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Hamlin RE, Blish CA. Challenges and opportunities in long COVID research. Immunity 2024; 57:1195-1214. [PMID: 38865966 PMCID: PMC11210969 DOI: 10.1016/j.immuni.2024.05.010] [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: 01/02/2024] [Revised: 04/19/2024] [Accepted: 05/10/2024] [Indexed: 06/14/2024]
Abstract
Long COVID (LC) is a condition in which patients do not fully recover from the initial SARS-CoV-2 infection but rather have persistent or new symptoms for months to years following the infection. Ongoing research efforts are investigating the pathophysiologic mechanisms of LC and exploring preventative and therapeutic treatment approaches for patients. As a burgeoning area of investigation, LC research can be structured to be more inclusive, innovative, and effective. In this perspective, we highlight opportunities for patient engagement and diverse research expertise, as well as the challenges of developing definitions and reproducible studies. Our intention is to provide a foundation for collaboration and progress in understanding the biomarkers and mechanisms driving LC.
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Affiliation(s)
| | - Catherine A Blish
- Department of Medicine, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Dehghan Z, Mirmotalebisohi SA, Mozafar M, Sameni M, Saberi F, Derakhshanfar A, Moaedi J, Zohrevand H, Zali H. Deciphering the similarities and disparities of molecular mechanisms behind respiratory epithelium response to HCoV-229E and SARS-CoV-2 and drug repurposing, a systems biology approach. Daru 2024; 32:215-235. [PMID: 38652363 PMCID: PMC11087451 DOI: 10.1007/s40199-024-00507-0] [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: 09/17/2022] [Accepted: 02/08/2024] [Indexed: 04/25/2024] Open
Abstract
PURPOSE Identifying the molecular mechanisms behind SARS-CoV-2 disparities and similarities will help find new treatments. The present study determines networks' shared and non-shared (specific) crucial elements in response to HCoV-229E and SARS-CoV-2 viruses to recommend candidate medications. METHODS We retrieved the omics data on respiratory cells infected with HCoV-229E and SARS-CoV-2, constructed PPIN and GRN, and detected clusters and motifs. Using a drug-gene interaction network, we determined the similarities and disparities of mechanisms behind their host response and drug-repurposed. RESULTS CXCL1, KLHL21, SMAD3, HIF1A, and STAT1 were the shared DEGs between both viruses' protein-protein interaction network (PPIN) and gene regulatory network (GRN). The NPM1 was a specific critical node for HCoV-229E and was a Hub-Bottleneck shared between PPI and GRN in HCoV-229E. The HLA-F, ADCY5, TRIM14, RPF1, and FGA were the seed proteins in subnetworks of the SARS-CoV-2 PPI network, and HSPA1A and RPL26 proteins were the seed in subnetworks of the PPI network of HCOV-229E. TRIM14, STAT2, and HLA-F played the same role for SARS-CoV-2. Top enriched KEGG pathways included cell cycle and proteasome in HCoV-229E and RIG-I-like receptor, Chemokine, Cytokine-cytokine, NOD-like receptor, and TNF signaling pathways in SARS-CoV-2. We suggest some candidate medications for COVID-19 patient lungs, including Noscapine, Isoetharine mesylate, Cycloserine, Ethamsylate, Cetylpyridinium, Tretinoin, Ixazomib, Vorinostat, Venetoclax, Vorinostat, Ixazomib, Venetoclax, and epoetin alfa for further in-vitro and in-vivo investigations. CONCLUSION We suggested CXCL1, KLHL21, SMAD3, HIF1A, and STAT1, ADCY5, TRIM14, RPF1, and FGA, STAT2, and HLA-F as critical genes and Cetylpyridinium, Cycloserine, Noscapine, Ethamsylate, Epoetin alfa, Isoetharine mesylate, Ribavirin, and Tretinoin drugs to study further their importance in treating COVID-19 lung complications.
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Affiliation(s)
- Zeinab Dehghan
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Amir Mirmotalebisohi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Mozafar
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzieh Sameni
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Saberi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amin Derakhshanfar
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
- Center of Comparative and Experimental Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Javad Moaedi
- Center of Comparative and Experimental Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Zohrevand
- Student Research Committee, Department of Biomedical Engineering and Medical Physics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biomedical Engineering and Medical Physics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Viox EG, Bosinger SE, Douek DC, Schreiber G, Paiardini M. Harnessing the power of IFN for therapeutic approaches to COVID-19. J Virol 2024; 98:e0120423. [PMID: 38651899 PMCID: PMC11092331 DOI: 10.1128/jvi.01204-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Interferons (IFNs) are essential for defense against viral infections but also drive recruitment of inflammatory cells to sites of infection, a key feature of severe COVID-19. Here, we explore the complexity of the IFN response in COVID-19, examine the effects of manipulating IFN on SARS-CoV-2 viral replication and pathogenesis, and highlight pre-clinical and clinical studies evaluating the therapeutic efficacy of IFN in limiting COVID-19 severity.
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Affiliation(s)
- Elise G. Viox
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
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Zhao H, Jiang G, Li C, Che Y, Long R, Pu J, Zhang Y, Li D, Liao Y, Yu L, Zhao Y, Yuan M, Li Y, Fan S, Liu L, Li Q. Evaluation of Binding and Neutralizing Antibodies for Inactivated SARS-CoV-2 Vaccine Immunization. Diseases 2024; 12:67. [PMID: 38667525 PMCID: PMC11048931 DOI: 10.3390/diseases12040067] [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: 01/30/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variant presents an ongoing challenge for surveillance and detection. It is important to establish an assay for SARS-CoV-2 antibodies in vaccinated individuals. Numerous studies have demonstrated that binding antibodies (such as S-IgG and N-IgG) and neutralizing antibodies (Nabs) can be detected in vaccinated individuals. However, it is still unclear how to evaluate the consistency and correlation between binding antibodies and Nabs induced by inactivated SARS-CoV-2 vaccines. In this study, serum samples from humans, rhesus macaques, and hamsters immunized with inactivated SARS-CoV-2 vaccines were analyzed for S-IgG, N-IgG, and Nabs. The results showed that the titer and seroconversion rate of S-IgG were significantly higher than those of N-IgG. The correlation between S-IgG and Nabs was higher compared to that of N-IgG. Based on this analysis, we further investigated the titer thresholds of S-IgG and N-IgG in predicting the seroconversion of Nabs. According to the threshold, we can quickly determine the positive and negative effects of the SARS-CoV-2 variant neutralizing antibody in individuals. These findings suggest that the S-IgG antibody is a better supplement to and confirmation of SARS-CoV-2 vaccine immunization.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Shengtao Fan
- Key Laboratory of Systemic Innovative Research on Virus Vaccine, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China; (H.Z.); (G.J.); (C.L.); (Y.C.); (R.L.); (J.P.); (Y.Z.); (D.L.); (Y.L.); (L.Y.); (Y.Z.); (M.Y.); (Y.L.); (L.L.)
| | | | - Qihan Li
- Key Laboratory of Systemic Innovative Research on Virus Vaccine, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China; (H.Z.); (G.J.); (C.L.); (Y.C.); (R.L.); (J.P.); (Y.Z.); (D.L.); (Y.L.); (L.Y.); (Y.Z.); (M.Y.); (Y.L.); (L.L.)
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Xu Y, Bao L, Cao S, Pang B, Zhang J, Zhang Y, Chen M, Wang Y, Sun Q, Zhao R, Guo S, Sun J, Cui X. Pharmacological effects and mechanism of Maxing Shigan decoction in the treatment of Pseudomonas aeruginosa pneumonia. JOURNAL OF ETHNOPHARMACOLOGY 2024; 320:117424. [PMID: 37984543 DOI: 10.1016/j.jep.2023.117424] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/05/2023] [Accepted: 11/11/2023] [Indexed: 11/22/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Maxing Shigan Decoction (MXSG) is a traditional Chinese Medicine effectively used in respiratory infections and bacterial pneumonia. However, the mechanism of MXSG treating acute Pseudomonas aeruginosa (P. aeruginosa) pneumonia is still unclear. AIM OF THE STUDY This study aimed to investigate the therapeutic effects of MXSG on acute P. aeruginosa pneumonia and explore its potential mechanisms. MATERIALS AND METHODS HPLC-MS analysis was performed to analyze the chemical composition. Antibacterial effects in vitro were evaluated by minimum inhibitory concentration (MIC). Forty-five male BALB/c mice were divided into control group, model group, levofloxacin group, MXSG-L (7.7 g/kg/d), and MXSG-H group (15.4 g/kg/d). Mice were intranasal instillation with P. aeruginosa to induce acute P. aeruginosa pneumonia model. Levofloxacin and MXSG were administered by oral gavage once a day. After 3 days of treatment, the lung index measurement, micro-CT, arterial blood gas analysis, bacteria load determination, and HE staining were performed. Network pharmacological analysis and transcriptome sequencing were employed to predict the potential mechanisms of MXSG on bacterial pneumonia. The expressions of relating genes were detected by immunofluorescence, Western blot, and RT-PCR. RESULTS In vitro, MIC of P. aeruginosa is greater than 500 mg/mL. In the treatment of acute P. aeruginosa pneumonia model, MXSG significantly improved body weight loss, lung index, and pulmonary lesions. MXSG treatment also reduced the bacterial load and ameliorated oxygen saturation significantly. Transcriptomes, immunofluorescence, Western blot, and RT-PCR analysis showed MXSG treating acute P. aeruginosa pneumonia through the IL-17 signaling pathway and HIF-1α/IL-6/STAT3 signaling pathway. CONCLUSIONS We demonstrated the efficacy and mechanism of MXSG in the treatment of acute P. aeruginosa pneumonia, which provides a scientific basis for its clinical application.
