1
|
Park SB, Khan M, Chiliveri SC, Hu X, Irvin P, Leek M, Grieshaber A, Hu Z, Jang ES, Bax A, Liang TJ. SARS-CoV-2 omicron variants harbor spike protein mutations responsible for their attenuated fusogenic phenotype. Commun Biol 2023; 6:556. [PMID: 37225764 DOI: 10.1038/s42003-023-04923-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/08/2023] [Indexed: 05/26/2023] Open
Abstract
Since the emergence of the Omicron variants at the end of 2021, they quickly became the dominant variants globally. The Omicron variants may be more easily transmitted compared to the earlier Wuhan and the other variants. In this study, we aimed to elucidate mechanisms of the altered infectivity associated with the Omicron variants. We systemically evaluated mutations located in the S2 sequence of spike and identified mutations that are responsible for altered viral fusion. We demonstrated that mutations near the S1/S2 cleavage site decrease S1/S2 cleavage, resulting in reduced fusogenicity. Mutations in the HR1 and other S2 sequences also affect cell-cell fusion. Based on nuclear magnetic resonance (NMR) studies and in silico modeling, these mutations affect fusogenicity possibly at multiple steps of the viral fusion. Our findings reveal that the Omicron variants have accumulated mutations that contribute to reduced syncytial formation and hence an attenuated pathogenicity.
Collapse
Affiliation(s)
- Seung Bum Park
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Mohsin Khan
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xin Hu
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, 20850, USA
| | - Parker Irvin
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Madeleine Leek
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ailis Grieshaber
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zongyi Hu
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eun Sun Jang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, 13620, Republic of Korea
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
2
|
Galão RP, Wilson H, Schierhorn KL, Debeljak F, Bodmer BS, Goldhill D, Hoenen T, Wilson SJ, Swanson CM, Neil SJD. TRIM25 and ZAP target the Ebola virus ribonucleoprotein complex to mediate interferon-induced restriction. PLoS Pathog 2022; 18:e1010530. [PMID: 35533151 PMCID: PMC9119685 DOI: 10.1371/journal.ppat.1010530] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 05/19/2022] [Accepted: 04/18/2022] [Indexed: 12/14/2022] Open
Abstract
Ebola virus (EBOV) causes highly pathogenic disease in primates. Through screening a library of human interferon-stimulated genes (ISGs), we identified TRIM25 as a potent inhibitor of EBOV transcription-and-replication-competent virus-like particle (trVLP) propagation. TRIM25 overexpression inhibited the accumulation of viral genomic and messenger RNAs independently of the RNA sensor RIG-I or secondary proinflammatory gene expression. Deletion of TRIM25 strongly attenuated the sensitivity of trVLPs to inhibition by type-I interferon. The antiviral activity of TRIM25 required ZAP and the effect of type-I interferon was modulated by the CpG dinucleotide content of the viral genome. We find that TRIM25 interacts with the EBOV vRNP, resulting in its autoubiquitination and ubiquitination of the viral nucleoprotein (NP). TRIM25 is recruited to incoming vRNPs shortly after cell entry and leads to dissociation of NP from the vRNA. We propose that TRIM25 targets the EBOV vRNP, exposing CpG-rich viral RNA species to restriction by ZAP.
Collapse
Affiliation(s)
- Rui Pedro Galão
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Harry Wilson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Kristina L. Schierhorn
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Franka Debeljak
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Bianca S. Bodmer
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Daniel Goldhill
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Thomas Hoenen
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Sam J. Wilson
- MRC Centre for Virus Research, University of Glasgow, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| |
Collapse
|
3
|
Drug Repurposing for Ebola Virus Disease: Principles of Consideration and the Animal Rule. J Pharm Sci 2018; 108:798-806. [PMID: 30244014 DOI: 10.1016/j.xphs.2018.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/29/2018] [Accepted: 09/11/2018] [Indexed: 11/21/2022]
Abstract
There are no approved drugs or biologics to treat Ebola virus disease (EVD). Literature reviews identified a list of 141 drugs with reports of preliminary in vitro potency and in vivo effectiveness in animals or with reports of clinical use/trials in EVD patients. The majority of these drugs have been individually approved by the U.S. Food and Drug Administration for treating various non-EVD diseases. The anti-Ebola potency data of these drugs were curated from literature and publicly accessible databases, along with their individual biopharmaceutical and pharmacokinetic characteristics. To facilitate the development of antiviral drugs including anti-EVD drugs, highlights include optimization of the exposure-response relationship, design of a safe and effective clinical dosing regimen to achieve an adequate high ratio of clinical Cmin to a plasma protein binding-adjusted EC95, and the pharmacokinetic studies needed in animal models (healthy and affected) and in healthy volunteers. The exposure/response relationship for human dose selection is summarized, as described in the U.S. Food and Drug Administration "Animal Rule'' guidance when human efficacy studies are not ethical or feasible.
