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Maloney SM, Shaw TM, Nennig KM, Larsen MS, Shah A, Kumar A, Marcotrigiano J, Grove J, Snijder EJ, Kirchdoerfer RN, Bailey AL. CD81 is a receptor for equine arteritis virus (family: Arteriviridae). mBio 2025:e0062325. [PMID: 40422661 DOI: 10.1128/mbio.00623-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Accepted: 05/07/2025] [Indexed: 05/28/2025] Open
Abstract
Arteriviruses are a family of single-stranded, positive-sense RNA (+ssRNA) viruses that infect diverse animal hosts. Many arteriviruses are macrophage-tropic, consistent with their utilization of the macrophage-specific molecule CD163 as a receptor. However, the horse arterivirus (equine arteritis virus, EAV), which infects additional cell types beyond macrophages, does not utilize CD163 in its entry mechanism. Here, we use a genome-wide CRISPR knockout screen to identify alternative receptors that could explain this discrepancy in arterivirus receptor utilization and tropism, identifying the plasma membrane tetraspanin CD81 as a required host factor for EAV infection. Genetic knockout of CD81 or pre-incubation with soluble CD81 protected cells from infection with EAV, but had no impact on susceptibility to other arteriviruses. Bypassing the entry step of the viral life cycle by transfecting the EAV genome into CD81-knockout cells produced infectious EAV, implicating CD81 in the EAV entry process. Screening of CD81 orthologs from natural arterivirus hosts identified the brushtail possum CD81 as unsupportive of EAV entry, indicating that CD81 incompatibility can serve as a barrier to cross-species infection. Horse/possum CD81 chimeras were then used to map the structural domains of CD81 engaged by EAV, identifying alpha helix "D" on the large extracellular loop of CD81 as critical for EAV entry. This study identifies the first example of receptor switching in the Arteriviridae family and, given the broad tissue distribution of CD81 expression, suggests that the adoption of CD81 enabled an expansion of EAV tropism.IMPORTANCEArteriviruses are a family of diverse positive-sense RNA viruses that can infect a wide range of animal hosts, but many details regarding how arteriviruses gain entry into cells remain unclear. Most arteriviruses are thought to utilize the macrophage-specific molecule CD163 as a receptor; however, the horse arterivirus (equine arteritis virus, EAV) infects additional cell types beyond macrophages and does not utilize CD163. In this study, we identified the host factor CD81 as a significant player in EAV entry. Beyond the implications that this discovery holds for equine health, this study adds to the increasingly complex picture of arterivirus entry and demonstrates that these viruses are capable of adopting new host molecules as receptors, with consequences for the types of cells these viruses infect, the disease they cause, and their mode(s) of transmission.
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Affiliation(s)
- Sara M Maloney
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
- University of Wisconsin-Madison Cellular and Molecular Pathology Graduate Program, Madison, Wisconsin, USA
| | - Teressa M Shaw
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Kylie M Nennig
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Malorie S Larsen
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Aadit Shah
- Stanford University School of Medicine, Stanford, California, USA
| | - Ashish Kumar
- Structural Virology Section, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph Marcotrigiano
- Structural Virology Section, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Joe Grove
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Eric J Snijder
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, South Holland, The Netherlands
| | - Robert N Kirchdoerfer
- Department of Biochemistry, Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Adam L Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
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2
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Zhu H, Liu X, He J, Lei J, Zhao J. High-affinity, broad-spectrum, "centipede-like" multi-branched drug conjugates, anchored to the S protein, for blocking coronavirus infection. Eur J Med Chem 2025; 289:117450. [PMID: 40022880 DOI: 10.1016/j.ejmech.2025.117450] [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: 11/04/2024] [Revised: 02/17/2025] [Accepted: 02/24/2025] [Indexed: 03/04/2025]
Abstract
Over the past two decades, various coronaviruses have posed a severe threat to human life and health, with the spike protein (S protein) being a critical protein for infecting host cells. Glycyrrhizic acid (GA), as a natural drug, can inhibit the infection of coronaviruses by binding to the receptor-binding domain (RBD) of the S protein. However, issues like poor water solubility and weak binding affinity with the S protein have hindered its further application. Therefore, drawing inspiration from the biological structure of centipedes, a ROS-responsive multi-branched drug conjugate (ODPAG) was constructed through a "polymer-drug linkage" strategy using dextran as the backbone and GA as the active "claw". ODPAG exhibited drug loading of 22.0 ± 0.2% (OD40kPAG) and 19.7 ± 0.1% (OD450kPAG), showing ROS responsiveness with a half-life 6.4 times that of GA (OD40kPAG) and 5.4 times longer (OD450kPAG). In in vitro antiviral experiments, ODPAG exhibited an enhanced binding affinity to the S protein, with IC50 values of 1.33 μM (OD40kPAG) and 0.89 μM (OD450kPAG) against SARS-CoV-2 pseudovirus, demonstrating exceptional antiviral efficacy. These results collectively indicate that ODPAG can block coronavirus infection by binding to the S protein, exhibiting significant potential in addressing the current challenges posed by the novel coronavirus. Additionally, the "polymer-drug conjugate" strategy employed in this process is efficient, cost-effective, and offers new insights for combating future emergent coronaviruses.
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Affiliation(s)
- Huatai Zhu
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, 100083, China; MOE Engineering Research Center of Forestry Biomass Materials and Bioenergy, Beijing Forestry University, Beijing, 100083, China
| | - Xuan Liu
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, 100083, China; MOE Engineering Research Center of Forestry Biomass Materials and Bioenergy, Beijing Forestry University, Beijing, 100083, China
| | - Jing He
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, 100083, China; MOE Engineering Research Center of Forestry Biomass Materials and Bioenergy, Beijing Forestry University, Beijing, 100083, China
| | - Jiandu Lei
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, 100083, China; MOE Engineering Research Center of Forestry Biomass Materials and Bioenergy, Beijing Forestry University, Beijing, 100083, China.
| | - Jingyang Zhao
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, China Academy of Sciences, Beijing, 100190, China.
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Tolentino JE, Lytras S, Ito J, Sato K. Beyond MERS: Merbecovirus receptor plasticity calls for emergence preparedness. Cell Host Microbe 2025; 33:453-456. [PMID: 40209670 DOI: 10.1016/j.chom.2025.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2025] [Accepted: 03/11/2025] [Indexed: 04/12/2025]
Abstract
Three studies recently published in Cell reveal distinct ACE2 binding interactions across the merbecoviruses, uncovering how HKU5 can use ACE2s of many non-human hosts and identifying a novel HKU5 lineage capable of using human ACE2. These findings highlight merbecovirus receptor plasticity and caution for preparedness against potential merbecovirus threats.
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Affiliation(s)
- Jarel Elgin Tolentino
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Spyros Lytras
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Department of Pathology, Immunology and Microbiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan; Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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4
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Sun S, He J, Liu L, Zhu Y, Zhang Q, Qiu Y, Han Y, Xue S, Peng X, Long Y, Lu T, Wu W, Xia A, Zhou Y, Yan Y, Gao Y, Lu L, Sun L, Xie M, Wang Q. Anti-S2 antibodies responsible for the SARS-CoV-2 infection-induced serological cross-reactivity against MERS-CoV and MERS-related coronaviruses. Front Immunol 2025; 16:1541269. [PMID: 40226608 PMCID: PMC11985752 DOI: 10.3389/fimmu.2025.1541269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2024] [Accepted: 03/06/2025] [Indexed: 04/15/2025] Open
Abstract
Sarbecoviruses, such as SARS-CoV-2, utilize angiotensin-converting enzyme 2 (ACE2) as the entry receptor; while merbecoviruses, such as MERS-CoV, use dipeptidyl peptidase 4 (DPP4) for viral entry. Recently, several MERS-related coronaviruses, NeoCoV and PDF-2180, were reported to use ACE2, the same receptor as SARS-CoV-2, to enter cells, raising the possibility of potential recombination between SARS-CoV-2 and MERS-related coronaviruses within the co-infected ACE2-expressing cells. However, facing this potential recombination risk, the serum and antibody cross-reactivity against MERS/MERS-related coronaviruses after SARS-CoV-2 vaccination and/or infection is still elusive. Here, in this study, we showed that the serological cross-reactivity against MERS/MERS-related S proteins could be induced by SARS-CoV-2 infection but not by inactivated SARS-CoV-2 vaccination. Further investigation revealed that this serum cross-reactivity is due to monoclonals recognizing relatively conserved S2 epitopes, such as fusion peptide and stem helix, but not by antibodies against the receptor-binding domain (RBD), N-terminal domain (NTD) or subdomain-1 (SD1). Some of these anti-S2 cross-reactive mAbs showed cross-neutralizing activity, while none of them exhibited antibody-dependent enhancement (ADE) effect of viral entry in vitro. Together, these results dissected the SARS-CoV-2 infection-induced serological cross-reactivity against MERS/MERS-related coronaviruses, and highlighted the significance of conserved S2 region for the design and development of pan-β-coronaviruses vaccines.
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Affiliation(s)
- Siyuan Sun
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jiaying He
- Microbiological Testing Department, Baoshan District Center for Disease Control and Prevention, Shanghai, China
| | - Luotian Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuzhen Zhu
- Department of Gastroenterology, Jingan District Central Hospitals, Fudan University, Shanghai, China
| | - Qingsong Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yinong Qiu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuru Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Song Xue
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiaofang Peng
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yiming Long
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Tianyu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wei Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Anqi Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yunjiao Zhou
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Medicine, Tongji University, Shanghai, China
| | - Yan Yan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yidan Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lei Sun
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Minxiang Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Fifth People’s Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
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5
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Park YJ, Liu C, Lee J, Brown JT, Ma CB, Liu P, Gen R, Xiong Q, Zepeda SK, Stewart C, Addetia A, Craig CJ, Tortorici MA, Alshukairi AN, Starr TN, Yan H, Veesler D. Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses. Cell 2025; 188:1711-1728.e21. [PMID: 39922192 DOI: 10.1016/j.cell.2024.12.032] [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: 08/16/2024] [Revised: 10/25/2024] [Accepted: 12/20/2024] [Indexed: 02/10/2025]
Abstract
DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity of ACE2 utilization among merbecoviruses and their receptor species tropism remain unknown. Here, we reveal that HKU5 enters host cells utilizing Pipistrellus abramus (P.abr) and several non-bat mammalian ACE2s through a binding mode distinct from that of any other known ACE2-using coronaviruses. We defined the molecular determinants of receptor species tropism and identified a single amino acid mutation enabling HKU5 to utilize human ACE2, providing proof of principle for machine-learning-assisted outbreak preparedness. We show that MERS-CoV and HKU5 have markedly distinct antigenicity and identified several HKU5 inhibitors, including two clinical compounds. Our findings profoundly alter our understanding of coronavirus evolution, as several merbecovirus clades independently evolved ACE2 utilization, and pave the way for developing countermeasures against viruses poised for human emergence.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Chen Liu
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack T Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cheng-Bao Ma
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Peng Liu
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Risako Gen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Qing Xiong
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Caroline J Craig
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | | | - Abeer N Alshukairi
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Tyler N Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Huan Yan
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, China.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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6
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Chen J, Zhang W, Li Y, Liu C, Dong T, Chen H, Wu C, Su J, Li B, Zhang W, Hu B, Jia J, Ma CB, Zhu Y, He X, Li A, Pan K, Lin H, Guo Z, Li C, Zhang L, Yan H, Zhou P, Peng W, Shi ZL. Bat-infecting merbecovirus HKU5-CoV lineage 2 can use human ACE2 as a cell entry receptor. Cell 2025; 188:1729-1742.e16. [PMID: 39970913 DOI: 10.1016/j.cell.2025.01.042] [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: 09/17/2024] [Revised: 12/16/2024] [Accepted: 01/29/2025] [Indexed: 02/21/2025]
Abstract
Merbecoviruses comprise four viral species with remarkable genetic diversity: MERS-related coronavirus, Tylonycteris bat coronavirus HKU4, Pipistrellus bat coronavirus HKU5, and Hedgehog coronavirus 1. However, the potential human spillover risk of animal merbecoviruses remains to be investigated. Here, we reported the discovery of HKU5-CoV lineage 2 (HKU5-CoV-2) in bats that efficiently utilize human angiotensin-converting enzyme 2 (ACE2) as a functional receptor and exhibits a broad host tropism. Cryo-EM analysis of HKU5-CoV-2 receptor-binding domain (RBD) and human ACE2 complex revealed an entirely distinct binding mode compared with other ACE2-utilizing merbecoviruses with RBD footprint largely shared with ACE2-using sarbecoviruses and NL63. Structural and functional analyses indicate that HKU5-CoV-2 has a better adaptation to human ACE2 than lineage 1 HKU5-CoV. Authentic HKU5-CoV-2 infected human ACE2-expressing cell lines and human respiratory and enteric organoids. This study reveals a distinct lineage of HKU5-CoVs in bats that efficiently use human ACE2 and underscores their potential zoonotic risk.
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Affiliation(s)
- Jing Chen
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Zhang
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, China; The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yang Li
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Chen Liu
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Tianyi Dong
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Huiyu Chen
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, China; The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Chunguang Wu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jia Su
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Bei Li
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Zhang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ben Hu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jingkun Jia
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Bao Ma
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yan Zhu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xiangyang He
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ang Li
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, China; The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Kaiyi Pan
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Haofeng Lin
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zishuo Guo
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Cong Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China.
| | - Huan Yan
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
| | - Peng Zhou
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, China; The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
| | - Wei Peng
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, China; The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
| | - Zheng-Li Shi
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, China.