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Affiliation(s)
- Yingli Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Lei Bao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Shan Cao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Bo Pang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Jingsheng Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Yu Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Mengping Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Yaxin Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Qiyue Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Ronghua Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Shanshan Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Jing Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Xiaolan Cui
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
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Di Pietro C, Haberman AM, Lindenbach BD, Smith PC, Bruscia EM, Allore HG, Vander Wyk B, Tyagi A, Zeiss CJ. Prior Influenza Infection Mitigates SARS-CoV-2 Disease in Syrian Hamsters. Viruses 2024; 16:246. [PMID: 38400021 PMCID: PMC10891789 DOI: 10.3390/v16020246] [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: 01/11/2024] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Seasonal infection rates of individual viruses are influenced by synergistic or inhibitory interactions between coincident viruses. Endemic patterns of SARS-CoV-2 and influenza infection overlap seasonally in the Northern hemisphere and may be similarly influenced. We explored the immunopathologic basis of SARS-CoV-2 and influenza A (H1N1pdm09) interactions in Syrian hamsters. H1N1 given 48 h prior to SARS-CoV-2 profoundly mitigated weight loss and lung pathology compared to SARS-CoV-2 infection alone. This was accompanied by the normalization of granulocyte dynamics and accelerated antigen-presenting populations in bronchoalveolar lavage and blood. Using nasal transcriptomics, we identified a rapid upregulation of innate and antiviral pathways induced by H1N1 by the time of SARS-CoV-2 inoculation in 48 h dual-infected animals. The animals that were infected with both viruses also showed a notable and temporary downregulation of mitochondrial and viral replication pathways. Quantitative RT-PCR confirmed a decrease in the SARS-CoV-2 viral load and lower cytokine levels in the lungs of animals infected with both viruses throughout the course of the disease. Our data confirm that H1N1 infection induces rapid and transient gene expression that is associated with the mitigation of SARS-CoV-2 pulmonary disease. These protective responses are likely to begin in the upper respiratory tract shortly after infection. On a population level, interaction between these two viruses may influence their relative seasonal infection rates.
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Affiliation(s)
- Caterina Di Pietro
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06519, USA; (C.D.P.); (E.M.B.)
| | - Ann M. Haberman
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06519, USA;
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06519, USA;
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06519, USA;
| | - Peter C. Smith
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06519, USA;
| | - Emanuela M. Bruscia
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06519, USA; (C.D.P.); (E.M.B.)
| | - Heather G. Allore
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06519, USA; (H.G.A.); (B.V.W.)
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06519, USA
| | - Brent Vander Wyk
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06519, USA; (H.G.A.); (B.V.W.)
| | - Antariksh Tyagi
- Department of Genetics, Yale Center for Genome Analysis, New Haven, CT 06519, USA;
| | - Caroline J. Zeiss
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06519, USA;
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Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L. Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted. EBioMedicine 2024; 100:104960. [PMID: 38232633 PMCID: PMC10803917 DOI: 10.1016/j.ebiom.2023.104960] [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: 05/01/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND SARS-CoV-2-neutralizing antibodies (nABs) showed great promise in the early phases of the COVID-19 pandemic. The emergence of resistant strains, however, quickly rendered the majority of clinically approved nABs ineffective. This underscored the imperative to develop nAB cocktails targeting non-overlapping epitopes. METHODS Undertaking a nAB discovery program, we employed a classical workflow, while integrating artificial intelligence (AI)-based prediction to select non-competing nABs very early in the pipeline. We identified and in vivo validated (in female Syrian hamsters) two highly potent nABs. FINDINGS Despite the promising results, in depth cryo-EM structural analysis demonstrated that the AI-based prediction employed with the intention to ensure non-overlapping epitopes was inaccurate. The two nABs in fact bound to the same receptor-binding epitope in a remarkably similar manner. INTERPRETATION Our findings indicate that, even in the Alphafold era, AI-based predictions of paratope-epitope interactions are rough and experimental validation of epitopes remains an essential cornerstone of a successful nAB lead selection. FUNDING Full list of funders is provided at the end of the manuscript.
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Affiliation(s)
- Delphine Diana Acar
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Wojciech Witkowski
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Magdalena Wejda
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Ruifang Wei
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Tim Desmet
- Department of Basic and Applied Medical Sciences, Ghent University, Ghent 9000, Belgium
| | - Bert Schepens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sieglinde De Cae
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Hannah Eeckhaut
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Daria Fijalkowska
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Kenny Roose
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sandrine Vanmarcke
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | | | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xin Zhang
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Rana Abdelnabi
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Caroline S Foo
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven 3000, Belgium
| | - Dirk Reiter
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Nico Callewaert
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Han Remaut
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels 1050, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sarah Gerlo
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent 9000, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
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Zhang J, Rissmann M, Kuiken T, Haagmans BL. Comparative Pathogenesis of Severe Acute Respiratory Syndrome Coronaviruses. ANNUAL REVIEW OF PATHOLOGY 2024; 19:423-451. [PMID: 37832946 DOI: 10.1146/annurev-pathol-052620-121224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Over the last two decades the world has witnessed the global spread of two genetically related highly pathogenic coronaviruses, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. However, the impact of these outbreaks differed significantly with respect to the hospitalizations and fatalities seen worldwide. While many studies have been performed recently on SARS-CoV-2, a comparative pathogenesis analysis with SARS-CoV may further provide critical insights into the mechanisms of disease that drive coronavirus-induced respiratory disease. In this review, we comprehensively describe clinical and experimental observations related to transmission and pathogenesis of SARS-CoV-2 in comparison with SARS-CoV, focusing on human, animal, and in vitro studies. By deciphering the similarities and disparities of SARS-CoV and SARS-CoV-2, in terms of transmission and pathogenesis mechanisms, we offer insights into the divergent characteristics of these two viruses. This information may also be relevant to assessing potential novel introductions of genetically related highly pathogenic coronaviruses.
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Affiliation(s)
- Jingshu Zhang
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands;
| | - Melanie Rissmann
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands;
| | - Thijs Kuiken
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands;
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands;
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Abdelnabi R, Lassaunière R, Maes P, Weynand B, Neyts J. Comparing the Infectivity of Recent SARS-CoV-2 Omicron Sub-Variants in Syrian Hamsters. Viruses 2024; 16:122. [PMID: 38257822 PMCID: PMC10819014 DOI: 10.3390/v16010122] [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: 12/18/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Since the emergence of the first omicron SARS-CoV-2 variant at the end of 2021, several sub-variants have evolved and become predominant in the human population, showing enhanced transmissibility and ability to (partly) escape the adaptive immune response. The XBB sub-variants (e.g., EG.5.1) have become globally dominant. Besides the XBB sub-variants, a phylogenetically distinct variant, i.e., BA.2.86, is also circulating; it carries several mutations in the spike protein as compared to its parental BA.2 variant. Here, we explored the infectivity of the BA.2.86 and EG.5.1 sub-variants compared to the preceding BA.5 sub-variant in Syrian hamsters. Such preclinical models are important for the evaluation of updated vaccine candidates and novel therapeutic modalities. Following intranasal infection with either variant, throat swabs and lung samples were collected on days 3 and 4 post infection. No significant differences in viral RNA loads in throat swabs were observed between these sub-variants. However, the infectious virus titers in the lungs of EG.5.1- and BA.2.86-infected animals were significantly lower compared to the BA.5-infected ones. The lung pathology scores of animals infected with EG.5.1 and BA.2.86 were also markedly lower than that of BA.5 sub-variant. Together, we show that EG.5.1 and BA.2.86 sub-variants exhibit an attenuated replication in hamsters' lungs as compared to the BA.5 sub-variant.
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Affiliation(s)
- Rana Abdelnabi
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, B-3000 Leuven, Belgium;
- Department of Microbiology, Immunology and Transplantation, VirusBank Platform, KU Leuven, B-3001 Leuven, Belgium
| | | | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Translational Cell and Tissue Research, Division of Translational Cell and Tissue Research, KU Leuven, B-3000 Leuven, Belgium;
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, B-3000 Leuven, Belgium;
- Department of Microbiology, Immunology and Transplantation, VirusBank Platform, KU Leuven, B-3001 Leuven, Belgium
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10
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Fenwick C, Turelli P, Duhoo Y, Lau K, Herate C, Marlin R, Lamrayah M, Campos J, Esteves-Leuenberger L, Farina A, Raclot C, Genet V, Fiscalini F, Cesborn J, Perez L, Dereuddre-Bosquet N, Contreras V, Lheureux K, Relouzat F, Abdelnabi R, Leyssen P, Lévy Y, Pojer F, Le Grand R, Trono D, Pantaleo G. Broadly potent anti-SARS-CoV-2 antibody shares 93% of epitope with ACE2 and provides full protection in monkeys. J Infect 2023; 87:524-537. [PMID: 37852477 DOI: 10.1016/j.jinf.2023.10.008] [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: 07/31/2023] [Revised: 10/08/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
Abstract
OBJECTIVES Due to the rapid evolution of SARS-CoV-2 to variants with reduced sensitivity to vaccine-induced humoral immunity and the near complete loss of protective efficacy of licensed therapeutic monoclonal antibodies, we isolated a potent, broad-spectrum neutralizing antibody that could potentially provide prophylactic protection to immunocompromised patient populations. METHODS Spike-specific B-cell clones isolated from a vaccinated post-infected donor were profiled for those producing potent neutralizing antibodies against a panel of SARS-CoV-2 variants. The P4J15 antibody was further characterized to define the structural binding epitope, viral resistance, and in vivo efficacy. RESULTS The P4J15 mAb shows <20 ng/ml neutralizing activity against all variants including the latest XBB.2.3 and EG.5.1 sub-lineages. Structural studies of P4J15 in complex with Omicron XBB.1 Spike show that the P4J15 epitope shares ∼93% of its buried surface area with the ACE2 contact region, consistent with an ACE2 mimetic antibody. In vitro selection of SARS-CoV-2 mutants escaping P4J15 neutralization showed reduced infectivity, poor ACE2 binding, and mutations are rare in public sequence databases. Using a SARS-CoV-2 XBB.1.5 monkey challenge model, P4J15-LS confers complete prophylactic protection with an exceptionally long in vivo half-life of 43 days. CONCLUSIONS The P4J15 mAb has potential as a broad-spectrum anti-SARS-CoV-2 drug for prophylactic protection of at-risk patient populations.
