in the post-pandemic era of COVID-19.
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Affiliation(s)
- Wenhao Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Zehong Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Jin Xiao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Yangtao Wu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Quan Yuan
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
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4
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Wang Q, Noettger S, Xie Q, Pastorio C, Seidel A, Müller JA, Jung C, Jacob T, Sparrer KMJ, Zech F, Kirchhoff F. Determinants of species-specific utilization of ACE2 by human and animal coronaviruses. Commun Biol 2023; 6:1051. [PMID: 37848611 PMCID: PMC10582019 DOI: 10.1038/s42003-023-05436-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023] Open
Abstract
Utilization of human ACE2 allowed several bat coronaviruses (CoVs), including the causative agent of COVID-19, to infect humans directly or via intermediate hosts. However, the determinants of species-specific differences in ACE2 usage and the frequency of the ability of animal CoVs to use human ACE2 are poorly understood. Here we applied VSV pseudoviruses to analyze the ability of Spike proteins from 26 human or animal CoVs to use ACE2 receptors across nine reservoir, potential intermediate and human hosts. We show that SARS-CoV-2 Omicron variants evolved towards more efficient ACE2 usage but mutation of R493Q in BA.4/5 and XBB Spike proteins disrupts utilization of ACE2 from Greater horseshoe bats. Variations in ACE2 residues 31, 41 and 354 govern species-specific differences in usage by coronaviral Spike proteins. Mutation of T403R allows the RaTG13 bat CoV Spike to efficiently use all ACE2 orthologs for viral entry. Sera from COVID-19 vaccinated individuals neutralize the Spike proteins of various bat Sarbecoviruses. Our results define determinants of ACE2 receptor usage of diverse CoVs and suggest that COVID-19 vaccination may protect against future zoonoses of bat coronaviruses.
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Affiliation(s)
- Qingxing Wang
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Sabrina Noettger
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Qinya Xie
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Chiara Pastorio
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Alina Seidel
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
- Institute of Virology, Philipps University Marburg, 35043, Marburg, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081, Ulm, Germany
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081, Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021, Karlsruhe, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, 89081, Ulm, Germany
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081, Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021, Karlsruhe, Germany
| | | | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
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5
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Han P, Meng Y, Zhang D, Xu Z, Li Z, Pan X, Zhao Z, Li L, Tang L, Qi J, Liu K, Gao GF. Structural basis of white-tailed deer, Odocoileus virginianus, ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity. J Virol 2023; 97:e0050523. [PMID: 37676003 PMCID: PMC10537675 DOI: 10.1128/jvi.00505-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/01/2023] [Indexed: 09/08/2023] Open
Abstract
SARS-CoV-2 has been expanding its host range, among which the white-tailed deer (WTD), Odocoileus virginianus, became the first wildlife species infected on a large scale and might serve as a host reservoir for variants of concern (VOCs) in case no longer circulating in humans. In this study, we comprehensively assessed the binding of the WTD angiotensin-converting enzyme 2 (ACE2) receptor to the spike (S) receptor-binding domains (RBDs) from the SARS-CoV-2 prototype (PT) strain and multiple variants. We found that WTD ACE2 could be broadly recognized by all of the tested RBDs. We further determined the complex structures of WTD ACE2 with PT, Omicron BA.1, and BA.4/5 S trimer. Detailed structural comparison revealed the important roles of RBD residues on 486, 498, and 501 sites for WTD ACE2 binding. This study deepens our understanding of the interspecies transmission mechanisms of SARS-CoV-2 and further addresses the importance of constant monitoring on SARS-CoV-2 infections in wild animals. IMPORTANCE Even if we manage to eliminate the virus among humans, it will still circulate among wildlife and continuously be transmitted back to humans. A recent study indicated that WTD may serve as reservoir for nearly extinct SARS-CoV-2 strains. Therefore, it is critical to evaluate the binding abilities of SARS-CoV-2 variants to the WTD ACE2 receptor and elucidate the molecular mechanisms of binding of the RBDs to assess the risk of spillback events.
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Affiliation(s)
- Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) , Beijing, China
| | - Yumin Meng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) , Beijing, China
- University of Chinese Academy of Sciences , Beijing, China
| | - Di Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) , Beijing, China
- Faculty of Health Sciences, University of Macau , Macau SAR, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) , Beijing, China
- Faculty of Health Sciences, University of Macau , Macau SAR, China
| | - Zhiyuan Li
- College of Veterinary Medicine, China Agricultural University , Beijing, China
| | - Xiaoqian Pan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) , Beijing, China
- University of Chinese Academy of Sciences , Beijing, China
| | - Zhennan Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) , Beijing, China
| | - Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) , Beijing, China
| | - Lingfeng Tang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) , Beijing, China
- Faculty of Health Sciences, University of Macau , Macau SAR, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) , Beijing, China
- University of Chinese Academy of Sciences , Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) , Beijing, China
- Beijing Life Science Academy , Beijing, China
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) , Beijing, China
- University of Chinese Academy of Sciences , Beijing, China
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6
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Si Y, Wu W, Xue X, Sun X, Qin Y, Li Y, Qiu C, Li Y, Zhuo Z, Mi Y, Zheng P. The evolution of SARS-CoV-2 and the COVID-19 pandemic. PeerJ 2023; 11:e15990. [PMID: 37701824 PMCID: PMC10493083 DOI: 10.7717/peerj.15990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/08/2023] [Indexed: 09/14/2023] Open
Abstract
Scientists have made great efforts to understand the evolution of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) to provide crucial information to public health experts on strategies to control this viral pathogen. The pandemic of the coronavirus disease that began in 2019, COVID-19, lasted nearly three years, and nearly all countries have set different epidemic prevention policies for this virus. The continuous evolution of SARS-CoV-2 alters its pathogenicity and infectivity in human hosts, thus the policy and treatments have been continually adjusted. Based on our previous study on the dynamics of binding ability prediction between the COVID-19 spike protein and human ACE2, the present study mined over 10 million sequences and epidemiological data of SARS-CoV-2 during 2020-2022 to understand the evolutionary path of SARS-CoV-2. We analyzed and predicted the mutation rates of the whole genome and main proteins of SARS-CoV-2 from different populations to understand the adaptive relationship between humans and COVID-19. Our study identified a correlation of the mutation rates from each protein of SARS-CoV-2 and various human populations. Overall, this analysis provides a scientific basis for developing data-driven strategies to confront human pathogens.