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7
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Jiang S, Wu F. Global surveillance and countermeasures for ACE2-using MERS-related coronaviruses with spillover risk. Cell 2025; 188:1465-1468. [PMID: 40118031 DOI: 10.1016/j.cell.2025.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2025] [Revised: 02/04/2025] [Accepted: 02/05/2025] [Indexed: 03/23/2025]
Abstract
Three studies published in this issue of Cell reveal that multiple MERS-related coronaviruses (MERSr-CoVs) utilize ACE2, rather than the canonical Merbecovirus receptor DPP4, for cell entry. These ACE2-dependent MERSr-CoVs pose a risk of zoonotic transmission to humans with high transmissibility potential like SARS-CoV-2, thus calling for global surveillance and countermeasures.
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Affiliation(s)
- Shibo Jiang
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, China.
| | - Fan Wu
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, China
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8
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Ma CB, Liu C, Park YJ, Tang J, Chen J, Xiong Q, Lee J, Stewart C, Asarnow D, Brown J, Tortorici MA, Yang X, Sun YH, Chen YM, Yu X, Si JY, Liu P, Tong F, Huang ML, Li J, Shi ZL, Deng Z, Veesler D, Yan H. Multiple independent acquisitions of ACE2 usage in MERS-related coronaviruses. Cell 2025; 188:1693-1710.e18. [PMID: 39922191 DOI: 10.1016/j.cell.2024.12.031] [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: 07/01/2024] [Revised: 09/20/2024] [Accepted: 12/20/2024] [Indexed: 02/10/2025]
Abstract
The angiotensin-converting enzyme 2 (ACE2) receptor is shared by various coronaviruses with distinct receptor-binding domain (RBD) architectures, yet our understanding of these convergent acquisition events remains elusive. Here, we report that two bat MERS-related coronaviruses (MERSr-CoVs) infecting Pipistrellus nathusii (P.nat)-MOW15-22 and PnNL2018B-use ACE2 as their receptor, with narrow ortholog specificity. Cryoelectron microscopy structures of the MOW15-22/PnNL2018B RBD-ACE2 complexes unveil an unexpected and entirely distinct binding mode, mapping >45 Å away from that of any other known ACE2-using coronaviruses. Functional profiling of ACE2 orthologs from 105 mammalian species led to the identification of host tropism determinants, including an ACE2 N432-glycosylation restricting viral recognition, and the design of a soluble P.nat ACE2 mutant with potent viral neutralizing activity. Our findings reveal convergent acquisition of ACE2 usage for merbecoviruses found in European bats, underscoring the extraordinary diversity of ACE2 recognition modes among coronaviruses and the promiscuity of this receptor.
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Affiliation(s)
- Cheng-Bao Ma
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Chen Liu
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Jingjing Tang
- State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jing Chen
- State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qing Xiong
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Xiao Yang
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Ye-Hui Sun
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Yuan-Mei Chen
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiao Yu
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Jun-Yu Si
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Peng Liu
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Fei Tong
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Mei-Ling Huang
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Jing Li
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Zheng-Li Shi
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou 510005, China.
| | - Zengqin Deng
- State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; Hubei Jiangxia Laboratory, Wuhan 430207, China.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
| | - Huan Yan
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, China.
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9
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Liu C, Park YJ, Ma CB, Stuart C, Gen R, Sun YC, Yang X, Lin MY, Xiong Q, Si JY, Liu P, Veesler D, Yan H. ACE2 utilization of HKU25 clade MERS-related coronaviruses with broad geographic distribution. RESEARCH SQUARE 2025:rs.3.rs-6097445. [PMID: 40162213 PMCID: PMC11952669 DOI: 10.21203/rs.3.rs-6097445/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Dipeptidyl peptidase-4 (DPP4) is a well-established receptor for several MERS-related coronaviruses (MERSr-CoVs) isolated from humans, camels, pangolins, and bats 1-6. However, the receptor usage of many genetically diverse bat MERSr-CoVs with broad geographical distributions remains poorly understood. Recent studies have identified angiotensin-converting enzyme 2 (ACE2) as an entry receptor for multiple merbecovirus clades. Here, using viral antigen and pseudovirus-based functional assays, we demonstrate that several bat merbecoviruses from the HKU25 clade previously thought to utilize DPP4 7, employ ACE2 as their functional receptor. Cryo-electron microscopy analysis revealed that HsItaly2011 and VsCoV-a7 recognize ACE2 with a binding mode sharing similarity with that of HKU5 but involving remodeled interfaces and distinct ortholog selectivity, suggesting a common evolutionary origin of ACE2 utilization for these two clades of viruses. EjCoV-3, a strain closely related to the DPP4-using MERSr-CoV BtCoV-422, exhibited relatively broad ACE2 ortholog tropism and could utilize human ACE2 albeit suboptimally. Despite differences in entry mechanisms and spike proteolytic activation compared to MERS-CoV, these viruses remain sensitive to several broadly neutralizing antibodies and entry inhibitors. These findings redefine our understanding of the evolution of receptor usage among MERSr-CoVs and highlight the versatility of ACE2 as a functional receptor for diverse coronaviruses.
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Affiliation(s)
- Chen Liu
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Young-Jun Park
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA
| | - Cheng-Bao Ma
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Cameron Stuart
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Risako Gen
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Yu-Cheng Sun
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Xiao Yang
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Mei-Yi Lin
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Qing Xiong
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Jun-Yu Si
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Peng Liu
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - David Veesler
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA
| | - Huan Yan
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
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10
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Lin MW, Lin CH, Chang JR, Chiang HH, Wu TH, Lin CS. The influence of PM2.5 exposure on SARS-CoV-2 infection via modulating the expression of angiotensin converting enzyme II. JOURNAL OF HAZARDOUS MATERIALS 2025; 485:136887. [PMID: 39700942 DOI: 10.1016/j.jhazmat.2024.136887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 11/22/2024] [Accepted: 12/13/2024] [Indexed: 12/21/2024]
Abstract
Particulate matter 2.5 (PM2.5) pollution and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic are the greatest environmental health issues worldwide. Several statistics revealed the significant positive correlation between the morbidity of coronavirus disease-19 (COVID-19) and the levels of air pollution. Nevertheless, there is no direct experimental evidence to indicate the effect of PM2.5 exposure on SARS-CoV-2 infection. The objective of this study was to evaluate whether the infection of SARS-CoV-2 affected by PM2.5 through angiotensin-converting enzyme II (ACE2) expression enhances and investigate the function of ACE2 in lung injury induced by PM2.5. An animal model of PM2.5-induced lung injury was established using wild-type (WT, C57BL/6), human ACE2 transgenic (K18-hACE2 TG), and murine ACE2 gene knockout (mACE2 KO) mice. The results indicate that PM2.5 exposure facilitates SARS-CoV-2 infection through inducing ACE2 expression in vitro (10 μg/mL) and in vivo (6.25 mg/kg/day in 50 μL saline). The levels of ACE, inflammatory cytokines, and mitogen-activated protein kinase (MAPK) proteins in WT, K18-hACE TG and mACE2 KO mice were significantly increased after PM2.5 instillation. The severest PM2.5-induced lung damage was observed in mACE2 KO mice. In summary, ACE2 plays a double-edged sword role in lung injury, PM2.5 exposure contributed to SARS-CoV-2 infection through inducing ACE2 expression, but ACE2 also protected pulmonary inflammation from PM2.5 challenge.
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Affiliation(s)
- Meng-Wei Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.
| | - Cheng-Han Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.
| | - Jia-Rong Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.
| | - Hua-Hsin Chiang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.
| | - Ting-Hsuan Wu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.
| | - Chih-Sheng Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan; Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.
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11
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Hills FR, Jorge F, Burga LN, Bostina M. Expression and Purification of SARS-related Spike Glycoproteins for Cryo-EM Analysis. Curr Protoc 2025; 5:e70115. [PMID: 40056094 PMCID: PMC11890022 DOI: 10.1002/cpz1.70115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2025]
Abstract
Coronaviridae spike glycoproteins mediate viral entry and fusion to host cells through binding to host receptors (i.e., ACE2, DPP4) and are key components in determining viral host range, making them targets for antiviral research. Here, we describe the expression, purification, and characterization of recombinant spike proteins to aid in protein characterization and analysis. These protocols were used for the production of spike glycoproteins from civet, pangolin, and bat coronaviruses, as well as high-resolution cryo-electron microscopy (cryo-EM) structural analysis of bat and civet host coronavirus spike glycoproteins (Hills et al., 2024). © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Expression and purification of SARS-CoV spike protein from ExpiCHO cells Basic Protocol 2: Preparation of SARS-CoV spike protein for visualization by negative-stain transmission electron microscopy and cryo-electron microscopy.
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Affiliation(s)
- Francesca R. Hills
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Fátima Jorge
- Otago Micro and Nano Imaging UnitUniversity of OtagoDunedinNew Zealand
| | - Laura N. Burga
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Mihnea Bostina
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
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12
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Hills FR, Geoghegan JL, Bostina M. Architects of infection: A structural overview of SARS-related coronavirus spike glycoproteins. Virology 2025; 604:110383. [PMID: 39983449 DOI: 10.1016/j.virol.2024.110383] [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: 10/20/2024] [Revised: 12/22/2024] [Accepted: 12/29/2024] [Indexed: 02/23/2025]
Abstract
The frequency of zoonotic viral emergence within the Coronaviridae family highlights the critical need to understand the structural features of spike proteins that govern viral entry and host adaptation. Investigating the structural conservation and variation in key regions of the spike protein-those involved in host range, binding affinity, viral entry, and immune evasion-is essential for predicting the evolutionary pathways of coronaviruses, assessing the risk of future host-jumping events, and discovering pan-neutralising antibodies. Here we summarise our current structural understanding of the spike proteins similar to SARS-CoV-2 from the Coronaviridae family and compare key functional similarities and differences. Our aim is to demonstrate the significant structural and sequence conservation between spike proteins from a range of host species and to outline the importance of animal coronavirus surveillance and structural investigation in our endeavour for pandemic preparedness against emerging viruses.
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Affiliation(s)
- Francesca R Hills
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
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13
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Sims AC, Schäfer A, Okuda K, Leist SR, Kocher JF, Cockrell AS, Hawkins PE, Furusho M, Jensen KL, Kyle JE, Burnum-Johnson KE, Stratton KG, Lamar NC, Niccora CD, Weitz KK, Smith RD, Metz TO, Waters KM, Boucher RC, Montgomery SA, Baric RS, Sheahan TP. Dysregulation of lung epithelial cell homeostasis and immunity contributes to Middle East respiratory syndrome coronavirus disease severity. mSphere 2025; 10:e0095124. [PMID: 39882872 PMCID: PMC11853001 DOI: 10.1128/msphere.00951-24] [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: 12/10/2024] [Accepted: 01/15/2025] [Indexed: 01/31/2025] Open
Abstract
Coronaviruses (CoV) emerge suddenly from animal reservoirs to cause novel diseases in new hosts. Discovered in 2012, the Middle East respiratory syndrome coronavirus (MERS-CoV) is endemic in camels in the Middle East and is continually causing local outbreaks and epidemics. While all three newly emerging human CoVs from the past 20 years (SARS-CoV, SARS-CoV-2, and MERS-CoV) cause respiratory disease, each CoV has unique host interactions that drive differential pathogeneses. To better understand the virus and host interactions driving lethal MERS-CoV infection, we performed a longitudinal multi-omics analysis of sublethal and lethal MERS-CoV infection in mice. Significant differences were observed in body weight loss, virus titers, and acute lung injury among lethal and sub-lethal virus doses. Virus-induced apoptosis of type I and II alveolar epithelial cells suggests that loss or dysregulation of these key cell populations was a major driver of severe disease. Omics analysis suggested differential pathogenesis was multi-factorial with clear differences among innate and adaptive immune pathways as well as those that regulate lung epithelial homeostasis. Infection of mice lacking functional T and B cells showed that adaptive immunity was important in controlling viral replication but also increased pathogenesis. In summary, we provide a high-resolution host response atlas for MERS-CoV infection and disease severity. Multi-omics studies of viral pathogenesis offer a unique opportunity to not only better understand the molecular mechanisms of disease but also to identify genes and pathways that can be exploited for therapeutic intervention all of which is important for our future pandemic preparedness.IMPORTANCEEmerging coronaviruses like SARS-CoV, SARS-CoV-2, and MERS-CoV cause a range of disease outcomes in humans from an asymptomatic, moderate, and severe respiratory disease that can progress to death but the factors causing these disparate outcomes remain unclear. Understanding host responses to mild and life-threatening infections provides insight into virus-host networks within and across organ systems that contribute to disease outcomes. We used multi-omics approaches to comprehensively define the host response to moderate and severe MERS-CoV infection. Severe respiratory disease was associated with dysregulation of the immune response. Key lung epithelial cell populations that are essential for lung function get infected and die. Mice lacking key immune cell populations experienced greater virus replication but decreased disease severity implicating the immune system in both protective and pathogenic roles in response to MERS-CoV. These data could be utilized to design new therapeutic strategies targeting specific pathways that contribute to severe disease.