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Affiliation(s)
- Craig Fenwick
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Yoan Duhoo
- School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne and Faculty of Biology and Medicine, UNIL, Lausanne, Switzerland
| | - Kelvin Lau
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Cécile Herate
- CEA, Université Paris Sud 11, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, Fontenay-aux-Roses, France
| | - Romain Marlin
- CEA, Université Paris Sud 11, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, Fontenay-aux-Roses, France
| | - Myriam Lamrayah
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jérémy Campos
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Line Esteves-Leuenberger
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Alex Farina
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Charlène Raclot
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Vanessa Genet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Flurin Fiscalini
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Julien Cesborn
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laurent Perez
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Nathalie Dereuddre-Bosquet
- CEA, Université Paris Sud 11, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, Fontenay-aux-Roses, France
| | - Vanessa Contreras
- CEA, Université Paris Sud 11, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, Fontenay-aux-Roses, France
| | - Kyllian Lheureux
- CEA, Université Paris Sud 11, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, Fontenay-aux-Roses, France
| | - Francis Relouzat
- CEA, Université Paris Sud 11, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, Fontenay-aux-Roses, France
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Pieter Leyssen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Yves Lévy
- VRI, Université Paris-Est Créteil, Faculté de Médicine, INSERM U955, 94010 Créteil, France; Inserm U955, Equipe 16, Créteil, France; AP-HP, Hôpital Henri-Mondor Albert-Chenevier, Service d'Immunologie Clinique et Maladies Infectieuses, Créteil, France
| | - Florence Pojer
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Roger Le Grand
- CEA, Université Paris Sud 11, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, Fontenay-aux-Roses, France
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; Swiss Vaccine Research Institute, Lausanne University Hospital and University of Lausanne, Switzerland.
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11
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Chauhan NR, Kundu S, Bal R, Chattopadhyay D, Sahu R, Mehto S, Yadav R, Krishna S, Jena KK, Satapathy S, Pv A, Murmu KC, Singh B, Patnaik S, Jena S, Harshan KH, Syed GH, Idris MM, Prasad P, Chauhan S. Transgenic mouse models support a protective role of type I IFN response in SARS-CoV-2 infection-related lung immunopathology and neuroinvasion. Cell Rep 2023; 42:113275. [PMID: 37874678 DOI: 10.1016/j.celrep.2023.113275] [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: 04/07/2023] [Revised: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023] Open
Abstract
Type I interferon (IFN-I) response is the first line of host defense against invading viruses. In the absence of definite mouse models, the role of IFN-I in SARS-CoV-2 infection remains perplexing. Here, we develop two mouse models, one with constitutively high IFN-I response (hACE2; Irgm1-/-) and the other with dampened IFN-I response (hACE2; Ifnar1-/-), to comprehend the role of IFN-I response. We report that hACE2; Irgm1-/- mice are resistant to lethal SARS-CoV-2 infection. In contrast, a severe SARS-CoV-2 infection along with immune cell infiltration, cytokine storm, and enhanced pathology is observed in the lungs and brain of hACE2; Ifnar1-/- mice. The hACE2; Irgm1-/-Ifnar1-/- double-knockout mice display loss of the protective phenotype observed in hACE2; Irgm1-/- mice, suggesting that heightened IFN-I response accounts for the observed immunity. Taking the results together, we demonstrate that IFN-I protects from lethal SARS-CoV-2 infection, and Irgm1 (IRGM) could be an excellent therapeutic target against SARS-CoV-2.
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Affiliation(s)
- Nishant Ranjan Chauhan
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India.
| | - Soumya Kundu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Ramyasingh Bal
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Diya Chattopadhyay
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Rinku Sahu
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Subhash Mehto
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Rina Yadav
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Sivaram Krishna
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Kautilya Kumar Jena
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Sameekshya Satapathy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Anusha Pv
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Krushna C Murmu
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Bharati Singh
- Virus-Host Interactions Lab, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | | | - Sarita Jena
- Experimental Animal Facility, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Krishnan H Harshan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Gulam Hussain Syed
- Virus-Host Interactions Lab, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Mohammed M Idris
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Punit Prasad
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Santosh Chauhan
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India.
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12
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Rudramurthy GR, Naveenkumar CN, Bharathkumar K, Shandil RK, Narayanan S. Genomic Mutations in SARS-CoV-2 Genome following Infection in Syrian Golden Hamster and Associated Lung Pathologies. Pathogens 2023; 12:1328. [PMID: 38003792 PMCID: PMC10674674 DOI: 10.3390/pathogens12111328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
The continuous evolution of the SARS-CoV-2 virus led to constant developments and efforts in understanding the significance and impacts of SARS-CoV-2 variants on human health. Our study aimed to determine the accumulation of genetic mutations and associated lung pathologies in male and female hamsters infected with the ancestral Wuhan strain of SARS-CoV-2. The present study showed no significant difference in the viral load between male and female hamsters and peak infection was found to be on day four post infection in both sexes of the animals. Live virus particles were detected up to 5 days post infection (dpi) through the TCID-50 assay, while qRT-PCR could detect viral RNA up to 14 dpi from all the infected animals. Further, the determination of the neutralizing antibody titer showed the onset of the humoral immune response as early as 4 dpi in both sexes against SARS-CoV-2, and a significant cross-protection against the delta variant of SARS-CoV-2 was observed. Histopathology showed edema, inflammation, inflammatory cell infiltration, necrosis, and degeneration of alveolar and bronchial epithelium cells from 3 dpi to 14 dpi in both sexes. Furthermore, next-generation sequencing (NGS) showed up to 10 single-nucleotide polymorphisms (SNPs) in the SARS-CoV-2 (ancestral Wuhan strain) genome isolated from both male and female hamsters. The mutation observed at the 23014 position (Glu484Asp) in the SARS-CoV-2 genome isolated from both sexes of the hamsters plays a significant role in the antiviral efficacy of small molecules, vaccines, and the Mabs-targeting S protein. The present study shows that either of the genders can be used in the pre-clinical efficacy of antiviral agents against SARS-CoV-2 in hamsters. However, considering the major mutation in the S protein, the understanding of the genetic mutation in SARS-CoV-2 after passing through hamsters is crucial in deciding the efficacy of the antiviral agents targeting the S protein. Importance: Our study findings indicate the accumulation of genomic mutations in SARS-CoV-2 after passing through the Syrian golden hamsters. Understanding the genomic mutations showed that either of the hamster genders can be used in the pre-clinical efficacy of antiviral agents and vaccines.
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Affiliation(s)
- Gudepalya Renukaiah Rudramurthy
- Foundation for Neglected Disease Research (FNDR), Plot No. 20A, KIADB Industrial Area, Bengaluru 561203, Karnataka, India; (C.N.N.); (K.B.); (R.K.S.); (S.N.)
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13
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Meehan GR, Herder V, Allan J, Huang X, Kerr K, Mendonca DC, Ilia G, Wright DW, Nomikou K, Gu Q, Molina Arias S, Hansmann F, Hardas A, Attipa C, De Lorenzo G, Cowton V, Upfold N, Palmalux N, Brown JC, Barclay WS, Filipe ADS, Furnon W, Patel AH, Palmarini M. Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning. PLoS Pathog 2023; 19:e1011589. [PMID: 37934791 PMCID: PMC10656012 DOI: 10.1371/journal.ppat.1011589] [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: 07/31/2023] [Revised: 11/17/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to evolve throughout the coronavirus disease-19 (COVID-19) pandemic, giving rise to multiple variants of concern (VOCs) with different biological properties. As the pandemic progresses, it will be essential to test in near real time the potential of any new emerging variant to cause severe disease. BA.1 (Omicron) was shown to be attenuated compared to the previous VOCs like Delta, but it is possible that newly emerging variants may regain a virulent phenotype. Hamsters have been proven to be an exceedingly good model for SARS-CoV-2 pathogenesis. Here, we aimed to develop robust quantitative pipelines to assess the virulence of SARS-CoV-2 variants in hamsters. We used various approaches including RNAseq, RNA in situ hybridization, immunohistochemistry, and digital pathology, including software assisted whole section imaging and downstream automatic analyses enhanced by machine learning, to develop methods to assess and quantify virus-induced pulmonary lesions in an unbiased manner. Initially, we used Delta and Omicron to develop our experimental pipelines. We then assessed the virulence of recent Omicron sub-lineages including BA.5, XBB, BQ.1.18, BA.2, BA.2.75 and EG.5.1. We show that in experimentally infected hamsters, accurate quantification of alveolar epithelial hyperplasia and macrophage infiltrates represent robust markers for assessing the extent of virus-induced pulmonary pathology, and hence virus virulence. In addition, using these pipelines, we could reveal how some Omicron sub-lineages (e.g., BA.2.75 and EG.5.1) have regained virulence compared to the original BA.1. Finally, to maximise the utility of the digital pathology pipelines reported in our study, we developed an online repository containing representative whole organ histopathology sections that can be visualised at variable magnifications (https://covid-atlas.cvr.gla.ac.uk). Overall, this pipeline can provide unbiased and invaluable data for rapidly assessing newly emerging variants and their potential to cause severe disease.