Collapse
|
4
|
Fu B, Wang L, Li S, Dorf ME. ZMPSTE24 defends against influenza and other pathogenic viruses. J Exp Med 2017; 214:919-929. [PMID: 28246125 PMCID: PMC5379977 DOI: 10.1084/jem.20161270] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/10/2016] [Accepted: 01/25/2017] [Indexed: 12/24/2022] Open
Abstract
Fu et al. show that ZMPSTE24 is a broad-spectrum antiviral protein that inhibits entry of selected fusogenic viruses by functioning as an effector in the IFITM pathway. ZMPSTE24 protease activity is dispensable for viral restriction. In mice, ZMPSTE24 deficiency increases susceptibility to influenza infection. Zinc metallopeptidase STE24 (ZMPSTE24) is a transmembrane metalloprotease whose catalytic activity is critical for processing lamin A on the inner nuclear membrane and clearing clogged translocons on the endoplasmic reticulum. We now report ZMPSTE24 is a virus-specific effector that restricts enveloped RNA and DNA viruses, including influenza A, Zika, Ebola, Sindbis, vesicular stomatitis, cowpox, and vaccinia, but not murine leukemia or adenovirus. ZMPSTE24-mediated antiviral action is independent of protease activity. Coimmunoprecipitation studies indicate ZMPSTE24 can complex with proteins of the interferon-induced transmembrane protein (IFITM) family. IFITM proteins impede viral entry, and ZMPSTE24 expression is necessary for IFITM antiviral activity. In vivo studies demonstrate ZMPSTE24-deficient mice display higher viral burdens, enhanced cytokine production, and increased mortality after influenza infection. Collectively, these findings identify ZMPSTE24 as an intrinsic broad-spectrum antiviral protein and provide insights into antiviral defense mechanisms.
Collapse
Affiliation(s)
- Bishi Fu
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Lingyan Wang
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078
| | - Shitao Li
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078
| | - Martin E Dorf
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| |
Collapse
|
5
|
Miao C, Li M, Zheng YM, Cohen FS, Liu SL. Cell-cell contact promotes Ebola virus GP-mediated infection. Virology 2015; 488:202-15. [PMID: 26655238 DOI: 10.1016/j.virol.2015.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 10/22/2022]
Abstract
Ebola virus (EBOV) is a highly pathogenic filovirus that causes hemorrhagic fever in humans and animals. Here we provide evidence that cell-cell contact promotes infection mediated by the glycoprotein (GP) of EBOV. Interestingly, expression of EBOV GP alone, even in the absence of retroviral Gag-Pol, is sufficient to transfer a retroviral vector encoding Tet-off from cell to cell. Cell-to-cell infection mediated by EBOV GP is blocked by inhibitors of actin polymerization, but appears to be less sensitive to KZ52 neutralization. Treatment of co-cultured cells with cathepsin B/L inhibitors, or an entry inhibitor 3.47 that targets the receptor NPC1 for virus binding, also blocks cell-to-cell infection. Cell-cell contact also enhances spread of rVSV bearing GP in monocytes and macrophages, the primary targets of natural EBOV infection. Altogether, our study reveals that cell-cell contact promotes EBOV GP-mediated infection, and provides new insight into understanding EBOV spread and viral pathogenesis.
Collapse
Affiliation(s)
- Chunhui Miao
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Minghua Li
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Yi-Min Zheng
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Fredric S Cohen
- Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Shan-Lu Liu
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| |
Collapse
|
6
|
Beyleveld G, White KM, Ayllon J, Shaw ML. New-generation screening assays for the detection of anti-influenza compounds targeting viral and host functions. Antiviral Res 2013; 100:120-32. [PMID: 23933115 DOI: 10.1016/j.antiviral.2013.07.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/23/2013] [Accepted: 07/26/2013] [Indexed: 01/08/2023]
Abstract
Current options for influenza antiviral therapy are limited to the neuraminidase inhibitors, and knowledge that high levels of oseltamivir resistance have been seen among previously circulating H1N1 viruses increases the urgency to find new influenza therapeutics. To feed this pipeline, assays that are appropriate for use in high-throughput screens are being developed and are discussed in this review. Particular emphasis is placed on cell-based assays that capture both inhibitors of viral functions as well as the host functions that facilitate optimal influenza virus replication. Success in this area has been fueled by a greater understanding of the genome structure of influenza viruses and the ability to generate replication-competent recombinant viruses that carry a reporter gene, allowing for easy monitoring of viral infection in a high-throughput setting. This article forms part of a symposium in Antiviral Research on "Treatment of influenza: targeting the virus or the host."
Collapse
Affiliation(s)
- Grant Beyleveld
- Department of Microbiology and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | |
Collapse
|
7
|
Nicholls JM. The battle between influenza and the innate immune response in the human respiratory tract. Infect Chemother 2013; 45:11-21. [PMID: 24265946 PMCID: PMC3780943 DOI: 10.3947/ic.2013.45.1.11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Indexed: 12/23/2022] Open
Abstract
Influenza is a viral infection of the respiratory tract. Infection is normally confined to the upper respiratory tract but certain viral strains have evolved the ability to infect the lower respiratory tract, including the alveoli, leading to inflammation and a disease pattern of diffuse alveolar damage. Factors leading to this sequence of events are novel influenza strains, or strains that have viral proteins, in particular the NS1 protein that allow it to escape the innate immune system. There are three main barriers that prevent infection of pneumocytes - mucin, host defence lectins and cells such as macrophages. Viruses have developed strategies such as neuraminidase and glycosylation patterns that allow this evasion. Though there has been much investment in antiviral drugs, it is proposed that more attention should be directed towards developing or utilizing compounds that enhance the ability of the innate immune system to combat viral infection.
Collapse
Affiliation(s)
- John M Nicholls
- Department of Pathology, Hong Kong University, Hong Kong, Hong Kong
| |
Collapse
|