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Affiliation(s)
- Amy C. Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jacob F. Kocher
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Adam S. Cockrell
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Padraig E. Hawkins
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Minako Furusho
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kara L. Jensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer E. Kyle
- Biological Sciences Division, Pacific Northwest National Laboratories, Richland, Washington, USA
| | | | - Kelly G. Stratton
- Biological Sciences Division, Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Natalie C. Lamar
- AI & Data Analytics Division, Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Carrie D. Niccora
- Biological Sciences Division, Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Karl K. Weitz
- Biological Sciences Division, Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Richard C. Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephanie A. Montgomery
- Department of Pathology & Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Timothy P. Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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14
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Liu C, Park YJ, Ma CB, Stuart C, Gen R, Sun YC, Yang X, Lin MY, Xiong Q, Si JY, Liu P, Veesler D, Yan H. ACE2 utilization of HKU25 clade MERS-related coronaviruses with broad geographic distribution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.19.639017. [PMID: 40027745 PMCID: PMC11870458 DOI: 10.1101/2025.02.19.639017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Dipeptidyl peptidase-4 (DPP4) is a well-established receptor for several MERS-related coronaviruses (MERSr-CoVs) isolated from humans, camels, pangolins, and bats (1-6). However, the receptor usage of many genetically diverse bat MERSr-CoVs with broad geographical distributions remains poorly understood. Recent studies have identified angiotensin-converting enzyme 2 (ACE2) as an entry receptor for multiple merbecovirus clades. Here, using viral antigen and pseudovirus-based functional assays, we demonstrate that several bat merbecoviruses from the HKU25 clade previously thought to utilize DPP4 (7), employ ACE2 as their functional receptor. Cryo-electron microscopy analysis revealed that HsItaly2011 and VsCoV-a7 recognize ACE2 with a binding mode sharing similarity with that of HKU5 but involving remodeled interfaces and distinct ortholog selectivity, suggesting a common evolutionary origin of ACE2 utilization for these two clades of viruses. EjCoV-3, a strain closely related to the DPP4-using MERSr-CoV BtCoV-422, exhibited relatively broad ACE2 ortholog tropism and could utilize human ACE2 albeit suboptimally. Despite differences in entry mechanisms and spike proteolytic activation compared to MERS-CoV, these viruses remain sensitive to several broadly neutralizing antibodies and entry inhibitors. These findings redefine our understanding of the evolution of receptor usage among MERSr-CoVs and highlight the versatility of ACE2 as a functional receptor for diverse coronaviruses. Significance Recent studies unexpectedly revealed that several merbecoviruses convergently evolved ACE2 receptor usage with distinct binding modes across three continents, challenging the dogma that DPP4 is their primary receptor. Here, we demonstrate that HKU25 clade MERS-related coronaviruses broadly distributed across Eurasia utilize ACE2 as host receptor through a binding mode shared with HKU5, challenging prior findings. These findings reveal a prevalence of ACE2 usage in diverse MERS-related coronaviruses in bats and show that EjCoV-3 is preadapted to use human ACE2, suggesting a potential for spillover. Our data provide a blueprint of host receptor barrier determinants which will facilitate global surveillance and development of countermeasures against these poorly characterized merbecoviruses.
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Affiliation(s)
- Chen Liu
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Young-Jun Park
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA
| | - Cheng-Bao Ma
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Cameron Stuart
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Risako Gen
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Yu-Cheng Sun
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Xiao Yang
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Mei-Yi Lin
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Qing Xiong
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Jun-Yu Si
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Peng Liu
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - David Veesler
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA
| | - Huan Yan
- State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
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15
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Luo YW, Huang AL, Tang KF. Angiotensin-converting enzyme 2 and hepatic SARS-CoV-2 infection: Regulation, association, and therapeutic implications. World J Gastroenterol 2025; 31:100864. [PMID: 39958440 PMCID: PMC11752700 DOI: 10.3748/wjg.v31.i6.100864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Revised: 12/07/2024] [Accepted: 12/20/2024] [Indexed: 01/10/2025] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells via the angiotensin-converting enzyme 2 (ACE2) receptor. Mounting evidence has indicated the presence of hepatic SARS-CoV-2 infection and liver injury in patients with coronavirus disease 2019 (COVID-19). Understanding the mechanisms of hepatic SARS-CoV-2 infection is crucial for addressing COVID-19-related liver pathology and developing targeted therapies. This editorial discusses the significance of ACE2 in hepatic SARS-CoV-2 infection, drawing on the research by Jacobs et al. Their findings indicate that hepatic ACE2 expression, frequency of hepatic SARS-CoV-2 infection, and severity of liver injury are elevated in patients with pre-existing chronic liver diseases. These data suggest that hepatic ACE2 could be a promising therapeutic target for COVID-19.
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Affiliation(s)
- Yu-Wei Luo
- Key Laboratory of Molecular Biology on Infectious Disease, Ministry of Education, Chongqing Medical University, Chongqing 400016, China
| | - Ai-Long Huang
- Key Laboratory of Molecular Biology on Infectious Disease, Ministry of Education, Chongqing Medical University, Chongqing 400016, China
| | - Kai-Fu Tang
- Key Laboratory of Molecular Biology on Infectious Disease, Ministry of Education, Chongqing Medical University, Chongqing 400016, China
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16
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Bihani S, Ray A, Borishetty D, Tuckley C, Salkar A, Acharjee A, Shrivastav P, Shrivastav O, Shastri J, Agrawal S, Duttagupta S, Srivastava S. Investigation of Immunoreactivity Profiles and Epitope Landscape in Divergent COVID-19 Trajectories and SARS-CoV-2 Variants. J Proteome Res 2025; 24:762-776. [PMID: 39873496 DOI: 10.1021/acs.jproteome.4c00791] [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] [Indexed: 01/30/2025]
Abstract
This study aimed to elucidate the complexity of the humoral immune response in COVID-19 patients with varying disease trajectories using a SARS-CoV-2 whole proteome peptide microarray chip. The microarray, containing 5347 peptides spanning the entire SARS-CoV-2 proteome and key variants of concern, was used to analyze IgG responses in 10 severe-to-recovered, 9 nonsevere-to-severe cases, and 10 control case (5 pre-pandemic and 5 SARS-CoV-2-negative) plasma samples. We identified 1151 IgG-reactive peptides corresponding to 647 epitopes, with 207 peptides being cross-reactive across 124 epitopes. Nonstructural protein 3 (nsp3) exhibited the highest number of total and unique epitopes, followed by the spike protein. nsp12 had the most number of cross-reactive epitopes. Peptides from the spike protein and nsps 2, 3, 5, and 13 were notably associated with recovery. Additionally, specific mutations in SARS-CoV-2 variants were found to alter peptide immunoreactivity, with some mutations (e.g., G142D, L452R, and N501Y) enhancing and others (e.g., R190S and E484 K) reducing immune recognition. These findings have critical implications for the development of diagnostics, vaccines, and therapeutics. Understanding the distribution of epitopes and the impact of viral mutations on antigenicity provides insights into immune evasion mechanisms, informing strategies for controlling COVID-19 and future coronavirus outbreaks.
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Affiliation(s)
- Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arka Ray
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Dhanush Borishetty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Chaitanya Tuckley
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arup Acharjee
- Molecular Omics Laboratory, Department of Zoology, Faculty of Science, University of Allahabad, Prayagraj 211002, India
| | | | - Om Shrivastav
- Kasturba Hospital for Infectious Disease, Mumbai 400011, India
| | | | - Sachee Agrawal
- Kasturba Hospital for Infectious Disease, Mumbai 400011, India
| | - Siddhartha Duttagupta
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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17
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Silvério BS, Guilardi MD, Martins JO, Duro RLS, de Sousa LLF, Cabral-Miranda G, Janini LMR, Poon LLM, Durães-Carvalho R. Coronavirus Cryptic Landscape and Draft Genome of a Novel CoV Clade Related to MERS From Bats Circulating in Northeastern Brazil. J Med Virol 2025; 97:e70173. [PMID: 39825725 DOI: 10.1002/jmv.70173] [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: 10/17/2024] [Revised: 12/03/2024] [Accepted: 01/05/2025] [Indexed: 01/20/2025]
Abstract
We identified seven distinct coronaviruses (CoVs) in bats from Brazil, classified into 229E-related (Alpha-CoV), Nobecovirus, Sarbecovirus, and Merbecovirus (Beta-CoV), including one closely related to MERS-like CoV with 82.8% genome coverage. To accomplish this, we screened 423 oral and rectal swabs from 16 different bat species using molecular assays, RNA sequencing, and evolutionary analysis. Notably, gaps in the spike-encoding gene led us to design new primers and perform Sanger sequencing, which revealed high similarities to MERS-related (MERSr) CoV strains found in humans and camels. Additionally, we identified key residues in the receptor-binding domain (RBD) of the spike protein, suggesting potential interactions with DPP4, the receptor for MERSr-CoV. Our analyses also revealed evidence of recombination involving our laboratory-produced sequences. These findings highlight the extensive genetic diversity of CoVs, the presence of novel viral lineages, and the occurrence of recombination events among bat CoVs circulating in Brazil, underscoring the critical role bats play as reservoirs for emerging viruses and emphasizing the necessity of ongoing surveillance to monitor the public health risks associated with CoV spillover events.
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Affiliation(s)
- Bruna Stefanie Silvério
- Department of Morphology and Genetics, Federal University of São Paulo, São Paulo-SP, Brazil
| | - Mariana Dias Guilardi
- Interunit Bioinformatics Graduate Program, Institute of Chemistry, University of São Paulo, São Paulo-SP, Brazil
| | - Junior Olímpio Martins
- Department of Morphology and Genetics, Federal University of São Paulo, São Paulo-SP, Brazil
| | - Rodrigo Lopes Sanz Duro
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Brazil
| | - Larissa Leão F de Sousa
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Brazil
- Rabies Diagnosis Laboratory, Central Laboratory of Public Health - LACEN, Fortaleza-CE, Brazil
| | | | - Luiz Mário Ramos Janini
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Brazil
| | - Leo L M Poon
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Ricardo Durães-Carvalho
- Department of Morphology and Genetics, Federal University of São Paulo, São Paulo-SP, Brazil
- Interunit Bioinformatics Graduate Program, Institute of Chemistry, University of São Paulo, São Paulo-SP, Brazil
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Brazil
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18
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López D, Zumárraga J. Bioinformatic Tools for Studying the Cellular Immune Response to SARS-CoV-2, Vaccine Efficacy, and Future Pandemics at the Global Population Level. Int J Mol Sci 2024; 25:13477. [PMID: 39769240 PMCID: PMC11678114 DOI: 10.3390/ijms252413477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 12/13/2024] [Accepted: 12/15/2024] [Indexed: 01/11/2025] Open
Abstract
Antigen recognition by human leukocyte antigen (HLA) restriction is critical for an adequate antiviral response in both natural infection and vaccination. However, the overwhelming polymorphism of HLA, with nearly 40,000 alleles identified, is an important limitation for the global analysis of cellular immune responses and vaccine efficacy. In this narrative review, we included several immunoinformatics studies performed in our laboratory to circumvent this limitation. These analyses focused on studying the cellular immune responses restricted by the most common HLA alleles, and their role in vaccine efficacy. Computational studies validated experimentally, such as our laboratory has carried out, represent a useful, rapid, and cost-effective strategy to combat future pandemics.
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Affiliation(s)
- Daniel López
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain;
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19
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Rexhepaj M, Asarnow D, Perruzza L, Park YJ, Guarino B, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Corti D, Starr TN, Benigni F, Veesler D. Isolation and escape mapping of broadly neutralizing antibodies against emerging delta-coronaviruses. Immunity 2024; 57:2914-2927.e7. [PMID: 39488210 DOI: 10.1016/j.immuni.2024.10.001] [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: 03/18/2024] [Revised: 08/06/2024] [Accepted: 10/02/2024] [Indexed: 11/04/2024]
Abstract
Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated PDCoV spike (S)-directed monoclonal antibodies (mAbs) from humanized mice and found that two, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryoelectron microscopy (cryo-EM) structures of PD33 and PD41 in complex with the S receptor-binding domain (RBD) and ectodomain trimer revealed the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs competitively interfere with host aminopeptidase N binding to neutralize PDCoV and used deep-mutational scanning epitope mapping to associate RBD antigenic sites with mAb-mediated neutralization potency. Our results indicate a PD33-PD41 mAb cocktail may heighten the barrier to escape. PD33 and PD41 are candidates for clinical advancement against future PDCoV outbreaks.