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Affiliation(s)
- Gavin R. Meehan
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Jay Allan
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Xinyi Huang
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Karen Kerr
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Diogo Correa Mendonca
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Georgios Ilia
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Derek W. Wright
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Sergi Molina Arias
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Florian Hansmann
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Germany
| | - Alexandros Hardas
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, North Mymms, United Kingdom
| | - Charalampos Attipa
- The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, United Kingdom
| | | | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Nicole Upfold
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Jonathan C. Brown
- Department of Infectious Disease, Imperial College London, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, United Kingdom
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
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14
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Abdelnabi R, Pérez P, Astorgano D, Albericio G, Kerstens W, Thibaut HJ, Coelmont L, Weynand B, Labiod N, Delgado R, Montenegro D, Puentes E, Rodríguez E, Neyts J, Dallmeier K, Esteban M, García-Arriaza J. Optimized vaccine candidate MVA-S(3P) fully protects against SARS-CoV-2 infection in hamsters. Front Immunol 2023; 14:1163159. [PMID: 37920464 PMCID: PMC10619667 DOI: 10.3389/fimmu.2023.1163159] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 09/27/2023] [Indexed: 11/04/2023] Open
Abstract
The development of novel optimized vaccines against coronavirus disease 2019 (COVID-19) that are capable of controlling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic and the appearance of different variants of concern (VoC) is needed to fully prevent the transmission of the virus. In the present study, we describe the enhanced immunogenicity and efficacy elicited in hamsters by a modified vaccinia virus Ankara (MVA) vector expressing a full-length prefusion-stabilized SARS-CoV-2 spike (S) protein [termed MVA-S(3P)]. Hamsters vaccinated with one or two doses of MVA-S(3P) developed high titers of S-binding IgG antibodies and neutralizing antibodies against the ancestral Wuhan SARS-CoV-2 virus and VoC beta, gamma, and delta, as well as against omicron, although with a somewhat lower neutralization activity. After SARS-CoV-2 challenge, vaccinated hamsters did not lose body weight as compared to matched placebo (MVA-WT) controls. Consistently, vaccinated hamsters exhibited significantly reduced viral RNA in the lungs and nasal washes, and no infectious virus was detected in the lungs in comparison to controls. Furthermore, almost no lung histopathology was detected in MVA-S(3P)-vaccinated hamsters, which also showed significantly reduced levels of proinflammatory cytokines in the lungs compared to unvaccinated hamsters. These results reinforce the use of MVA-S(3P) as a vaccine candidate against COVID-19 in clinical trials.
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Affiliation(s)
- Rana Abdelnabi
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, KU Leuven, Leuven, Belgium
| | - Patricia Pérez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - David Astorgano
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Guillermo Albericio
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Winnie Kerstens
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Hendrik Jan Thibaut
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Lotte Coelmont
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, KU Leuven, Leuven, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Translational Cell and Tissue Research, Division of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Nuria Labiod
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Rafael Delgado
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Department of Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Medicine, Medical School, Universidad Complutense de Madrid, Madrid, Spain
| | | | | | | | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, KU Leuven, Leuven, Belgium
| | - Kai Dallmeier
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, KU Leuven, Leuven, Belgium
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Juan García-Arriaza
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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15
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Kehrer T, Cupic A, Ye C, Yildiz S, Bouhaddou M, Crossland NA, Barrall EA, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena I, Aslam S, Saqi A, Rutkowska M, Ummadi MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Ak B, Marin A, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. Cell Host Microbe 2023; 31:1668-1684.e12. [PMID: 37738983 PMCID: PMC10750313 DOI: 10.1016/j.chom.2023.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/01/2023] [Accepted: 08/07/2023] [Indexed: 09/24/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes several proteins that inhibit host interferon responses. Among these, ORF6 antagonizes interferon signaling by disrupting nucleocytoplasmic trafficking through interactions with the nuclear pore complex components Nup98-Rae1. However, the roles and contributions of ORF6 during physiological infection remain unexplored. We assessed the role of ORF6 during infection using recombinant viruses carrying a deletion or loss-of-function (LoF) mutation in ORF6. ORF6 plays key roles in interferon antagonism and viral pathogenesis by interfering with nuclear import and specifically the translocation of IRF and STAT transcription factors. Additionally, ORF6 inhibits cellular mRNA export, resulting in the remodeling of the host cell proteome, and regulates viral protein expression. Interestingly, the ORF6:D61L mutation that emerged in the Omicron BA.2 and BA.4 variants exhibits reduced interactions with Nup98-Rae1 and consequently impairs immune evasion. Our findings highlight the role of ORF6 in antagonizing innate immunity and emphasize the importance of studying the immune evasion strategies of SARS-CoV-2.
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Affiliation(s)
- Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anastasija Cupic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Soner Yildiz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA 90024, USA; Institute for Quantitative and Computational Biosciences (OCBio), University of California, Los Angeles, Los Angeles, CA 90024, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02215, USA; Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Erika A Barrall
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Phillip Cohen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Tseng
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02215, USA; Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Tolga Çağatay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Flores
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Fahmida Alam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sadaf Aslam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Magdalena Rutkowska
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Manisha R Ummadi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Giuseppe Pisanelli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy
| | - R Blake Richardson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ethan C Veit
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Baran Ak
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arturo Marin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew J Evans
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emilia M Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Harm van Bakel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lorena Zuliani-Alvarez
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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16
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Lachhab S, El Mansouri AE, Mehdi A, Dennemont I, Neyts J, Jochmans D, Andrei G, Snoeck R, Sanghvi YS, Ait Ali M, Loiseau PM, Lazrek HB. Synthesis of new 3-acetyl-1,3,4-oxadiazolines combined with pyrimidines as antileishmanial and antiviral agents. Mol Divers 2023; 27:2147-2159. [PMID: 36251201 PMCID: PMC9573813 DOI: 10.1007/s11030-022-10548-9] [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] [Received: 06/12/2022] [Accepted: 10/07/2022] [Indexed: 11/25/2022]
Abstract
A new series of 3-acetyl-1,3,4-oxadiazoline hybrid molecules was designed and synthesized using a condensation between acyclonucleosides and substituted phenylhydrazone. All intermediates and final products were screened against Leishmania donovani, a Protozoan parasite and against three viruses SARS-CoV-2, HCMV and VZV. While no significant activity was observed against the viruses, the intermediate with 6-azatymine as thymine and 5-azathymine-3-acetyl-1,3,4-oxadiazoline hybrid exhibited a significant antileishmanial activity. The later compound was the most promising, exhibiting an IC50 value at 8.98 µM on L. donovani intramacrophage amastigotes and a moderate selectivity index value at 2.4.
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Affiliation(s)
- Saida Lachhab
- Laboratory of Biomolecular and Medicinal Chemistry, Faculty of Science Semlalia, University Cadi Ayyad, Marrakech, Morocco
| | - Az-Eddine El Mansouri
- Department of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Ahmad Mehdi
- ICGM, Université Montpellier, CNRS, ENSCM, Montpellier, France
| | - Indira Dennemont
- Antiparasite Chemotherapy, CNRS, BioCIS, Université Paris-Saclay, Chatenay-Malabry, 92290, Paris, France
| | - Johan Neyts
- Rega Institute for Medical Research, KULeuven, Louvain, Belgium
| | - Dirk Jochmans
- Rega Institute for Medical Research, KULeuven, Louvain, Belgium
| | - Graciela Andrei
- Rega Institute for Medical Research, KULeuven, Louvain, Belgium
| | - Robert Snoeck
- Rega Institute for Medical Research, KULeuven, Louvain, Belgium
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, CA, 92024-6615, USA
| | - Mustapha Ait Ali
- Laboratory of Biomolecular and Medicinal Chemistry, Faculty of Science Semlalia, University Cadi Ayyad, Marrakech, Morocco
| | - Philippe M Loiseau
- Antiparasite Chemotherapy, CNRS, BioCIS, Université Paris-Saclay, Chatenay-Malabry, 92290, Paris, France
| | - Hassan B Lazrek
- Laboratory of Biomolecular and Medicinal Chemistry, Faculty of Science Semlalia, University Cadi Ayyad, Marrakech, Morocco.
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17
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Han Q, Wang S, Wang Z, Zhang C, Wang X, Feng N, Wang T, Zhao Y, Chi H, Yan F, Xia X. Nanobodies with cross-neutralizing activity provide prominent therapeutic efficacy in mild and severe COVID-19 rodent models. Virol Sin 2023; 38:787-800. [PMID: 37423308 PMCID: PMC10590698 DOI: 10.1016/j.virs.2023.07.003] [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: 03/16/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023] Open
Abstract
The weakened protective efficacy of COVID-19 vaccines and antibodies caused by SARS-CoV-2 variants presents a global health emergency, which underscores the urgent need for universal therapeutic antibody intervention for clinical patients. Here, we screened three alpacas-derived nanobodies (Nbs) with neutralizing activity from twenty RBD-specific Nbs. The three Nbs were fused with the Fc domain of human IgG, namely aVHH-11-Fc, aVHH-13-Fc and aVHH-14-Fc, which could specifically bind RBD protein and competitively inhibit the binding of ACE2 receptor to RBD. They effectively neutralized SARS-CoV-2 pseudoviruses D614G, Alpha, Beta, Gamma, Delta, and Omicron sub-lineages BA.1, BA.2, BA.4, and BA.5 and authentic SARS-CoV-2 prototype, Delta, and Omicron BA.1, BA.2 strains. In mice-adapted COVID-19 severe model, intranasal administration of aVHH-11-Fc, aVHH-13-Fc and aVHH-14-Fc effectively protected mice from lethal challenges and reduced viral loads in both the upper and lower respiratory tracts. In the COVID-19 mild model, aVHH-13-Fc, which represents the optimal neutralizing activity among the above three Nbs, effectively protected hamsters from the challenge of SARS-CoV-2 prototype, Delta, Omicron BA.1 and BA.2 by significantly reducing viral replication and pathological alterations in the lungs. In structural modeling of aVHH-13 and RBD, aVHH-13 binds to the receptor-binding motif region of RBD and interacts with some highly conserved epitopes. Taken together, our study illustrated that alpaca-derived Nbs offered a therapeutic countermeasure against SARS-CoV-2, including those Delta and Omicron variants which have evolved into global pandemic strains.