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Affiliation(s)
- Yuanfang Si
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Weidong Wu
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xia Xue
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiangdong Sun
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Yaping Qin
- School of Basic Medical Sciences, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ya Li
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Chunjing Qiu
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Yingying Li
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Ziran Zhuo
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Mi
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Pengyuan Zheng
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
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7
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Zhao Z, Xie Y, Bai B, Luo C, Zhou J, Li W, Meng Y, Li L, Li D, Li X, Li X, Wang X, Sun J, Xu Z, Sun Y, Zhang W, Fan Z, Zhao X, Wu L, Ma J, Li OY, Shang G, Chai Y, Liu K, Wang P, Gao GF, Qi J. Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants. Nat Commun 2023; 14:4405. [PMID: 37479708 PMCID: PMC10362042 DOI: 10.1038/s41467-023-39942-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/29/2023] [Indexed: 07/23/2023] Open
Abstract
Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly increasing in some countries. Exploring their receptor binding and interspecies transmission risk is urgently needed. Herein, we examine the binding capacities of human and other 28 animal ACE2 orthologs covering nine orders towards S proteins of these sub-variants. The binding affinities between hACE2 and these sub-variants remain in the range as that of previous variants of concerns (VOCs) or interests (VOIs). Notably, R493Q reverse mutation enhances the bindings towards ACE2s from humans and many animals closely related to human life, suggesting an increased risk of cross-species transmission. Structures of S/hACE2 or RBD/hACE2 complexes for these sub-variants and BA.2 S binding to ACE2 of mouse, rat or golden hamster are determined to reveal the molecular basis for receptor binding and broader interspecies recognition.
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Affiliation(s)
- Zhennan Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yufeng Xie
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Bin Bai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunliang Luo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Jingya Zhou
- University of Chinese Academy of Sciences, Beijing, China
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Weiwei Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yumin Meng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dedong Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaomei Li
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Xiaoxiong Li
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Xiaoyun Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Junqing Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Yeping Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zheng Fan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Linhuan Wu
- Chinese National Microbiology Data Center (NMDC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Juncai Ma
- Chinese National Microbiology Data Center (NMDC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Odel Y Li
- NHC Key Laboratory of Parasite and Vector Biology, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Guijun Shang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Peiyi Wang
- Cryo-EM Center, Department of Biology, Southern University of Science and Technology, Shenzhen, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
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Hu Y, Liu K, Han P, Xu Z, Zheng A, Pan X, Jia Y, Su C, Tang L, Wu L, Bai B, Zhao X, Tian D, Chen Z, Qi J, Wang Q, Gao GF. Host range and structural analysis of bat-origin RshSTT182/200 coronavirus binding to human ACE2 and its animal orthologs. EMBO J 2023; 42:e111737. [PMID: 36519268 PMCID: PMC9877840 DOI: 10.15252/embj.2022111737] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/07/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
Bat-origin RshSTT182 and RshSTT200 coronaviruses (CoV) from Rhinolophus shameli in Southeast Asia (Cambodia) share 92.6% whole-genome identity with SARS-CoV-2 and show identical receptor-binding domains (RBDs). In this study, we determined the structure of the RshSTT182/200 receptor binding domain (RBD) in complex with human angiotensin-converting enzyme 2 (hACE2) and identified the key residues that influence receptor binding. The binding of the RshSTT182/200 RBD to ACE2 orthologs from 39 animal species, including 18 bat species, was used to evaluate its host range. The RshSTT182/200 RBD broadly recognized 21 of 39 ACE2 orthologs, although its binding affinities for the orthologs were weaker than those of the RBD of SARS-CoV-2. Furthermore, RshSTT182 pseudovirus could utilize human, fox, and Rhinolophus affinis ACE2 receptors for cell entry. Moreover, we found that SARS-CoV-2 induces cross-neutralizing antibodies against RshSTT182 pseudovirus. Taken together, these findings indicate that RshSTT182/200 can potentially infect susceptible animals, but requires further evolution to obtain strong interspecies transmission abilities like SARS-CoV-2.
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Affiliation(s)
- Yu Hu
- School of Life Sciences, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Zepeng Xu
- Faculty of Health SciencesUniversity of MacauMacau SARChina
| | - Anqi Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoqian Pan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yunfei Jia
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
| | - Chao Su
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- Department of Biomedical SciencesCity University of Hong KongHong Kong SARChina
| | - Lingfeng Tang
- Faculty of Health SciencesUniversity of MacauMacau SARChina
| | - Lili Wu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Bin Bai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Di Tian
- Center of Infectious Disease, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Zhihai Chen
- Center of Infectious Disease, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - George F Gao
- School of Life Sciences, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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