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Affiliation(s)
- Megi Rexhepaj
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Lisa Perruzza
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Barbara Guarino
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Mathew Mccallum
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Katja Culap
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Giada Leoni
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Alessio Balmelli
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Miles S Dickinson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jack T Brown
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ashley L Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Davide Corti
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Tyler N Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Fabio Benigni
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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20
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Li M, Zhao C, Shi J, Wang X, Liu Y, Zhao X, Cai G, Chu H, Wang P. Bispecific antibodies provide broad neutralization of emerging beta-coronaviruses by targeting ACE2 and viral spikes. Emerg Microbes Infect 2024; 13:2404166. [PMID: 39258934 PMCID: PMC11421165 DOI: 10.1080/22221751.2024.2404166] [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: 04/19/2024] [Revised: 08/15/2024] [Accepted: 09/10/2024] [Indexed: 09/12/2024]
Abstract
Human coronaviruses such as SARS-CoV, MERS-CoV, and SARS-CoV-2 have recurrently emerged as significant pathogens, causing severe respiratory illnesses and presenting challenges to monoclonal antibody therapeutics due to their rapid evolution, particularly the diverse variants of SARS-CoV-2. In this study, we utilized "Knob-into-Hole" and "IgG-scFv" technologies to engineer bispecific antibodies (bsAbs) that target both the viral receptor and spike protein, enhancing their neutralization breadth and potency. Our bsAbs, combining anti-SARS-CoV-2 or anti-MERS-CoV antibodies with an anti-ACE2 antibody, demonstrated effective neutralization across a range of SARS-CoV-2 variants, SARS-CoV and MERS-CoV in both pseudovirus and authentic virus assays. Notably, the "IgG-scFv" bsAbs format exhibited superior binding and neutralization capabilities compared to the "Knob-into-Hole" configurations. The most effective of these, "IgG-scFv" H11B11_m336, displayed exceptional neutralization potency against a panel of 24 pseudotyped Beta-Coronaviruses, with IC50 values ranging from 0.001-0.183 μg/mL. Overall, our findings underscore the potential of bsAbs as an effective strategy to meet the immediate challenges posed by existing and emerging pathogens, thereby enhancing global pandemic preparedness.
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Affiliation(s)
- Minghui Li
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People's Republic of China
| | - Chaoyue Zhao
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People's Republic of China
| | - Jialu Shi
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Xun Wang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People's Republic of China
| | - Yuanchen Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Xiaoyu Zhao
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People's Republic of China
| | - Guonan Cai
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People's Republic of China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Pengfei Wang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People's Republic of China
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21
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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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22
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Stich M, Magalhães VG, Bürger F, Garbade SF, Jeltsch K, Mohr K, Haddad A, Elling R, Lang P, Rabsteyn A, Jacobsen E, Bode SFN, Müller B, Kräusslich H, Hoffmann GF, Okun JG, Bartenschlager R, Binder M, Janda A, Renk H, Tönshoff B. Elevated Soluble ACE2 Activity in Children and Adults After SARS-CoV-2 Exposure Irrespective of Laboratory-Confirmed Infection. J Med Virol 2024; 96:e70098. [PMID: 39624009 PMCID: PMC11612704 DOI: 10.1002/jmv.70098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 10/21/2024] [Accepted: 11/15/2024] [Indexed: 12/06/2024]
Abstract
The pivotal role of the cell entry receptor ACE2 for SARS-CoV-2 infection is well-established. When ACE2 is shed from cell surface into plasma as soluble ACE2 (sACE2), it can effectively neutralize SARS-CoV-2. This longitudinal prospective cohort study analyzed sACE2 activity in 1192 participants, aged 4 months to 81 years, 3 and 12 months after SARS-CoV-2 household exposure. Following SARS-CoV-2 exposure, participants exhibited significantly elevated sACE2 activity, irrespective of confirmed infection, with the highest levels observed in exposed children. Longitudinal analysis revealed a decline in sACE2 levels over time, reaching levels comparable to age- and sex-matched pre-pandemic controls. An increase in sACE2 activity was also confirmed in vitro in Calu-3 (human lung) cells within hours of SARS-CoV-2 exposure, providing a direct link between SARS-CoV-2 exposure and elevated sACE2. This study, therefore, challenges the dichotomy of categorizing SARS-CoV-2 exposed participants as infected or not infected solely on currently established diagnostic assays. It demonstrates lasting host responses independent of B- and T-cell memory and may help to keep SARS-CoV-2 infections in balance and contribute to successful virus clearance in children and adults lacking humoral and cellular immune responses following SARS-CoV-2 exposure. Trial Registration: German Registry for Clinical Studies; Identifier: D 00021521.
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Affiliation(s)
- Maximilian Stich
- Heidelberg UniversityMedical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department of Pediatrics IHeidelbergGermany
- Heidelberg UniversityMedical Faculty Heidelberg, Department of Infectious Diseases, Molecular VirologyHeidelbergGermany
- German Cancer Research Center (DKFZ)Division Virus‐Associated CarcinogenesisHeidelbergGermany
- German Center for Infection Research (DZIF)Heidelberg Partner SiteHeidelbergGermany
| | - Vladimir Gonçalves Magalhães
- German Cancer Research Center (DKFZ)Division Virus‐Associated Carcinogenesis, Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”HeidelbergGermany
| | - Friederike Bürger
- Heidelberg UniversityMedical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department of Pediatrics IHeidelbergGermany
| | - Sven F. Garbade
- Heidelberg UniversityMedical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department of Pediatrics IHeidelbergGermany
| | - Kathrin Jeltsch
- Heidelberg UniversityMedical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department of Pediatrics IHeidelbergGermany
| | - Kerstin Mohr
- German Cancer Research Center (DKFZ)Division Virus‐Associated Carcinogenesis, Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”HeidelbergGermany
| | - Anneke Haddad
- Institute for Infection Prevention and ControlUniversity Medical Centre and Faculty of Medicine FreiburgFreiburg im BreisgauGermany
- Center for Pediatrics and Adolescent MedicineUniversity Medical Centre and Faculty of Medicine FreiburgFreiburg im BreisgauGermany
| | - Roland Elling
- Center for Pediatrics and Adolescent MedicineUniversity Medical Centre and Faculty of Medicine FreiburgFreiburg im BreisgauGermany
- Institute for ImmunodeficiencyMedical Center Freiburg, Germany and Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Peter Lang
- University Children's Hospital TübingenDepartment of Hematology/OncologyTübingenGermany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)Partner Site TübingenTübingenGermany
| | - Armin Rabsteyn
- University Children's Hospital TübingenDepartment of Hematology/OncologyTübingenGermany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)Partner Site TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) “Image‐Guided and Functionally Instructed Tumor Therapies”University of TübingenTübingenGermany
| | - Eva‐Maria Jacobsen
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Sebastian F. N. Bode
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Barbara Müller
- Heidelberg UniversityMedical Faculty Heidelberg, Department of Infectious Diseases, VirologyHeidelbergGermany
| | - Hans‐Georg Kräusslich
- German Center for Infection Research (DZIF)Heidelberg Partner SiteHeidelbergGermany
- Heidelberg UniversityMedical Faculty Heidelberg, Department of Infectious Diseases, VirologyHeidelbergGermany
| | - Georg Friedrich Hoffmann
- Heidelberg UniversityMedical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department of Pediatrics IHeidelbergGermany
| | - Jürgen G. Okun
- Heidelberg UniversityMedical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department of Pediatrics IHeidelbergGermany
| | - Ralf Bartenschlager
- Heidelberg UniversityMedical Faculty Heidelberg, Department of Infectious Diseases, Molecular VirologyHeidelbergGermany
- German Cancer Research Center (DKFZ)Division Virus‐Associated CarcinogenesisHeidelbergGermany
- German Center for Infection Research (DZIF)Heidelberg Partner SiteHeidelbergGermany
| | - Marco Binder
- German Cancer Research Center (DKFZ)Division Virus‐Associated Carcinogenesis, Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”HeidelbergGermany
| | - Aleš Janda
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Hanna Renk
- University Children's Hospital TübingenDepartment of Pediatric Neurology and Developmental MedicineTübingenGermany
| | - Burkhard Tönshoff
- Heidelberg UniversityMedical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department of Pediatrics IHeidelbergGermany
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23
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Xu L, Song M, Tian X, Sun J, Wang Y, Bie M, Bi Y, Holmes EC, Guan Y, Chen J, Li J, Shi W. Five-year longitudinal surveillance reveals the continual circulation of both alpha- and beta-coronaviruses in Plateau and Gansu pikas ( Ochotona spp.) at Qinghai Lake, China 1. Emerg Microbes Infect 2024; 13:2392693. [PMID: 39137298 PMCID: PMC11346322 DOI: 10.1080/22221751.2024.2392693] [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: 07/01/2024] [Revised: 08/03/2024] [Accepted: 08/11/2024] [Indexed: 08/15/2024]
Abstract
The discovery of alphacoronaviruses and betacoronaviruses in plateau pikas (Ochotona curzoniae) expanded the host range of mammalian coronavirus (CoV) to a new order - Lagomorpha. However, the diversity and evolutionary relationships of CoVs in these plateau-region-specific animal population remains uncertain. We conducted a five-year longitudinal surveillance of CoVs harboured by pikas around Qinghai Lake, China. CoVs were identified in 33 of 236 plateau pikas and 2 of 6 Gansu pikas (Ochotona cansus), with a total positivity rate of 14.5%, and exhibiting a wide spatiotemporal distribution across seven sampling sites and six time points. Through meta-transcriptomic sequencing and RT-PCR, we recovered 16 near-complete viral genome sequences. Phylogenetic analyses classified the viruses as variants of either pika alphacoronaviruses or betacoronaviruses endemic to plateau pikas from the Qinghai-Tibet Plateau region. Of particular note, the pika-associated betacoronaviruses may represent a novel subgenus within the genus Betacoronavirus. Tissue tropism, evaluated using quantitative real-time PCR, revealed the presence of CoV in the rectal and/or lung tissues, with the highest viral loads at 103.55 or 102.80 RNA copies/μL. Surface plasmon resonance (SPR) assays indicated that the newly identified betacoronavirus did not bind to human or pika Angiotensin-converting enzyme 2 (ACE2) or Dipeptidyl peptidase 4 (DPP4). The findings highlight the ongoing circulation and broadening host spectrum of CoVs among pikas, emphasizing the necessity for further investigation to evaluate their potential public health risks.
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Affiliation(s)
- Lin Xu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
| | - Meiqing Song
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
| | - Xianzhi Tian
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
| | - Ju Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
| | - Yanjun Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
| | - Mengyu Bie
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Edward C. Holmes
- School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Yi Guan
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Jianjun Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Juan Li
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
| | - Weifeng Shi
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
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24
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Cruz AV, Santos-Silva S, Queirós-Reis L, Rodrigues C, Soeiro V, Tarlinton RE, Mesquita JR. Genomic characterization and cross-species transmission potential of hedgehog coronavirus. One Health 2024; 19:100940. [PMID: 39650145 PMCID: PMC11621562 DOI: 10.1016/j.onehlt.2024.100940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 11/15/2024] [Accepted: 11/16/2024] [Indexed: 12/11/2024] Open
Abstract
In the 21st century, three betacoronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have emerged in humans worldwide as a result of animal spillover, causing severe respiratory infections and resulting in more than seven million deaths. In 2013, a novel Betacoronavirus closely related to MERS-CoV (Betacoronavirus cameli) was discovered in European hedgehogs (Erinaceus europaeus), raising questions on the possibility of hedgehog-to-human transmission. Hence, the present study aimed to investigate and characterize the presence and genetic diversity of coronaviruses in hedgehogs from Portugal, as well as their potential for cross-species transmission. To achieve this, fecal samples from 110 hedgehogs at two recovery centers and one environmental non-governmental organization were tested for coronaviruses using a broad-spectrum nested RT-PCR assay targeting the RdRp gene. Of these samples, 24.5 % tested positive, most belonging to the Betacoronavirus genus. However, the present study also reports, for the first time, Alphacoronaviruses in hedgehogs, showing 100 % identity with a Bat coronavirus (a variant of Alphacoronavirus miniopteri). The genome sequencing of one betacoronavirus-positive sample yielded 65 % of a full-length genome, with the closest homology (93.5 %) to Betacoronavirus erinacei from the United Kingdom. Computational protein-protein docking studies predicted the binding affinity between the spike protein of hedgehog coronavirus and cell receptors of mammal species that interact with hedgehogs. The results obtained raise the question of whether hedgehog CoV uses the same receptor as MERS-CoV or a different receptor to enter host cells. Thus, this study enhances our understanding of the epidemiology of coronaviruses, emphasizing the need for further investigation into cross-species transmission risks.
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Affiliation(s)
- Andreia V.S. Cruz
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
| | - Sérgio Santos-Silva
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
| | - Luís Queirós-Reis
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
| | - Clarisse Rodrigues
- Centro de Recuperação e Interpretação do Ouriço, 4470-372 Maia, Portugal
| | - Vanessa Soeiro
- Centro de Recuperação de Fauna do Parque Biológico de Gaia, 4430-812 Vila Nova de Gaia, Portugal
| | - Rachael E. Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - João R. Mesquita
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, 4050-600 Porto, Portugal
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-600 Porto, Portugal
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25
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Ragotte RJ, Tortorici MA, Catanzaro NJ, Addetia A, Coventry B, Froggatt HM, Lee J, Stewart C, Brown JT, Goreshnik I, Sims JN, Milles LF, Wicky BI, Glögl M, Gerben S, Kang A, Bera AK, Sharkey W, Schäfer A, Baric RS, Baker D, Veesler D. Designed miniproteins potently inhibit and protect against MERS-CoV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.03.621760. [PMID: 39574666 PMCID: PMC11580849 DOI: 10.1101/2024.11.03.621760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2024]
Abstract
Middle-East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic pathogen with 36% case-fatality rate in humans. No vaccines or specific therapeutics are currently approved to use in humans or the camel host reservoir. Here, we computationally designed monomeric and homo-oligomeric miniproteins binding with high affinity to the MERS-CoV spike (S) glycoprotein, the main target of neutralizing antibodies and vaccine development. We show that these miniproteins broadly neutralize a panel of MERS-CoV S variants, spanning the known antigenic diversity of this pathogen, by targeting a conserved site in the receptor-binding domain (RBD). The miniproteins directly compete with binding of the DPP4 receptor to MERS-CoV S, thereby blocking viral attachment to the host entry receptor and subsequent membrane fusion. Intranasal administration of a lead miniprotein provides prophylactic protection against stringent MERS-CoV challenge in mice motivating future clinical development as a next-generation countermeasure against this virus with pandemic potential.