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Affiliation(s)
- Qiuxue Han
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Shen Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Zhenshan Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Cheng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Xinyue Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Na Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China
| | - Yongkun Zhao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China; Jiangsu Co-innovation Centre for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Hang Chi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China.
| | - Feihu Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China; Jiangsu Co-innovation Centre for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
| | - Xianzhu Xia
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 132122, China; Jiangsu Co-innovation Centre for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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18
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Baker PJ, Amaral EP, Castro E, Bohrer AC, Torres-Juárez F, Jordan CM, Nelson CE, Barber DL, Johnson RF, Hilligan KL, Mayer-Barber KD. Co-infection of mice with SARS-CoV-2 and Mycobacterium tuberculosis limits early viral replication but does not affect mycobacterial loads. Front Immunol 2023; 14:1240419. [PMID: 37720210 PMCID: PMC10502726 DOI: 10.3389/fimmu.2023.1240419] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
Viral co-infections have been implicated in worsening tuberculosis (TB) and during the COVID-19 pandemic, the global rate of TB-related deaths has increased for the first time in over a decade. We and others have previously shown that a resolved prior or concurrent influenza A virus infection in Mycobacterium tuberculosis (Mtb)-infected mice resulted in increased pulmonary bacterial burden, partly through type I interferon (IFN-I)-dependent mechanisms. Here we investigated whether SARS-CoV-2 (SCV2) co-infection could also negatively affect bacterial control of Mtb. Importantly, we found that K18-hACE2 transgenic mice infected with SCV2 one month before, or months after aerosol Mtb exposure did not display exacerbated Mtb infection-associated pathology, weight loss, nor did they have increased pulmonary bacterial loads. However, pre-existing Mtb infection at the time of exposure to the ancestral SCV2 strain in infected K18-hACE2 transgenic mice or the beta variant (B.1.351) in WT C57Bl/6 mice significantly limited early SCV2 replication in the lung. Mtb-driven protection against SCV2 increased with higher bacterial doses and did not require IFN-I, TLR2 or TLR9 signaling. These data suggest that SCV2 co-infection does not exacerbate Mtb infection in mice, but rather the inflammatory response generated by Mtb infection in the lungs at the time of SCV2 exposure restricts viral replication.
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Affiliation(s)
- Paul J. Baker
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Eduardo P. Amaral
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Ehydel Castro
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Andrea C. Bohrer
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Flor Torres-Juárez
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Cassandra M. Jordan
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Christine E. Nelson
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, United States
| | - Daniel L. Barber
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, United States
| | - Reed F. Johnson
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, United States
| | - Kerry L. Hilligan
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, United States
| | - Katrin D. Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
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19
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Vanker M, Särekannu K, Fekkar A, Jørgensen SE, Haljasmägi L, Kallaste A, Kisand K, Lember M, Peterson P, Menon M, Hussell T, Knight S, Moore-Stanley J, Bastard P, Zhang SY, Mogensen TH, Philippot Q, Zhang Q, Puel A, Casanova JL, Kisand K. Autoantibodies Neutralizing Type III Interferons Are Uncommon in Patients with Severe Coronavirus Disease 2019 Pneumonia. J Interferon Cytokine Res 2023; 43:379-393. [PMID: 37253131 PMCID: PMC10517334 DOI: 10.1089/jir.2023.0003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/07/2023] [Indexed: 06/01/2023] Open
Abstract
Autoantibodies (AABs) neutralizing type I interferons (IFN) underlie about 15% of cases of critical coronavirus disease 2019 (COVID-19) pneumonia. The impact of autoimmunity toward type III IFNs remains unexplored. We included samples from 1,002 patients with COVID-19 (50% with severe disease) and 1,489 SARS-CoV-2-naive individuals. We studied the prevalence and neutralizing capacity of AABs toward IFNλ and IFNα. Luciferase-based immunoprecipitation method was applied using pooled IFNα (subtypes 1, 2, 8, and 21) or pooled IFNλ1-IFNλ3 as antigens, followed by reporter cell-based neutralization assay. In the SARS-CoV-2-naive cohort, IFNλ AABs were more common (8.5%) than those targeting IFNα2 (2.9%) and were related with older age. In the COVID-19 cohort the presence of autoreactivity to IFNλ did not associate with severe disease [odds ratio (OR) 0.84; 95% confidence interval (CI) 0.40-1.73], unlike to IFNα (OR 4.88; 95% CI 2.40-11.06; P < 0.001). Most IFNλ AAB-positive COVID-19 samples (67%) did not neutralize any of the 3 IFNλ subtypes. Pan-IFNλ neutralization occurred in 5 patients (0.50%), who all suffered from severe COVID-19 pneumonia, and 4 of them neutralized IFNα2 in addition to IFNλ. Overall, AABs to type III IFNs are rarely neutralizing, and do not seem to predispose to severe COVID-19 pneumonia on their own.
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Affiliation(s)
- Martti Vanker
- Institute of Biomedicine and Translational Medicine; Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Karita Särekannu
- Institute of Biomedicine and Translational Medicine; Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Arnaud Fekkar
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Service de Parasitologie-Mycologie, Groupe Hospitalier Pitié Salpêtrière, AP-HP, Paris, France
| | - Sofie Eg Jørgensen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus N, Denmark
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Liis Haljasmägi
- Institute of Biomedicine and Translational Medicine; Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Anne Kallaste
- Department of Internal Medicine, Tartu University Hospital, Tartu, Estonia
| | - Kalle Kisand
- Department of Internal Medicine, Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Margus Lember
- Department of Internal Medicine, Tartu University Hospital, Tartu, Estonia
- Department of Internal Medicine, Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Pärt Peterson
- Institute of Biomedicine and Translational Medicine; Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
| | - Madhvi Menon
- Lydia Becker Institute of Immunology and Inflammation, Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Tracy Hussell
- Lydia Becker Institute of Immunology and Inflammation, Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Sean Knight
- Lydia Becker Institute of Immunology and Inflammation, Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Respiratory Department, Salford Care Organisation, Northern Care Alliance Foundation Trust, Manchester, United Kingdom
| | - James Moore-Stanley
- Lydia Becker Institute of Immunology and Inflammation, Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Trine H. Mogensen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus N, Denmark
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
- Howard Hughes Medical Institute, New York, New York, USA
| | - Kai Kisand
- Institute of Biomedicine and Translational Medicine; Institute of Clinical Medicine; University of Tartu, Tartu, Estonia
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20
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Baggen J, Jacquemyn M, Persoons L, Vanstreels E, Pye VE, Wrobel AG, Calvaresi V, Martin SR, Roustan C, Cronin NB, Reading E, Thibaut HJ, Vercruysse T, Maes P, De Smet F, Yee A, Nivitchanyong T, Roell M, Franco-Hernandez N, Rhinn H, Mamchak AA, Ah Young-Chapon M, Brown E, Cherepanov P, Daelemans D. TMEM106B is a receptor mediating ACE2-independent SARS-CoV-2 cell entry. Cell 2023; 186:3427-3442.e22. [PMID: 37421949 PMCID: PMC10409496 DOI: 10.1016/j.cell.2023.06.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/24/2023] [Accepted: 06/08/2023] [Indexed: 07/10/2023]
Abstract
SARS-CoV-2 is associated with broad tissue tropism, a characteristic often determined by the availability of entry receptors on host cells. Here, we show that TMEM106B, a lysosomal transmembrane protein, can serve as an alternative receptor for SARS-CoV-2 entry into angiotensin-converting enzyme 2 (ACE2)-negative cells. Spike substitution E484D increased TMEM106B binding, thereby enhancing TMEM106B-mediated entry. TMEM106B-specific monoclonal antibodies blocked SARS-CoV-2 infection, demonstrating a role of TMEM106B in viral entry. Using X-ray crystallography, cryogenic electron microscopy (cryo-EM), and hydrogen-deuterium exchange mass spectrometry (HDX-MS), we show that the luminal domain (LD) of TMEM106B engages the receptor-binding motif of SARS-CoV-2 spike. Finally, we show that TMEM106B promotes spike-mediated syncytium formation, suggesting a role of TMEM106B in viral fusion. Together, our findings identify an ACE2-independent SARS-CoV-2 infection mechanism that involves cooperative interactions with the receptors heparan sulfate and TMEM106B.