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Affiliation(s)
- Robert J. Ragotte
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | - Nicholas J. Catanzaro
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Heather M. Froggatt
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack T. Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jeremiah N. Sims
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lukas F. Milles
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Basile I.M. Wicky
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Matthias Glögl
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - William Sharkey
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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26
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Liu P, Huang ML, Guo H, McCallum M, Si JY, Chen YM, Wang CL, Yu X, Shi LL, Xiong Q, Ma CB, Bowen JE, Tong F, Liu C, Sun YH, Yang X, Chen J, Guo M, Li J, Corti D, Veesler D, Shi ZL, Yan H. Design of customized coronavirus receptors. Nature 2024; 635:978-986. [PMID: 39478224 DOI: 10.1038/s41586-024-08121-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 09/25/2024] [Indexed: 11/29/2024]
Abstract
Although coronaviruses use diverse receptors, the characterization of coronaviruses with unknown receptors has been impeded by a lack of infection models1,2. Here we introduce a strategy to engineer functional customized viral receptors (CVRs). The modular design relies on building artificial receptor scaffolds comprising various modules and generating specific virus-binding domains. We identify key factors for CVRs to functionally mimic native receptors by facilitating spike proteolytic cleavage, membrane fusion, pseudovirus entry and propagation for various coronaviruses. We delineate functional SARS-CoV-2 spike receptor-binding sites for CVR design and reveal the mechanism of cell entry promoted by the N-terminal domain-targeting S2L20-CVR. We generated CVR-expressing cells for 12 representative coronaviruses from 6 subgenera, most of which lack known receptors, and show that a pan-sarbecovirus CVR supports propagation of a propagation-competent HKU3 pseudovirus and of authentic RsHuB2019A3. Using an HKU5-specific CVR, we successfully rescued wild-type and ZsGreen-HiBiT-incorporated HKU5-1 (LMH03f) and isolated a HKU5 strain from bat samples. Our study demonstrates the potential of the CVR strategy for establishing native receptor-independent infection models, providing a tool for studying viruses that lack known susceptible target cells.
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Affiliation(s)
- Peng Liu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Mei-Ling Huang
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Hua Guo
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jun-Yu Si
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yuan-Mei Chen
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Chun-Li Wang
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Xiao Yu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Lu-Lu Shi
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Qing Xiong
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Cheng-Bao Ma
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Fei Tong
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Chen Liu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Ye-Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Xiao Yang
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jing Chen
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ming Guo
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jing Li
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Davide Corti
- Humabs BioMed SA, subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - Zheng-Li Shi
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China.
| | - Huan Yan
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
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27
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Zhang L, Cheng HH, Krüger N, Hörnich B, Graichen L, Hahn AS, Schulz SR, Jäck HM, Stankov MV, Behrens GMN, Müller MA, Drosten C, Mörer O, Winkler MS, Qian Z, Pöhlmann S, Hoffmann M. ACE2-independent sarbecovirus cell entry can be supported by TMPRSS2-related enzymes and can reduce sensitivity to antibody-mediated neutralization. PLoS Pathog 2024; 20:e1012653. [PMID: 39536058 PMCID: PMC11559990 DOI: 10.1371/journal.ppat.1012653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Accepted: 10/10/2024] [Indexed: 11/16/2024] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, demonstrated that zoonotic transmission of animal sarbecoviruses threatens human health but the determinants of transmission are incompletely understood. Here, we show that most spike (S) proteins of horseshoe bat and Malayan pangolin sarbecoviruses employ ACE2 for entry, with human and raccoon dog ACE2 exhibiting broad receptor activity. The insertion of a multibasic cleavage site into the S proteins increased entry into human lung cells driven by most S proteins tested, suggesting that acquisition of a multibasic cleavage site might increase infectivity of diverse animal sarbecoviruses for the human respiratory tract. In contrast, two bat sarbecovirus S proteins drove cell entry in an ACE2-independent, trypsin-dependent fashion and several ACE2-dependent S proteins could switch to the ACE2-independent entry pathway when exposed to trypsin. Several TMPRSS2-related cellular proteases but not the insertion of a multibasic cleavage site into the S protein allowed for ACE2-independent entry in the absence of trypsin and may support viral spread in the respiratory tract. Finally, the pan-sarbecovirus antibody S2H97 enhanced cell entry driven by two S proteins and this effect was reversed by trypsin while trypsin protected entry driven by a third S protein from neutralization by S2H97. Similarly, plasma from quadruple vaccinated individuals neutralized entry driven by all S proteins studied, and availability of the ACE2-independent, trypsin-dependent pathway reduced neutralization sensitivity. In sum, our study reports a pathway for entry into human cells that is ACE2-independent, can be supported by TMPRSS2-related proteases and may be associated with antibody evasion.
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Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Hsiu-Hsin Cheng
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Nadine Krüger
- Platform Infection Models, German Primate Center, Göttingen, Germany
| | - Bojan Hörnich
- Junior Research Group Herpesviruses, German Primate Center, Göttingen, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Alexander S. Hahn
- Junior Research Group Herpesviruses, German Primate Center, Göttingen, Germany
| | - Sebastian R. Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Metodi V. Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Georg M. N. Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Marcel A. Müller
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Berlin, Berlin, Germany
| | - Onnen Mörer
- Department of Anesthesiology, University of Göttingen Medical Center, Göttingen, Georg-August University of Göttingen, Göttingen, Germany
| | - Martin Sebastian Winkler
- Department of Anesthesiology, University of Göttingen Medical Center, Göttingen, Georg-August University of Göttingen, Göttingen, Germany
| | - ZhaoHui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
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28
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Yang M, Li Z, Chen J, Li Y, Xu R, Wang M, Xu Y, Chen R, Ji W, Li X, Wei J, Zhou Z, Ren M, Ma K, Guan J, Mo G, Zhou P, Shu B, Guo J, Yuan Y, Shi ZL, Zhang S. Structural basis for human DPP4 receptor recognition by a pangolin MERS-like coronavirus. PLoS Pathog 2024; 20:e1012695. [PMID: 39514585 DOI: 10.1371/journal.ppat.1012695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 11/20/2024] [Accepted: 10/24/2024] [Indexed: 11/16/2024] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) and the pangolin MERS-like coronavirus MjHKU4r-CoV-1 employ dipeptidyl peptidase 4 (DPP4) as an entry receptor. MjHKU4r-CoV-1 could infect transgenic mice expressing human DPP4. To understand the mechanism of MjHKU4r-CoV-1 entry into cells, we determined the crystal structures of the receptor binding domain (RBD) of MjHKU4r-CoV-1 spike protein bound to human DPP4 (hDPP4) and Malayan pangolin DPP4 (MjDPP4), respectively. The overall hDPP4-binding mode of MjHKU4r-CoV-1 RBD is similar to that of MERS-CoV RBD. MjHKU4r-CoV-1 RBD shows higher binding affinity to hDPP4 compared to the bat MERS-like coronavirus Ty-BatCoV-HKU4. Via swapping residues between MjHKU4r-CoV-1 RBD and Ty-BatCoV-HKU4 RBD, we identified critical determinants on MjHKU4r-CoV-1 that are responsible for virus usage of hDPP4. Our study suggests that MjHKU4r-CoV-1 is more adapted to the human receptor compared to the bat HKU4 coronavirus and highlights the potential of virus emergence into the human population.
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Affiliation(s)
- Mo Yang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zehou Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jing Chen
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yang Li
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ran Xu
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Meihua Wang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ying Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Rong Chen
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, China
| | - Weiwei Ji
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxia Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiayu Wei
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhengrong Zhou
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Minjie Ren
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ke Ma
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiayu Guan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Guoxiang Mo
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Peng Zhou
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Bo Shu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Yuan Yuan
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Zheng-Li Shi
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Shuijun Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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29
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Si JY, Chen YM, Sun YH, Gu MX, Huang ML, Shi LL, Yu X, Yang X, Xiong Q, Ma CB, Liu P, Shi ZL, Yan H. Sarbecovirus RBD indels and specific residues dictating multi-species ACE2 adaptiveness. Nat Commun 2024; 15:8869. [PMID: 39402048 PMCID: PMC11473667 DOI: 10.1038/s41467-024-53029-3] [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: 03/06/2024] [Accepted: 09/24/2024] [Indexed: 10/17/2024] Open
Abstract
Our comprehensive understanding of the multi-species ACE2 adaptiveness of sarbecoviruses remains elusive, particularly for those with various receptor binding motif (RBM) insertions/deletions (indels). Here, we analyzed RBM sequences from 268 sarbecoviruses categorized into four RBM indel types. We examined the ability of 20 representative sarbecovirus Spike glycoproteins (S) and derivatives in utilizing ACE2 from various bats and several other mammalian species. We reveal that sarbecoviruses with long RBMs (type-I) can achieve broad ACE2 tropism, whereas viruses with single deletions in Region 1 (type-II) or Region 2 (type-III) exhibit narrower ACE2 tropism. Sarbecoviruses with double region deletions (type-IV) completely lost ACE2 usage, which is restricted by clade-specific residues within and outside RBM. Lastly, we propose the evolution of sarbecovirus RBM indels and illustrate how loop lengths, disulfide, and residue determinants shape multi-species ACE2 adaptiveness. This study provides profound insights into the mechanisms governing ACE2 usage and spillover risks of sarbecoviruses.
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Affiliation(s)
- Jun-Yu Si
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yuan-Mei Chen
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Ye-Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Meng-Xue Gu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Mei-Ling Huang
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Lu-Lu Shi
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xiao Yu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xiao Yang
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Qing Xiong
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Cheng-Bao Ma
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Peng Liu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Zheng-Li Shi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Huan Yan
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China.
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30
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Jiang B, Yang Y, Zhao R, Chen D, Wang Y, Liu J, Long F, Chen R, Hao R. A multifunctional evanescent wave biosensor for the universal assay of SARS-CoV-2 variants and affinity analysis of coronavirus spike protein-hACE2 interactions. Biosens Bioelectron 2024; 260:116426. [PMID: 38815461 DOI: 10.1016/j.bios.2024.116426] [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: 03/26/2024] [Revised: 05/12/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024]
Abstract
The conventional detection model of passive adaptation to pathogen mutations, i.e., developing assays using corresponding antibodies or nucleic acid probes, is difficult to address frequent outbreaks of emerging infectious diseases. In particular, adaptive mutations observed in coronaviruses, which increase the affinity of the spike protein with the human cellular receptor hACE2, play pivotal roles in the transmission and immune evasion of coronaviruses. Herein, we developed a multifunctional optical fiber evanescent wave biosensor for the universal assay of coronavirus and affinity analysis of the spike protein interacting with hACE2, namely, My-SPACE. By competitively binding with Cy5.5-hACE2 between coronavirus spike proteins in mobile buffer and that modified on optical fibers from the SARS-CoV-2 wild type, My-SPACE could automatically detect SARS-CoV-2 and its variants within 10 min. My-SPACE demonstrated greater sensitivity and faster results than ELISA for SARS-CoV-2 variants, achieving 100% specificity and 94.10% sensitivity in detecting the Omicron variant in 18 clinical samples. Moreover, the interaction between hACE2 and the coronavirus spike protein was accurately characterized across SARS-CoV-2 mutants, SARS-CoV and hCoV-NL63. The accuracy of the affinity determined by My-SPACE was verified by SPR. This approach enables preliminary assessment of the transmissibility and hazards of emerging coronaviruses. The sensor fibers of My-SPACE can be reused more than 40 times, and the device is compact and easy to use; moreover, it is available as a rapid and cost-effective on-site detection tool adapted to coronavirus variability and as an effective assessment platform for early warning of coronavirus transmission risk.
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Affiliation(s)
- Bo Jiang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China
| | - Yi Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Rongtao Zhao
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Dan Chen
- School of Environment and Natural Resources, Renmin University of China, Beijing, China
| | - Yule Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Junwen Liu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China
| | - Feng Long
- School of Environment and Natural Resources, Renmin University of China, Beijing, China.
| | - Rui Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China.
| | - Rongzhang Hao
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China.
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31
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Bolinger AA, Li J, Xie X, Li H, Zhou J. Lessons learnt from broad-spectrum coronavirus antiviral drug discovery. Expert Opin Drug Discov 2024; 19:1023-1041. [PMID: 39078037 PMCID: PMC11390334 DOI: 10.1080/17460441.2024.2385598] [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: 02/22/2024] [Accepted: 07/24/2024] [Indexed: 07/31/2024]
Abstract
INTRODUCTION Highly pathogenic coronaviruses (CoVs), such as severe acute respiratory syndrome CoV (SARS-CoV), Middle East respiratory syndrome CoV (MERS-CoV), and the most recent SARS-CoV-2 responsible for the COVID-19 pandemic, pose significant threats to human populations over the past two decades. These CoVs have caused a broad spectrum of clinical manifestations ranging from asymptomatic to severe distress syndromes (ARDS), resulting in high morbidity and mortality. AREAS COVERED The accelerated advancements in antiviral drug discovery, spurred by the COVID-19 pandemic, have shed new light on the imperative to develop treatments effective against a broad spectrum of CoVs. This perspective discusses strategies and lessons learnt in targeting viral non-structural proteins, structural proteins, drug repurposing, and combinational approaches for the development of antivirals against CoVs. EXPERT OPINION Drawing lessons from the pandemic, it becomes evident that the absence of efficient broad-spectrum antiviral drugs increases the vulnerability of public health systems to the potential onslaught by highly pathogenic CoVs. The rapid and sustained spread of novel CoVs can have devastating consequences without effective and specifically targeted treatments. Prioritizing the effective development of broad-spectrum antivirals is imperative for bolstering the resilience of public health systems and mitigating the potential impact of future highly pathogenic CoVs.
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Affiliation(s)
- Andrew A. Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jun Li
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX 77555, USA
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32
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Park YJ, Liu C, Lee J, Brown JT, Ma CB, Liu P, Xiong Q, Stewart C, Addetia A, Craig CJ, Tortorici MA, Alshukari A, Starr T, Yan H, Veesler D. Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.608351. [PMID: 39253417 PMCID: PMC11383307 DOI: 10.1101/2024.08.28.608351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity with which merbecoviruses engage ACE2 and their receptor species tropism remain unknown. Here, we reveal that HKU5 enters host cells utilizing Pipistrellus abramus (P.abr) and several non-bat mammalian ACE2s through a binding mode distinct from that of any other known ACE2-using coronaviruses. These results show that several merbecovirus clades independently evolved ACE2 utilization, which appears to be a broadly shared property among these pathogens, through an extraordinary diversity of ACE2 recognition modes. We show that MERS-CoV and HKU5 have markedly distinct antigenicity, due to extensive genetic divergence, and identified several HKU5 inhibitors, including two clinical compounds. Our findings profoundly alter our understanding of coronavirus evolution and pave the way for developing countermeasures against viruses poised for human emergence.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA
| | - Chen Liu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Jimin Lee
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Jack T Brown
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Chen-Bao Ma
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Peng Liu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Qing Xiong
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Cameron Stewart
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Caroline J. Craig
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | | | - Abeer Alshukari
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Tyler Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Huan Yan
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - David Veesler
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA
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Addetia A, Stewart C, Seo AJ, Sprouse KR, Asiri AY, Al-Mozaini M, Memish ZA, Alshukairi AN, Veesler D. Mapping immunodominant sites on the MERS-CoV spike glycoprotein targeted by infection-elicited antibodies in humans. Cell Rep 2024; 43:114530. [PMID: 39058596 DOI: 10.1016/j.celrep.2024.114530] [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: 03/26/2024] [Revised: 05/31/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) first emerged in 2012 and causes human infections in endemic regions. Vaccines and therapeutics in development against MERS-CoV focus on the spike (S) glycoprotein to prevent viral entry into target cells. These efforts are limited by a poor understanding of antibody responses elicited by infection. Here, we analyze S-directed antibody responses in plasma collected from MERS-CoV-infected individuals. We observe that binding and neutralizing antibodies peak 1-6 weeks after symptom onset/hospitalization, persist for at least 6 months, and neutralize human and camel MERS-CoV strains. We show that the MERS-CoV S1 subunit is immunodominant and that antibodies targeting S1, particularly the receptor-binding domain (RBD), account for most plasma neutralizing activity. Antigenic site mapping reveals that plasma antibodies frequently target RBD epitopes, whereas targeting of S2 subunit epitopes is rare. Our data reveal the humoral immune responses elicited by MERS-CoV infection, which will guide vaccine and therapeutic design.
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Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA; Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Albert J Seo
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ayed Y Asiri
- Al-Hayat National Hospital, Riyadh, Saudi Arabia
| | - Maha Al-Mozaini
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ziad A Memish
- King Saud Medical City, Ministry of Health, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA; Kyung Hee University, Seoul, South Korea
| | - Abeer N Alshukairi
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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Catanzaro NJ, Wu Z, Fan C, Schäfer A, Yount BL, Bjorkman PJ, Baric R, Letko M. ACE2 from Pipistrellus abramus bats is a receptor for HKU5 coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584892. [PMID: 38559009 PMCID: PMC10980018 DOI: 10.1101/2024.03.13.584892] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The merbecovirus subgenus of coronaviruses includes Middle East Respiratory Syndrome Coronavirus (MERS-CoV), a zoonotic pathogen transmitted from dromedary camels to humans that causes severe respiratory disease. Viral discovery efforts have uncovered hundreds of merbecoviruses in different species across multiple continents, but few have been studied under laboratory conditions, leaving basic questions regarding their human threat potential unresolved. Viral entry into host cells is a critical step for transmission between hosts. Here, a scalable approach that assesses novel merbecovirus cell entry was developed and used to evaluate receptor use across the entire merbecovirus subgenus. Merbecoviruses are sorted into clades based on the receptor-binding domain of the spike glycoprotein. Receptor tropism is clade-specific, with the clade including MERS-CoV using DPP4 and multiple clades using ACE2, including HKU5 bat coronaviruses. Mutational analysis identified possible structural limitations to HKU5 adaptability and a cryo-EM structure of the HKU5-20s spike trimer revealed only 'down' RBDs.
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Affiliation(s)
- Nicholas J. Catanzaro
- Department of Epidemiology, Gillings School of Global Public Heath, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Ziyan Wu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Alexandra Schäfer
- Department of Epidemiology, Gillings School of Global Public Heath, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Boyd L. Yount
- Department of Epidemiology, Gillings School of Global Public Heath, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Ralph Baric
- Department of Epidemiology, Gillings School of Global Public Heath, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Michael Letko
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, 99163
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35
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Ren X, Sun J, Kuang W, Yu F, Wang B, Wang Y, Deng W, Xu Z, Yang S, Wang H, Hu Y, Deng Z, Ning YJ, Zhao H. A broadly protective antibody targeting glycoprotein Gn inhibits severe fever with thrombocytopenia syndrome virus infection. Nat Commun 2024; 15:7009. [PMID: 39147753 PMCID: PMC11327358 DOI: 10.1038/s41467-024-51108-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: 02/15/2024] [Accepted: 07/29/2024] [Indexed: 08/17/2024] Open
Abstract
Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging bunyavirus that causes severe viral hemorrhagic fever and thrombocytopenia syndrome with a fatality rate of up to 30%. No licensed vaccines or therapeutics are currently available for humans. Here, we develop seven monoclonal antibodies (mAbs) against SFTSV surface glycoprotein Gn. Mechanistic studies show that three neutralizing mAbs (S2A5, S1G3, and S1H7) block multiple steps during SFTSV infection, including viral attachment and membrane fusion, whereas another neutralizing mAb (B1G11) primarily inhibits the viral attachment step. Epitope binning and X-ray crystallographic analyses reveal four distinct antigenic sites on Gn, three of which have not previously been reported, corresponding to domain I, domain II, and spanning domain I and domain II. One of the most potent neutralizing mAbs, S2A5, binds to a conserved epitope on Gn domain I and broadly neutralizes infection of six SFTSV strains corresponding to genotypes A to F. A single dose treatment of S2A5 affords both pre- and post-exposure protection of mice against lethal SFTSV challenge without apparent weight loss. Our results support the importance of glycoprotein Gn for eliciting a robust humoral response and pave a path for developing prophylactic and therapeutic antibodies against SFTSV infection.
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Affiliation(s)
- Xuanxiu Ren
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Jiawen Sun
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenhua Kuang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Feiyang Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Bingjie Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yong Wang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Deng
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhao Xu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shangyu Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Hualin Wang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, China
| | - Yangbo Hu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, China
| | - Zengqin Deng
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.
- Hubei Jiangxia Laboratory, Wuhan, Hubei, China.
| | - Yun-Jia Ning
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.
- Hubei Jiangxia Laboratory, Wuhan, Hubei, China.
| | - Haiyan Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.
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36
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Gagne M, Flynn BJ, Honeycutt CC, Flebbe DR, Andrew SF, Provost SJ, McCormick L, Van Ry A, McCarthy E, Todd JPM, Bao S, Teng IT, Marciano S, Rudich Y, Li C, Jain S, Wali B, Pessaint L, Dodson A, Cook A, Lewis MG, Andersen H, Zahradník J, Suthar MS, Nason MC, Foulds KE, Kwong PD, Roederer M, Schreiber G, Seder RA, Douek DC. Variant-proof high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways. Nat Commun 2024; 15:6894. [PMID: 39134521 PMCID: PMC11319446 DOI: 10.1038/s41467-024-51046-w] [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: 11/21/2023] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
SARS-CoV-2 has the capacity to evolve mutations that escape vaccine- and infection-acquired immunity and antiviral drugs. A variant-agnostic therapeutic agent that protects against severe disease without putting selective pressure on the virus would thus be a valuable biomedical tool that would maintain its efficacy despite the ongoing emergence of new variants. Here, we challenge male rhesus macaques with SARS-CoV-2 Delta-the most pathogenic variant in a highly susceptible animal model. At the time of challenge, we also treat the macaques with aerosolized RBD-62, a protein developed through multiple rounds of in vitro evolution of SARS-CoV-2 RBD to acquire 1000-fold enhanced ACE2 binding affinity. RBD-62 treatment equivalently suppresses virus replication in both upper and lower airways, a phenomenon not previously observed with clinically approved vaccines. Importantly, RBD-62 does not block the development of virus-specific T- and B-cell responses and does not elicit anti-drug immunity. These data provide proof-of-concept that RBD-62 can prevent severe disease from a highly virulent variant.
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Affiliation(s)
- Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Barbara J Flynn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Cole Honeycutt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dillon R Flebbe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shayne F Andrew
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samantha J Provost
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lauren McCormick
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Elizabeth McCarthy
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Fred Hutch Cancer Center, Seattle, WA, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Saran Bao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shir Marciano
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Chunlin Li
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shilpi Jain
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | - Bushra Wali
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | | | | | | | | | | | - Jiří Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mehul S Suthar
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Martha C Nason
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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37
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McCallum M, Park YJ, Stewart C, Sprouse KR, Addetia A, Brown J, Tortorici MA, Gibson C, Wong E, Ieven M, Telenti A, Veesler D. Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. Cell 2024; 187:4231-4245.e13. [PMID: 38964328 DOI: 10.1016/j.cell.2024.06.006] [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: 01/02/2024] [Revised: 04/26/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. We designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2, providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among orthologous proteases. We identified TMPRSS2 orthologs from five mammalian orders promoting HKU1 S-mediated entry into cells along with key residues governing host receptor usage. Our data show that the TMPRSS2 binding motif is a site of vulnerability to neutralizing antibodies and suggest that HKU1 uses S conformational masking and glycan shielding to balance immune evasion and receptor engagement.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Cecily Gibson
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Emily Wong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Margareta Ieven
- Laboratory of Clinical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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38
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Leekha A, Saeedi A, Sefat KMSR, Kumar M, Martinez-Paniagua M, Damian A, Kulkarni R, Reichel K, Rezvan A, Masoumi S, Liu X, Cooper LJN, Sebastian M, Sands CM, Das VE, Patel NB, Hurst B, Varadarajan N. Multi-antigen intranasal vaccine protects against challenge with sarbecoviruses and prevents transmission in hamsters. Nat Commun 2024; 15:6193. [PMID: 39043645 PMCID: PMC11266618 DOI: 10.1038/s41467-024-50133-2] [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: 08/01/2023] [Accepted: 07/01/2024] [Indexed: 07/25/2024] Open
Abstract
Immunization programs against SARS-CoV-2 with commercial intramuscular vaccines prevent disease but are less efficient in preventing infections. Mucosal vaccines can provide improved protection against transmission, ideally for different variants of concern (VOCs) and related sarbecoviruses. Here, we report a multi-antigen, intranasal vaccine, NanoSTING-SN (NanoSTING-Spike-Nucleocapsid), eliminates virus replication in both the lungs and the nostrils upon challenge with the pathogenic SARS-CoV-2 Delta VOC. We further demonstrate that NanoSTING-SN prevents transmission of the SARS-CoV-2 Omicron VOC (BA.5) to vaccine-naïve hamsters. To evaluate protection against other sarbecoviruses, we immunized mice with NanoSTING-SN. We showed that immunization affords protection against SARS-CoV, leading to protection from weight loss and 100% survival in mice. In non-human primates, animals immunized with NanoSTING-SN show durable serum IgG responses (6 months) and nasal wash IgA responses cross-reactive to SARS-CoV-2 (XBB1.5), SARS-CoV and MERS-CoV antigens. These observations have two implications: (1) mucosal multi-antigen vaccines present a pathway to reducing transmission of respiratory viruses, and (2) eliciting immunity against multiple antigens can be advantageous in engineering pan-sarbecovirus vaccines.