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Affiliation(s)
- Jim Baggen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium.
| | - Maarten Jacquemyn
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium
| | - Leentje Persoons
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium
| | - Els Vanstreels
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Valeria Calvaresi
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London SE1 1DB, UK
| | - Stephen R Martin
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Chloë Roustan
- Structural Biology Science Technology Platform, Francis Crick Institute, London NW1 1AT, UK
| | - Nora B Cronin
- LonCEM Facility, Francis Crick Institute, London NW1 1AT, UK
| | - Eamonn Reading
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London SE1 1DB, UK
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium
| | - Thomas Vercruysse
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium
| | - Piet Maes
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Leuven 3000, Belgium
| | - Frederik De Smet
- KU Leuven Department of Imaging and Pathology, Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Leuven 3000, Belgium
| | - Angie Yee
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | - Toey Nivitchanyong
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | - Marina Roell
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | | | - Herve Rhinn
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | - Alusha Andre Mamchak
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | | | - Eric Brown
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London NW1 1AT, UK; Department of Infectious Disease, Section of Virology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK.
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium.
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21
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Adler JM, Martin Vidal R, Voß A, Kunder S, Nascimento M, Abdelgawad A, Langner C, Vladimirova D, Osterrieder N, Gruber AD, Kunec D, Trimpert J. A non-transmissible live attenuated SARS-CoV-2 vaccine. Mol Ther 2023; 31:2391-2407. [PMID: 37263272 PMCID: PMC10214529 DOI: 10.1016/j.ymthe.2023.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 03/23/2023] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
Live attenuated vaccines (LAVs) administered via the mucosal route may offer better control of the COVID-19 pandemic than non-replicating vaccines injected intramuscularly. Conceptionally, LAVs have several advantages, including presentation of the entire antigenic repertoire of the virus, and the induction of strong mucosal immunity. Thus, immunity induced by LAV could offer superior protection against future surges of COVID-19 cases caused by emerging SARS-CoV-2 variants. However, LAVs carry the risk of unintentional transmission. To address this issue, we investigated whether transmission of a SARS-CoV-2 LAV candidate can be blocked by removing the furin cleavage site (FCS) from the spike protein. The level of protection and immunity induced by the attenuated virus with the intact FCS was virtually identical to the one induced by the attenuated virus lacking the FCS. Most importantly, removal of the FCS completely abolished horizontal transmission of vaccine virus between cohoused hamsters. Furthermore, the vaccine was safe in immunosuppressed animals and showed no tendency to recombine in vitro or in vivo with a SARS-CoV-2 field strain. These results indicate that removal of the FCS from SARS-CoV-2 LAV is a promising strategy to increase vaccine safety and prevent vaccine transmission without compromising vaccine efficacy.
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Affiliation(s)
- Julia M Adler
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Anne Voß
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Sandra Kunder
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Azza Abdelgawad
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Christine Langner
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Daria Vladimirova
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Achim D Gruber
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Dusan Kunec
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany.
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22
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Sheng J, Li L, Lv X, Gao M, Chen Z, Zhou Z, Wang J, Wu A, Jiang T. Integrated interactome and transcriptome analysis reveals key host factors critical for SARS-CoV-2 infection. Virol Sin 2023; 38:508-519. [PMID: 37169126 PMCID: PMC10166720 DOI: 10.1016/j.virs.2023.05.004] [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: 01/16/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has seriously threatened global public health and caused huge economic losses. Omics studies of SARS-CoV-2 can help understand the interaction between the virus and host, thereby providing a new perspective in guiding the intervention and treatment of the SARS-CoV-2 infection. Since large amount of SARS-CoV-2 omics data have been accumulated in public databases, this study aimed to identify key host factors involved in SARS-CoV-2 infection through systematic integration of transcriptome and interactome data. By manually curating published studies, we obtained a comprehensive SARS-CoV-2-human protein-protein interactions (PPIs) network, comprising 3591 human proteins interacting with 31 SARS-CoV-2 viral proteins. Using the RobustRankAggregation method, we identified 123 multiple cell line common genes (CLCGs), of which 115 up-regulated CLCGs showed host enhanced innate immunity and chemotactic response signatures. Combined with network analysis, co-expression and functional enrichment analysis, we discovered four key host factors involved in SARS-CoV-2 infection: IFITM1, SERPINE1, DDX60, and TNFAIP2. Furthermore, SERPINE1 was found to facilitate SARS-CoV-2 replication, and can alleviate the endoplasmic reticulum (ER) stress induced by ORF8 protein through interaction with ORF8. Our findings highlight the importance of systematic integration analysis in understanding SARS-CoV-2-human interactions and provide valuable insights for future research on potential therapeutic targets against SARS-CoV-2 infection.
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Affiliation(s)
- Jie Sheng
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China; Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Lili Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Xueying Lv
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China; Department of Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, China
| | - Meiling Gao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Ziyi Chen
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Zhuo Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Jingfeng Wang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China.
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China.
| | - Taijiao Jiang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China; Guangzhou Laboratory, Guangzhou, 510005, China; State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, China.
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23
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Carrau L, Frere JJ, Golynker I, Fajardo A, Rivera CF, Horiuchi S, Roonprapunt T, Minkoff JM, Blanco-Melo D, TenOever B. Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19. Sci Signal 2023; 16:eadg5470. [PMID: 37311033 DOI: 10.1126/scisignal.adg5470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/26/2023] [Indexed: 06/15/2023]
Abstract
Clinical presentations that develop in response to infection result from interactions between the pathogen and host defenses. SARS-CoV-2, the etiologic agent of COVID-19, directly antagonizes these defenses, leading to delayed immune engagement in the lungs that materializes only as cells succumb to infection and are phagocytosed. Leveraging the golden hamster model of COVID-19, we sought to understand the dynamics between SARS-CoV-2 infection in the airways and the systemic host response that ensues. We found that early SARS-CoV-2 replication was largely confined to the respiratory tract and olfactory system and, to a lesser extent, the heart and gastrointestinal tract but generated a host antiviral response in every organ as a result of circulating type I and III interferons. Moreover, we showed that diminishing the response in the airways by immunosuppression or administration of SARS-CoV-2 intravenously resulted in decreased immune priming, viremia, and increased viral tropism, including productive infection of the liver, kidney, spleen, and brain. Last, we showed that productive infection of the airways was required for mounting an effective and system-wide antiviral response. Together, these data illustrate how COVID-19 can result in diverse clinical presentations in which disease outcomes can be a by-product of the speed and strength of immune engagement. These studies provide additional evidence for the mechanistic basis of the diverse clinical presentations of COVID-19 and highlight the ability of the respiratory tract to generate a systemic immune defense after pathogen recognition.
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Affiliation(s)
- Lucia Carrau
- Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Justin J Frere
- Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Ilona Golynker
- Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Alvaro Fajardo
- Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Cristobal F Rivera
- Department of Cell Biology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Shu Horiuchi
- Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Tyler Roonprapunt
- Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Judith M Minkoff
- Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Daniel Blanco-Melo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98104, USA
| | - Benjamin TenOever
- Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA
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24
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Tada T, Minnee J, Landau NR. Vectored immunoprophylaxis and treatment of SARS-CoV-2 infection in a preclinical model. Proc Natl Acad Sci U S A 2023; 120:e2303509120. [PMID: 37252952 PMCID: PMC10266030 DOI: 10.1073/pnas.2303509120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
Vectored immunoprophylaxis was first developed as a means of establishing engineered immunity to HIV using an adenoassociated viral vector expressing a broadly neutralizing antibody. We applied this concept to establish long-term prophylaxis against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a mouse model using adenoassociated virus and lentiviral vectors expressing a high-affinity angiotensin-converting enzyme 2 (ACE2) decoy. Administration of decoy-expressing (adenoassociated virus) AAV2.retro and AAV6.2 vectors by intranasal instillation or intramuscular injection protected mice against high-titered SARS-CoV-2 infection. AAV and lentiviral vectored immunoprophylaxis was durable and was active against SARS-CoV-2 Omicron subvariants. The AAV vectors were also effective therapeutically when administered postinfection. Vectored immunoprophylaxis could be of value for immunocompromised individuals for whom vaccination is not practical and as a means to rapidly establish protection from infection. Unlike monoclonal antibody therapy, the approach is expected to remain active despite continued evolution viral variants.
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, New York University (NYU) Grossman School of Medicine, New York, NY10016
| | - Julia Minnee
- Department of Microbiology, New York University (NYU) Grossman School of Medicine, New York, NY10016
| | - Nathaniel R. Landau
- Department of Microbiology, New York University (NYU) Grossman School of Medicine, New York, NY10016
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25
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Cuypers L, Keyaerts E, Hong SL, Gorissen S, Menezes SM, Starick M, Van Elslande J, Weemaes M, Wawina-Bokalanga T, Marti-Carreras J, Vanmechelen B, Van Holm B, Bloemen M, Dogne JM, Dufrasne F, Durkin K, Ruelle J, De Mendonca R, Wollants E, Vermeersch P, Boulouffe C, Djiena A, Broucke C, Catry B, Lagrou K, Van Ranst M, Neyts J, Baele G, Maes P, André E, Dellicour S, Van Weyenbergh J. Immunovirological and environmental screening reveals actionable risk factors for fatal COVID-19 during post-vaccination nursing home outbreaks. NATURE AGING 2023:10.1038/s43587-023-00421-1. [PMID: 37217661 DOI: 10.1038/s43587-023-00421-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023]
Abstract
Coronavirus Disease 2019 (COVID-19) vaccination has resulted in excellent protection against fatal disease, including in older adults. However, risk factors for post-vaccination fatal COVID-19 are largely unknown. We comprehensively studied three large nursing home outbreaks (20-35% fatal cases among residents) by combining severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) aerosol monitoring, whole-genome phylogenetic analysis and immunovirological profiling of nasal mucosa by digital nCounter transcriptomics. Phylogenetic investigations indicated that each outbreak stemmed from a single introduction event, although with different variants (Delta, Gamma and Mu). SARS-CoV-2 was detected in aerosol samples up to 52 d after the initial infection. Combining demographic, immune and viral parameters, the best predictive models for mortality comprised IFNB1 or age, viral ORF7a and ACE2 receptor transcripts. Comparison with published pre-vaccine fatal COVID-19 transcriptomic and genomic signatures uncovered a unique IRF3 low/IRF7 high immune signature in post-vaccine fatal COVID-19 outbreaks. A multi-layered strategy, including environmental sampling, immunomonitoring and early antiviral therapy, should be considered to prevent post-vaccination COVID-19 mortality in nursing homes.