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Affiliation(s)
- Ankita Leekha
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Arash Saeedi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - K M Samiur Rahman Sefat
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Monish Kumar
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Melisa Martinez-Paniagua
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Adrian Damian
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Rohan Kulkarni
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Kate Reichel
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Ali Rezvan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Shalaleh Masoumi
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Xinli Liu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | | | | | | | - Vallabh E Das
- College of Optometry, University of Houston, Houston, TX, USA
| | - Nimesh B Patel
- College of Optometry, University of Houston, Houston, TX, USA
| | - Brett Hurst
- Institute of Antiviral Research, Utah State University, UT, Logan, USA
| | - Navin Varadarajan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
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Padín JF, Pérez-Ortiz JM, Redondo-Calvo FJ. Aprotinin (II): Inhalational Administration for the Treatment of COVID-19 and Other Viral Conditions. Int J Mol Sci 2024; 25:7209. [PMID: 39000315 PMCID: PMC11241800 DOI: 10.3390/ijms25137209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Aprotinin is a broad-spectrum inhibitor of human proteases that has been approved for the treatment of bleeding in single coronary artery bypass surgery because of its potent antifibrinolytic actions. Following the outbreak of the COVID-19 pandemic, there was an urgent need to find new antiviral drugs. Aprotinin is a good candidate for therapeutic repositioning as a broad-spectrum antiviral drug and for treating the symptomatic processes that characterise viral respiratory diseases, including COVID-19. This is due to its strong pharmacological ability to inhibit a plethora of host proteases used by respiratory viruses in their infective mechanisms. The proteases allow the cleavage and conformational change of proteins that make up their viral capsid, and thus enable them to anchor themselves by recognition of their target in the epithelial cell. In addition, the activation of these proteases initiates the inflammatory process that triggers the infection. The attraction of the drug is not only its pharmacodynamic characteristics but also the possibility of administration by the inhalation route, avoiding unwanted systemic effects. This, together with the low cost of treatment (≈2 Euro/dose), makes it a good candidate to reach countries with lower economic means. In this article, we will discuss the pharmacodynamic, pharmacokinetic, and toxicological characteristics of aprotinin administered by the inhalation route; analyse the main advances in our knowledge of this medication; and the future directions that should be taken in research in order to reposition this medication in therapeutics.
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Affiliation(s)
- Juan-Fernando Padín
- Department of Medical Sciences, School of Medicine at Ciudad Real, University of Castilla-La Mancha, 13971 Ciudad Real, Spain
| | - José Manuel Pérez-Ortiz
- Facultad HM de Ciencias de la Salud, Universidad Camilo José Cela, 28692 Madrid, Spain
- Instituto de Investigación Sanitaria HM Hospitales, 28015 Madrid, Spain
| | - Francisco Javier Redondo-Calvo
- Department of Medical Sciences, School of Medicine at Ciudad Real, University of Castilla-La Mancha, 13971 Ciudad Real, Spain
- Department of Anaesthesiology and Critical Care Medicine, University General Hospital, 13005 Ciudad Real, Spain
- Translational Research Unit, University General Hospital and Research Institute of Castilla-La Mancha (IDISCAM), 13005 Ciudad Real, Spain
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Wang Y, Hao A, Ji P, Ma Y, Zhang Z, Chen J, Mao Q, Xiong X, Rehati P, Wang Y, Wang Y, Wen Y, Lu L, Chen Z, Zhao J, Wu F, Huang J, Sun L. A bispecific antibody exhibits broad neutralization against SARS-CoV-2 Omicron variants XBB.1.16, BQ.1.1 and sarbecoviruses. Nat Commun 2024; 15:5127. [PMID: 38879565 PMCID: PMC11180174 DOI: 10.1038/s41467-024-49096-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 05/22/2024] [Indexed: 06/19/2024] Open
Abstract
The Omicron subvariants BQ.1.1, XBB.1.5, and XBB.1.16 of SARS-CoV-2 are known for their adeptness at evading immune responses. Here, we isolate a neutralizing antibody, 7F3, with the capacity to neutralize all tested SARS-CoV-2 variants, including BQ.1.1, XBB.1.5, and XBB.1.16. 7F3 targets the receptor-binding motif (RBM) region and exhibits broad binding to a panel of 37 RBD mutant proteins. We develop the IgG-like bispecific antibody G7-Fc using 7F3 and the cross-neutralizing antibody GW01. G7-Fc demonstrates robust neutralizing activity against all 28 tested SARS-CoV-2 variants and sarbecoviruses, providing potent prophylaxis and therapeutic efficacy against XBB.1 infection in both K18-ACE and BALB/c female mice. Cryo-EM structure analysis of the G7-Fc in complex with the Omicron XBB spike (S) trimer reveals a trimer-dimer conformation, with G7-Fc synergistically targeting two distinct RBD epitopes and blocking ACE2 binding. Comparative analysis of 7F3 and LY-CoV1404 epitopes highlights a distinct and highly conserved epitope in the RBM region bound by 7F3, facilitating neutralization of the immune-evasive Omicron variant XBB.1.16. G7-Fc holds promise as a potential prophylactic countermeasure against SARS-CoV-2, particularly against circulating and emerging variants.
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Affiliation(s)
- Yingdan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Aihua Hao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ping Ji
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yunping Ma
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiali Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qiyu Mao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xinyi Xiong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Palizhati Rehati
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yajie Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yumei Wen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhenguo Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Fan Wu
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai, China.
| | - Jinghe Huang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China.
- Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Lei Sun
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China.
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Shen X, Wang S, Hao Y, Fu Y, Ren L, Li D, Tang W, Li J, Chen R, Zhu M, Wang S, Liu Y, Shao Y. DNA vaccine prime and replicating vaccinia vaccine boost induce robust humoral and cellular immune responses against MERS-CoV in mice. Virol Sin 2024; 39:490-500. [PMID: 38768713 PMCID: PMC11279798 DOI: 10.1016/j.virs.2024.05.005] [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: 11/04/2023] [Accepted: 05/15/2024] [Indexed: 05/22/2024] Open
Abstract
As of December 2022, 2603 laboratory-identified Middle East respiratory syndrome coronavirus (MERS-CoV) infections and 935 associated deaths, with a mortality rate of 36%, had been reported to the World Health Organization (WHO). However, there are still no vaccines for MERS-CoV, which makes the prevention and control of MERS-CoV difficult. In this study, we generated two DNA vaccine candidates by integrating MERS-CoV Spike (S) gene into a replicating Vaccinia Tian Tan (VTT) vector. Compared to homologous immunization with either vaccine, mice immunized with DNA vaccine prime and VTT vaccine boost exhibited much stronger and durable humoral and cellular immune responses. The immunized mice produced robust binding antibodies and broad neutralizing antibodies against the EMC2012, England1 and KNIH strains of MERS-CoV. Prime-Boost immunization also induced strong MERS-S specific T cells responses, with high memory and poly-functional (CD107a-IFN-γ-TNF-α) effector CD8+ T cells. In conclusion, the research demonstrated that DNA-Prime/VTT-Boost strategy could elicit robust and balanced humoral and cellular immune responses against MERS-CoV-S. This study not only provides a promising set of MERS-CoV vaccine candidates, but also proposes a heterologous sequential immunization strategy worthy of further development.
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MESH Headings
- Animals
- Vaccines, DNA/immunology
- Vaccines, DNA/administration & dosage
- Vaccines, DNA/genetics
- Middle East Respiratory Syndrome Coronavirus/immunology
- Middle East Respiratory Syndrome Coronavirus/genetics
- Immunity, Cellular
- Antibodies, Viral/blood
- Mice
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Immunity, Humoral
- Viral Vaccines/immunology
- Viral Vaccines/administration & dosage
- Viral Vaccines/genetics
- Female
- Coronavirus Infections/prevention & control
- Coronavirus Infections/immunology
- Mice, Inbred BALB C
- CD8-Positive T-Lymphocytes/immunology
- Vaccinia virus/genetics
- Vaccinia virus/immunology
- Immunization, Secondary
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
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Affiliation(s)
- Xiuli Shen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shuhui Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanling Hao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yuyu Fu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Li Ren
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Dan Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Wenqi Tang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jing Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ran Chen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Meiling Zhu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shuo Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ying Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Yiming Shao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China; State 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, School of Medicine, Zhejiang University, Hangzhou 310003, China.
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Zumla A, Peiris M, Memish ZA, Perlman S. Anticipating a MERS-like coronavirus as a potential pandemic threat. Lancet 2024; 403:1729-1731. [PMID: 38604210 DOI: 10.1016/s0140-6736(24)00641-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024]
Affiliation(s)
- Alimuddin Zumla
- Department of Infection, Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, London, UK; NIHR Biomedical Research Centre, University College London Hospitals, London, UK
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong Special Administrative Region, China
| | - Ziad A Memish
- Research and Innovation Center, King Saud Medical City, Ministry of Health and College of Medicine, Al Faisal University, Riyadh, Saudi Arabia; Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA; Division of Infectious Diseases, Kyung Hee University, Seoul, South Korea
| | - Stanley Perlman
- Department of Microbiology and Immunology and Department of Pediatrics, University of Iowa, Iowa City, IA 52246, USA.
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Tolentino JE, Lytras S, Ito J, Sato K. Recombination analysis on the receptor switching event of MERS-CoV and its close relatives: implications for the emergence of MERS-CoV. Virol J 2024; 21:84. [PMID: 38600521 PMCID: PMC11008012 DOI: 10.1186/s12985-024-02358-2] [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: 11/21/2023] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND PlMERS-CoV is a coronavirus known to cause severe disease in humans, taxonomically classified under the subgenus Merbecovirus. Recent findings showed that the close relatives of MERS-CoV infecting vespertillionid bats (family Vespertillionidae), named NeoCoV and PDF-2180, use their hosts' ACE2 as their entry receptor, unlike the DPP4 receptor usage of MERS-CoV. Previous research suggests that this difference in receptor usage between these related viruses is a result of recombination. However, the precise location of the recombination breakpoints and the details of the recombination event leading to the change of receptor usage remain unclear. METHODS We used maximum likelihood-based phylogenetics and genetic similarity comparisons to characterise the evolutionary history of all complete Merbecovirus genome sequences. Recombination events were detected by multiple computational methods implemented in the recombination detection program. To verify the influence of recombination, we inferred the phylogenetic relation of the merbecovirus genomes excluding recombinant segments and that of the viruses' receptor binding domains and examined the level of congruency between the phylogenies. Finally, the geographic distribution of the genomes was inspected to identify the possible location where the recombination event occurred. RESULTS Similarity plot analysis and the recombination-partitioned phylogenetic inference showed that MERS-CoV is highly similar to NeoCoV (and PDF-2180) across its whole genome except for the spike-encoding region. This is confirmed to be due to recombination by confidently detecting a recombination event between the proximal ancestor of MERS-CoV and a currently unsampled merbecovirus clade. Notably, the upstream recombination breakpoint was detected in the N-terminal domain and the downstream breakpoint at the S2 subunit of spike, indicating that the acquired recombined fragment includes the receptor-binding domain. A tanglegram comparison further confirmed that the receptor binding domain-encoding region of MERS-CoV was acquired via recombination. Geographic mapping analysis on sampling sites suggests the possibility that the recombination event occurred in Africa. CONCLUSION Together, our results suggest that recombination can lead to receptor switching of merbecoviruses during circulation in bats. These results are useful for future epidemiological assessments and surveillance to understand the spillover risk of bat coronaviruses to the human population.
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Affiliation(s)
- Jarel Elgin Tolentino
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Spyros Lytras
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
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Addetia A, Stewart C, Seo AJ, Sprouse KR, Asiri AY, Al-Mozaini M, Memish ZA, Alshukairi A, Veesler D. Mapping immunodominant sites on the MERS-CoV spike glycoprotein targeted by infection-elicited antibodies in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.586409. [PMID: 38617298 PMCID: PMC11014493 DOI: 10.1101/2024.03.31.586409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Middle-East respiratory syndrome coronavirus (MERS-CoV) first emerged in 2012 and causes human infections in endemic regions. Most vaccines and therapeutics in development against MERS-CoV focus on the spike (S) glycoprotein to prevent viral entry into target cells. These efforts, however, are limited by a poor understanding of antibody responses elicited by infection along with their durability, fine specificity and contribution of distinct S antigenic sites to neutralization. To address this knowledge gap, we analyzed S-directed binding and neutralizing antibody titers in plasma collected from individuals infected with MERS-CoV in 2017-2019 (prior to the COVID-19 pandemic). We observed that binding and neutralizing antibodies peak 1 to 6 weeks after symptom onset/hospitalization, persist for at least 6 months, and broadly neutralize human and camel MERS-CoV strains. We show that the MERS-CoV S1 subunit is immunodominant and that antibodies targeting S1, particularly the RBD, account for most plasma neutralizing activity. Antigenic site mapping revealed that polyclonal plasma antibodies frequently target RBD epitopes, particularly a site exposed irrespective of the S trimer conformation, whereas targeting of S2 subunit epitopes is rare, similar to SARS-CoV-2. Our data reveal in unprecedented details the humoral immune responses elicited by MERS-CoV infection, which will guide vaccine and therapeutic design.