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Affiliation(s)
- Lize Cuypers
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Els Keyaerts
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Samuel Leandro Hong
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sarah Gorissen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Soraya Maria Menezes
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marick Starick
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jan Van Elslande
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Matthias Weemaes
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Tony Wawina-Bokalanga
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Joan Marti-Carreras
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Bert Vanmechelen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Bram Van Holm
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mandy Bloemen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jean-Michel Dogne
- Department of Pharmacy, Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - François Dufrasne
- Laboratory of Proteomics and Microbiology, University of Mons, Mons, Belgium
- Department of Infectious Diseases, Laboratory of Viral Diseases, National Institute for Public Health (Sciensano), Brussels, Belgium
| | - Keith Durkin
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | - Jean Ruelle
- Medical Microbiology Unit (MBLG), Institute of Experimental and Clinical Research (IREC), Université Catholique de Louvain, Brussels, Belgium
| | | | - Elke Wollants
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Pieter Vermeersch
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Caroline Boulouffe
- Infectious Disease Surveillance Unit, Agence pour une vie de qualité (AVIQ), Wallonia, Belgium
| | - Achille Djiena
- Infectious Disease Surveillance Unit, Agence pour une vie de qualité (AVIQ), Wallonia, Belgium
| | - Caroline Broucke
- Outbreak Investigation Team, Agentschap zorg en gezondheid, Flanders, Belgium
| | - Boudewijn Catry
- Unit Healthcare-Associated Infections and Antimicrobial Resistance, Sciensano, Brussels, Belgium
| | - Katrien Lagrou
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation, Laboratory Virology and Chemotherapy, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Emmanuel André
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Johan Van Weyenbergh
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium.
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26
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Wouters E, Verbrugghe C, Abdelnabi R, Devloo R, De Clippel D, Jochmans D, De Bleser D, Weynand B, Compernolle V, Neyts J, Feys HB. Intranasal administration of convalescent plasma protects against SARS-CoV-2 infection in hamsters. EBioMedicine 2023; 92:104597. [PMID: 37148586 PMCID: PMC10171892 DOI: 10.1016/j.ebiom.2023.104597] [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: 02/09/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND Convalescent plasma (CP) transfusion is an early option for treating infections with pandemic potential, often preceding vaccine or antiviral drug rollout. Heterogenous findings from randomized clinical trials on transfusion of COVID-19 CP (CCP) have been reported. However, meta-analysis suggests that transfusion of high titer CCP is associated with a mortality benefit for COVID-19 outpatients or inpatients treated within 5 days after symptom onset, indicating the importance of early administration. METHODS We tested if CCP is an effective prophylactic against SARS-CoV-2 infection by the intranasal administration of 25 μL CCP/nostril (i.e. 0.01-0.06 mg anti-RBD antibodies/kg) in hamsters exposed to infected littermates. FINDINGS In this model, 40% of CCP treated hamsters were fully protected and 40% had significantly reduced viral loads, the remaining 20% was not protected. The effect seems dose-dependent because high-titer CCP from a vaccinated donor was more effective than low-titer CCP from a donation prior to vaccine rollout. Intranasal administration of human CCP resulted in a reactive (immune) response in hamster lungs, however this was not observed upon administration of hamster CCP. INTERPRETATION We conclude that CCP is an effective prophylactic when used directly at the site of primary infection. This option should be considered in future prepandemic preparedness plans. FUNDING Flanders Innovation & Entrepreneurship (VLAIO) and the Foundation for Scientific Research of the Belgian Red Cross Flanders.
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Affiliation(s)
- Elise Wouters
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium
| | - Caro Verbrugghe
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium; Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | - Rosalie Devloo
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium
| | | | - Dirk Jochmans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | | | - Birgit Weynand
- KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, Division of Translational Cell and Tissue Research, B-3000, Leuven, Belgium
| | - Veerle Compernolle
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium; Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Blood Services of the Belgian Red Cross-Flanders, Mechelen, Belgium; Transfusion Innovation Center, Belgian Red Cross-Flanders, Ghent, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | - Hendrik B Feys
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium; Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Blood Services of the Belgian Red Cross-Flanders, Mechelen, Belgium.
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27
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Abdelnabi R, Jochmans D, Donckers K, Trüeb B, Ebert N, Weynand B, Thiel V, Neyts J. Nirmatrelvir-resistant SARS-CoV-2 is efficiently transmitted in female Syrian hamsters and retains partial susceptibility to treatment. Nat Commun 2023; 14:2124. [PMID: 37059708 PMCID: PMC10101821 DOI: 10.1038/s41467-023-37773-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/24/2023] [Indexed: 04/16/2023] Open
Abstract
The SARS-CoV-2 main protease (3CLpro) is one of the promising therapeutic targets for the treatment of COVID-19. Nirmatrelvir is the first 3CLpro inhibitor authorized for treatment of COVID-19 patients at high risk of hospitalization. We recently reported on the in vitro selection of SARS-CoV-2 3CLpro resistant virus (L50F-E166A-L167F; 3CLprores) that is cross-resistant with nirmatrelvir and other 3CLpro inhibitors. Here, we demonstrate that the 3CLprores virus replicates efficiently in the lungs of intranasally infected female Syrian hamsters and causes lung pathology comparable to that caused by the WT virus. Moreover, hamsters infected with 3CLprores virus transmit the virus efficiently to co-housed non-infected contact hamsters. Importantly, at a dose of 200 mg/kg (BID) of nirmatrelvir, the compound was still able to reduce the lung infectious virus titers of 3CLprores-infected hamsters by 1.4 log10 with a modest improvement in the lung histopathology as compared to the vehicle control. Fortunately, resistance to Nirmatrelvir does not readily develop in clinical setting. Yet, as we demonstrate, in case drug-resistant viruses emerge, they may spread easily which may thus impact therapeutic options. Therefore, the use of 3CLpro inhibitors in combination with other drugs may be considered, especially in immunodeficient patients, to avoid the development of drug-resistant viruses.
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Affiliation(s)
- Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
- The VirusBank Platform, Gaston Geenslaan, B-3000, Leuven, Belgium
| | - Dirk Jochmans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | - Kim Donckers
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | - Bettina Trüeb
- Institute of Virology and Immunology, University of Bern, 3012, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology, University of Bern, 3012, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Birgit Weynand
- KU Leuven Department of Imaging and Pathology, Division of Translational Cell and Tissue Research, B-3000, Leuven, Belgium
| | - Volker Thiel
- Institute of Virology and Immunology, University of Bern, 3012, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium.
- The VirusBank Platform, Gaston Geenslaan, B-3000, Leuven, Belgium.
- Global Virus Network, GVN, Baltimore, US.
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28
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Le NTH, De Jonghe S, Erven K, Vermeyen T, Baldé AM, Herrebout WA, Neyts J, Pannecouque C, Pieters L, Tuenter E. Anti-SARS-CoV-2 Activity and Cytotoxicity of Amaryllidaceae Alkaloids from Hymenocallis littoralis. Molecules 2023; 28:molecules28073222. [PMID: 37049986 PMCID: PMC10096449 DOI: 10.3390/molecules28073222] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/24/2023] [Accepted: 04/03/2023] [Indexed: 04/09/2023] Open
Abstract
The Amaryllidaceae species are well-known as a rich source of bioactive compounds in nature. Although Hymenocallis littoralis has been studied for decades, its polar components were rarely explored. The current phytochemical investigation of Amaryllidaceae alkaloids from H. littoralis led to the identification of three previously undescribed compounds: O-demethyl-norlycoramine (1), (−)-2-epi-pseudolycorine (2) and (+)-2-epi-pseudolycorine (3), together with eight known compounds: 6α-hydroxyhippeastidine (4), 6β-hydroxyhippeastidine (5), lycorine (6), 2-epi-lycorine (7), zephyranthine (8), ungeremine (9), pancratistatin (10) and 9-O-demethyl-7-O-methyllycorenine (11). Among the eight previously reported compounds, five were isolated from H. littoralis for the first time (compounds 4, 5, 7, 8, and 9). Compounds 1, 4, 5, 7, 8, and 11 exhibited weak anti-SARS-CoV-2 activity (EC50 = 40–77 µM) at non-cytotoxic concentrations. Assessment of cytotoxicity on the Vero-E6 cell line revealed lycorine and pancratistatin as cytotoxic substances with CC50 values of 1.2 µM and 0.13 µM, respectively. The preliminary structure-activity relationship for the lycorine-type alkaloids in this study was further investigated, and as a result ring C appears to play a crucial role in their anti-SARS-CoV-2 activity.