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Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Albert J Seo
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ayed Y Asiri
- Al-Hayat National Hospital, Riyadh, Saudi Arabia
| | - Maha Al-Mozaini
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ziad A Memish
- King Saud Medical City, Ministry of Health, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Kyung Hee University, Seoul, South Korea
| | - Abeer Alshukairi
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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Sun L, Man Q, Zhang H, Xia S, Lu L, Wang X, Xiong L, Jiang S. Strong cross immune responses against sarbecoviruses but not merbecoviruses in SARS-CoV-2 BA.5/BF.7-infected individuals with or without inactivated COVID-19 vaccination. J Infect 2024; 88:106138. [PMID: 38490275 DOI: 10.1016/j.jinf.2024.106138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/04/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Affiliation(s)
- Lujia Sun
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Qiuhong Man
- Department of Laboratory Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Hui Zhang
- Department of Laboratory Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Shuai Xia
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lu Lu
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xinling Wang
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Lize Xiong
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Shibo Jiang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
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Maity S, Acharya A. Many Roles of Carbohydrates: A Computational Spotlight on the Coronavirus S Protein Binding. ACS APPLIED BIO MATERIALS 2024; 7:646-656. [PMID: 36947738 PMCID: PMC10880061 DOI: 10.1021/acsabm.2c01064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 03/24/2023]
Abstract
Glycosylation is one of the post-translational modifications with more than 50% of human proteins being glycosylated. The exact nature and chemical composition of glycans are inaccessible to X-ray or cryo-electron microscopy imaging techniques. Therefore, computational modeling studies and molecular dynamics must be used as a "computational microscope". The spike (S) protein of SARS-CoV-2 is heavily glycosylated, and a few glycans play a more functional role "beyond shielding". In this mini-review, we discuss computational investigations of the roles of specific S-protein and ACE2 glycans in the overall ACE2-S protein binding. We highlight different functions of specific glycans demonstrated in myriad computational models and simulations in the context of the SARS-CoV-2 virus binding to the receptor. We also discuss interactions between glycocalyx and the S protein, which may be utilized to design prophylactic polysaccharide-based therapeutics targeting the S protein. In addition, we underline the recent emergence of coronavirus variants and their impact on the S protein and its glycans.
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Affiliation(s)
- Suman Maity
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Atanu Acharya
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse, Syracuse University, Syracuse, New York 13244, United States
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Xia LY, Wang ZF, Cui XM, Li YG, Ye RZ, Zhu DY, Li FX, Zhang J, Wang WH, Zhang MZ, Gao WY, Li LF, Que TC, Wang TC, Jia N, Jiang JF, Gao YW, Cao WC. Isolation and characterization of a pangolin-borne HKU4-related coronavirus that potentially infects human-DPP4-transgenic mice. Nat Commun 2024; 15:1048. [PMID: 38316817 PMCID: PMC10844334 DOI: 10.1038/s41467-024-45453-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 01/23/2024] [Indexed: 02/07/2024] Open
Abstract
We recently detected a HKU4-related coronavirus in subgenus Merbecovirus (named pangolin-CoV-HKU4-P251T) from a Malayan pangolin1. Here we report isolation and characterization of pangolin-CoV-HKU4-P251T, the genome sequence of which is closest to that of a coronavirus from the greater bamboo bat (Tylonycteris robustula) in Yunnan Province, China, with a 94.3% nucleotide identity. Pangolin-CoV-HKU4-P251T is able to infect human cell lines, and replicates more efficiently in cells that express human-dipeptidyl-peptidase-4 (hDPP4)-expressing and pangolin-DPP4-expressing cells than in bat-DPP4-expressing cells. After intranasal inoculation with pangolin-CoV-HKU4-P251, hDPP4-transgenic female mice are likely infected, showing persistent viral RNA copy numbers in the lungs. Progressive interstitial pneumonia developed in the infected mice, characterized by the accumulation of macrophages, and increase of antiviral cytokines, proinflammatory cytokines, and chemokines in lung tissues. These findings suggest that the pangolin-borne HKU4-related coronavirus has a potential for emerging as a human pathogen by using hDPP4.
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Affiliation(s)
- Luo-Yuan Xia
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, P. R. China
| | - Zhen-Fei Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, P. R. China
- Changchun Veterinary Research Institute, Changchun, 130122, Jilin, P. R. China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, P. R. China
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, 100071, P. R. China
| | - Yuan-Guo Li
- Changchun Veterinary Research Institute, Changchun, 130122, Jilin, P. R. China
| | - Run-Ze Ye
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, P. R. China
| | - Dai-Yun Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, P. R. China
| | - Fang-Xu Li
- Changchun Veterinary Research Institute, Changchun, 130122, Jilin, P. R. China
| | - Jie Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, P. R. China
| | - Wen-Hao Wang
- Changchun Veterinary Research Institute, Changchun, 130122, Jilin, P. R. China
| | - Ming-Zhu Zhang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, P. R. China
| | - Wan-Ying Gao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, P. R. China
| | - Lian-Feng Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, P. R. China
| | - Teng-Cheng Que
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, P. R. China
| | - Tie-Cheng Wang
- Changchun Veterinary Research Institute, Changchun, 130122, Jilin, P. R. China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, P. R. China
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, 100071, P. R. China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, P. R. China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, 100071, P. R. China.
| | - Yu-Wei Gao
- Changchun Veterinary Research Institute, Changchun, 130122, Jilin, P. R. China.
| | - Wu-Chun Cao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, P. R. China.
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, P. R. China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, 100071, P. R. China.
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48
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Xiong Q, Ma C, Liu C, Tong F, Huang M, Yan H. ACE2-using merbecoviruses: Further evidence of convergent evolution of ACE2 recognition by NeoCoV and other MERS-CoV related viruses. CELL INSIGHT 2024; 3:100145. [PMID: 38476250 PMCID: PMC10928290 DOI: 10.1016/j.cellin.2023.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 03/14/2024]
Abstract
Angiotensin-converting enzyme 2 (ACE2) was recognized as an entry receptor shared by coronaviruses from Sarbecovirus and Setracovirus subgenera, including three human coronaviruses: SARS-CoV, SARS-CoV-2, and NL63. We recently disclosed that NeoCoV and three other merbecoviruses (PDF-2180, MOW15-22, PnNL 2018B), which are MERS-CoV relatives found in African and European bats, also utilize ACE2 as their functional receptors through unique receptor binding mechanisms. This unexpected receptor usage assumes significance, particularly in light of the prior recognition of Dipeptidyl peptidase-4 (DPP4) as the only known protein receptor for merbecoviruses. In contrast to other ACE2-using coronaviruses, NeoCoV and PDF-2180 engage a distinct and relatively compact binding surface on ACE2, facilitated by protein-glycan interactions, which is demonstrated by the Cryo-EM structures of the receptor binding domains (RBDs) of these viruses in complex with a bat ACE2 orthologue. These findings further support the hypothesis that phylogenetically distant coronaviruses, characterized by distinct RBD structures, can independently evolve to acquire ACE2 affinity during inter-species transmission and adaptive evolution. To date, these viruses have exhibited limited efficiency in entering human cells, although single mutations like T510F in NeoCoV can overcome the incompatibility with human ACE2. In this review, we present a comprehensive overview of ACE2-using merbecoviruses, summarize our current knowledge regarding receptor usage and host tropism determination, and deliberate on potential strategies for prevention and intervention, with the goal of mitigating potential future outbreaks caused by spillover of these viruses.
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Affiliation(s)
- Qing Xiong
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Chengbao Ma
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Chen Liu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Fei Tong
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Meiling Huang
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Huan Yan
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
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Barros ALAN, Silva VC, Ribeiro-Junior AF, Cardoso MG, Costa SR, Moraes CB, Barbosa CG, Coleone AP, Simões RP, Cabral WF, Falcão RM, Vasconcelos AG, Rocha JA, Arcanjo DDR, Batagin-Neto A, Borges TKS, Gonçalves J, Brand GD, Freitas-Junior LHG, Eaton P, Marani M, Kato MJ, Plácido A, Leite JRSA. Antiviral Action against SARS-CoV-2 of a Synthetic Peptide Based on a Novel Defensin Present in the Transcriptome of the Fire Salamander ( Salamandra salamandra). Pharmaceutics 2024; 16:190. [PMID: 38399250 PMCID: PMC10892092 DOI: 10.3390/pharmaceutics16020190] [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: 12/14/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The potential emergence of zoonotic diseases has raised significant concerns, particularly in light of the recent pandemic, emphasizing the urgent need for scientific preparedness. The bioprospection and characterization of new molecules are strategically relevant to the research and development of innovative drugs for viral and bacterial treatment and disease management. Amphibian species possess a diverse array of compounds, including antimicrobial peptides. This study identified the first bioactive peptide from Salamandra salamandra in a transcriptome analysis. The synthetic peptide sequence, which belongs to the defensin family, was characterized through MALDI TOF/TOF mass spectrometry. Molecular docking assays hypothesized the interaction between the identified peptide and the active binding site of the spike WT RBD/hACE2 complex. Although additional studies are required, the preliminary evaluation of the antiviral potential of synthetic SS-I was conducted through an in vitro cell-based SARS-CoV-2 infection assay. Additionally, the cytotoxic and hemolytic effects of the synthesized peptide were assessed. These preliminary findings highlighted the potential of SS-I as a chemical scaffold for drug development against COVID-19, hindering viral infection. The peptide demonstrated hemolytic activity while not exhibiting cytotoxicity at the antiviral concentration.
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Affiliation(s)
- Ana Luisa A N Barros
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
- Programa de Pós-graduação em Medicina Tropical, PGMT, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Vladimir C Silva
- Laboratório de Vigilância Genômica e Biologia Molecular-Fundação Oswaldo Cruz Piauí, Teresina 64001-350, PI, Brazil
| | - Atvaldo F Ribeiro-Junior
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Miguel G Cardoso
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
- imed.ULisboa-Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, 1649-003 Lisbon, Portugal
| | - Samuel R Costa
- Instituto de Química, IQ, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Carolina B Moraes
- Department of Pharmaceutical Sciences, Federal University of São Paulo, Diadema 09913-030, SP, Brazil
| | - Cecília G Barbosa
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo 05508-000, SP, Brazil
| | - Alex P Coleone
- Programa de Pós-Graduação em Ciência e Tecnologia de Materiais (POSMAT), School of Sciences, São Paulo State University (UNESP), Bauru 17033-360, SP, Brazil
| | - Rafael P Simões
- School of Agriculture, Department of Bioprocess and Biotechnology, São Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil
| | - Wanessa F Cabral
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Raul M Falcão
- Bioinformatics Postgraduate Program, Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal 59078-900, RN, Brazil
| | - Andreanne G Vasconcelos
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
- People&Science Pesquisa Desenvolvimento e Inovação LTDA, Centro de Desenvolvimento Tecnológico (CDT), Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Jefferson A Rocha
- Campus São Bernardo, Universidade Federal do Maranhão, UFMA, São Bernardo 65550-000, MA, Brazil
| | - Daniel D R Arcanjo
- Department of Biophysics and Physiology, Federal University of Piauí, Teresina 64049-550, PI, Brazil
| | - Augusto Batagin-Neto
- Programa de Pós-Graduação em Ciência e Tecnologia de Materiais (POSMAT), School of Sciences, São Paulo State University (UNESP), Bauru 17033-360, SP, Brazil
- Institute of Sciences and Engineering, São Paulo State University (UNESP), Itapeva 18409-010, SP, Brazil
| | - Tatiana Karla S Borges
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - João Gonçalves
- imed.ULisboa-Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, 1649-003 Lisbon, Portugal
| | - Guilherme D Brand
- Instituto de Química, IQ, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Lucio H G Freitas-Junior
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo 05508-000, SP, Brazil
| | - Peter Eaton
- Laboratório Associado para a Química Verde/Rede de Química e Tecnologia (LAQV/REQUIMTE), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- School of Chemistry, The Bridge, University of Lincoln, Lincoln LN6 7EL, UK
| | - Mariela Marani
- IPEEC-CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn 9120, Argentina
| | - Massuo J Kato
- Instituto de Química (IQ), Universidade de São Paulo (USP), São Paulo 05508-900, SP, Brazil
| | - Alexandra Plácido
- Laboratório Associado para a Química Verde/Rede de Química e Tecnologia (LAQV/REQUIMTE), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - José Roberto S A Leite
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
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50
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Zech F, Jung C, Jacob T, Kirchhoff F. Causes and Consequences of Coronavirus Spike Protein Variability. Viruses 2024; 16:177. [PMID: 38399953 PMCID: PMC10892391 DOI: 10.3390/v16020177] [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: 12/28/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Coronaviruses are a large family of enveloped RNA viruses found in numerous animal species. They are well known for their ability to cross species barriers and have been transmitted from bats or intermediate hosts to humans on several occasions. Four of the seven human coronaviruses (hCoVs) are responsible for approximately 20% of common colds (hCoV-229E, -NL63, -OC43, -HKU1). Two others (SARS-CoV-1 and MERS-CoV) cause severe and frequently lethal respiratory syndromes but have only spread to very limited extents in the human population. In contrast the most recent human hCoV, SARS-CoV-2, while exhibiting intermediate pathogenicity, has a profound impact on public health due to its enormous spread. In this review, we discuss which initial features of the SARS-CoV-2 Spike protein and subsequent adaptations to the new human host may have helped this pathogen to cause the COVID-19 pandemic. Our focus is on host forces driving changes in the Spike protein and their consequences for virus infectivity, pathogenicity, immune evasion and resistance to preventive or therapeutic agents. In addition, we briefly address the significance and perspectives of broad-spectrum therapeutics and vaccines.
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Affiliation(s)
- Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- 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; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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