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Affiliation(s)
- Ngoc-Thao-Hien Le
- Natural Products and Food Research and Analysis (NatuRA), Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Kristien Erven
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Tom Vermeyen
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
- Ghent Quantum Chemistry Group, Department of Chemistry, Ghent University, Krijgslaan 281, B-9000 Ghent, Belgium
| | - Aliou M. Baldé
- Department of Pharmacy, University Gamal Abdel Nasser of Conakry, Conakry 00224, Guinea
| | - Wouter A. Herrebout
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Luc Pieters
- Natural Products and Food Research and Analysis (NatuRA), Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Emmy Tuenter
- Natural Products and Food Research and Analysis (NatuRA), Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
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29
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Roy SS, Sharma S, Rizvi ZA, Sinha D, Gupta D, Rophina M, Sehgal P, Sadhu S, Tripathy MR, Samal S, Maiti S, Scaria V, Sivasubbu S, Awasthi A, Harshan KH, Jain S, Chowdhury S. G4-binding drugs, chlorpromazine and prochlorperazine, repurposed against COVID-19 infection in hamsters. Front Mol Biosci 2023; 10:1133123. [PMID: 37006620 PMCID: PMC10061221 DOI: 10.3389/fmolb.2023.1133123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has caused millions of infections and deaths worldwide. Limited treatment options and the threat from emerging variants underline the need for novel and widely accessible therapeutics. G-quadruplexes (G4s) are nucleic acid secondary structures known to affect many cellular processes including viral replication and transcription. We identified heretofore not reported G4s with remarkably low mutation frequency across >5 million SARS-CoV-2 genomes. The G4 structure was targeted using FDA-approved drugs that can bind G4s - Chlorpromazine (CPZ) and Prochlorperazine (PCZ). We found significant inhibition in lung pathology and lung viral load of SARS-CoV-2 challenged hamsters when treated with CPZ or PCZ that was comparable to the widely used antiviral drug Remdesivir. In support, in vitro G4 binding, inhibition of reverse transcription from RNA isolated from COVID-infected humans, and attenuated viral replication and infectivity in Vero cell cultures were clear in case of both CPZ and PCZ. Apart from the wide accessibility of CPZ/PCZ, targeting relatively invariant nucleic acid structures poses an attractive strategy against viruses like SARS-CoV-2, which spread fast and accumulate mutations quickly.
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Affiliation(s)
- Shuvra Shekhar Roy
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shalu Sharma
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Zaigham Abbas Rizvi
- Immuno-biology Laboratory, Infection and Immunology Centre, Translational Health Science and Technology Institute, Faridabad, 121001, India
| | - Dipanjali Sinha
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Divya Gupta
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Mercy Rophina
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Paras Sehgal
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Srikanth Sadhu
- Immuno-biology Laboratory, Infection and Immunology Centre, Translational Health Science and Technology Institute, Faridabad, 121001, India
| | - Manas Ranjan Tripathy
- Immuno-biology Laboratory, Infection and Immunology Centre, Translational Health Science and Technology Institute, Faridabad, 121001, India
| | - Sweety Samal
- Translational Health Science and Technology Institute, Faridabad, 411008, India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-National Chemical Laboratory, Pune, 121001, India
| | - Vinod Scaria
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Amit Awasthi
- Immuno-biology Laboratory, Infection and Immunology Centre, Translational Health Science and Technology Institute, Faridabad, 121001, India
| | - Krishnan H. Harshan
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Sanjeev Jain
- Molecular Genetics Laboratory, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Shantanu Chowdhury
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- *Correspondence: Shantanu Chowdhury,
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30
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Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has been associated with substantial global morbidity and mortality. Despite a tropism that is largely confined to the airways, COVID-19 is associated with multiorgan dysfunction and long-term cognitive pathologies. A major driver of this biology stems from the combined effects of virus-mediated interference with the host antiviral defences in infected cells and the sensing of pathogen-associated material by bystander cells. Such a dynamic results in delayed induction of type I and III interferons (IFN-I and IFN-III) at the site of infection, but systemic IFN-I and IFN-III priming in distal organs and barrier epithelial surfaces, respectively. In this Review, we examine the relationship between SARS-CoV-2 biology and the cellular response to infection, detailing how antagonism and dysregulation of host innate immune defences contribute to disease severity of COVID-19.
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Affiliation(s)
- Judith M Minkoff
- Department of Microbiology, New York University Langone Health, New York, NY, USA
| | - Benjamin tenOever
- Department of Microbiology, New York University Langone Health, New York, NY, USA.
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31
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The Substitutions L50F, E166A, and L167F in SARS-CoV-2 3CLpro Are Selected by a Protease Inhibitor In Vitro and Confer Resistance To Nirmatrelvir. mBio 2023; 14:e0281522. [PMID: 36625640 PMCID: PMC9973015 DOI: 10.1128/mbio.02815-22] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The SARS-CoV-2 main protease (3CLpro) has an indispensable role in the viral life cycle and is a therapeutic target for the treatment of COVID-19. The potential of 3CLpro-inhibitors to select for drug-resistant variants needs to be established. Therefore, SARS-CoV-2 was passaged in vitro in the presence of increasing concentrations of ALG-097161, a probe compound designed in the context of a 3CLpro drug discovery program. We identified a combination of amino acid substitutions in 3CLpro (L50F E166A L167F) that is associated with a >20× increase in 50% effective concentration (EC50) values for ALG-097161, nirmatrelvir (PF-07321332), PF-00835231, and ensitrelvir. While two of the single substitutions (E166A and L167F) provide low-level resistance to the inhibitors in a biochemical assay, the triple mutant results in the highest levels of resistance (6× to 72×). All substitutions are associated with a significant loss of enzymatic 3CLpro activity, suggesting a reduction in viral fitness. Structural biology analysis indicates that the different substitutions reduce the number of inhibitor/enzyme interactions while the binding of the substrate is maintained. These observations will be important for the interpretation of resistance development to 3CLpro inhibitors in the clinical setting. IMPORTANCE Paxlovid is the first oral antiviral approved for treatment of SARS-CoV-2 infection. Antiviral treatments are often associated with the development of drug-resistant viruses. In order to guide the use of novel antivirals, it is essential to understand the risk of resistance development and to characterize the associated changes in the viral genes and proteins. In this work, we describe for the first time a pathway that allows SARS-CoV-2 to develop resistance against Paxlovid in vitro. The characteristics of in vitro antiviral resistance development may be predictive for the clinical situation. Therefore, our work will be important for the management of COVID-19 with Paxlovid and next-generation SARS-CoV-2 3CLpro inhibitors.
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32
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Jochmans D, Liu C, Donckers K, Stoycheva A, Boland S, Stevens SK, De Vita C, Vanmechelen B, Maes P, Trüeb B, Ebert N, Thiel V, De Jonghe S, Vangeel L, Bardiot D, Jekle A, Blatt LM, Beigelman L, Symons JA, Raboisson P, Chaltin P, Marchand A, Neyts J, Deval J, Vandyck K. The Substitutions L50F, E166A, and L167F in SARS-CoV-2 3CLpro Are Selected by a Protease Inhibitor In Vitro and Confer Resistance To Nirmatrelvir. mBio 2023. [PMID: 36625640 DOI: 10.1101/2022.06.07.495116] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
The SARS-CoV-2 main protease (3CLpro) has an indispensable role in the viral life cycle and is a therapeutic target for the treatment of COVID-19. The potential of 3CLpro-inhibitors to select for drug-resistant variants needs to be established. Therefore, SARS-CoV-2 was passaged in vitro in the presence of increasing concentrations of ALG-097161, a probe compound designed in the context of a 3CLpro drug discovery program. We identified a combination of amino acid substitutions in 3CLpro (L50F E166A L167F) that is associated with a >20× increase in 50% effective concentration (EC50) values for ALG-097161, nirmatrelvir (PF-07321332), PF-00835231, and ensitrelvir. While two of the single substitutions (E166A and L167F) provide low-level resistance to the inhibitors in a biochemical assay, the triple mutant results in the highest levels of resistance (6× to 72×). All substitutions are associated with a significant loss of enzymatic 3CLpro activity, suggesting a reduction in viral fitness. Structural biology analysis indicates that the different substitutions reduce the number of inhibitor/enzyme interactions while the binding of the substrate is maintained. These observations will be important for the interpretation of resistance development to 3CLpro inhibitors in the clinical setting. IMPORTANCE Paxlovid is the first oral antiviral approved for treatment of SARS-CoV-2 infection. Antiviral treatments are often associated with the development of drug-resistant viruses. In order to guide the use of novel antivirals, it is essential to understand the risk of resistance development and to characterize the associated changes in the viral genes and proteins. In this work, we describe for the first time a pathway that allows SARS-CoV-2 to develop resistance against Paxlovid in vitro. The characteristics of in vitro antiviral resistance development may be predictive for the clinical situation. Therefore, our work will be important for the management of COVID-19 with Paxlovid and next-generation SARS-CoV-2 3CLpro inhibitors.
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Affiliation(s)
- Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology & Transplantation, Rega Institute, Laboratory of Virology & Chemotherapy, Leuven, Belgium
| | - Cheng Liu
- Aligos Therapeutics, Inc., South San Francisco, California, USA
| | - Kim Donckers
- KU Leuven, Department of Microbiology, Immunology & Transplantation, Rega Institute, Laboratory of Virology & Chemotherapy, Leuven, Belgium
| | | | | | - Sarah K Stevens
- Aligos Therapeutics, Inc., South San Francisco, California, USA
| | - Chloe De Vita
- Aligos Therapeutics, Inc., South San Francisco, California, USA
| | - Bert Vanmechelen
- KU Leuven, Department of Microbiology, Immunology & Transplantation, Rega Institute, Laboratory of Clinical & Epidemiological Virology, Leuven, Belgium
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology & Transplantation, Rega Institute, Laboratory of Clinical & Epidemiological Virology, Leuven, Belgium
| | - Bettina Trüeb
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology & Transplantation, Rega Institute, Laboratory of Virology & Chemotherapy, Leuven, Belgium
| | - Laura Vangeel
- KU Leuven, Department of Microbiology, Immunology & Transplantation, Rega Institute, Laboratory of Virology & Chemotherapy, Leuven, Belgium
| | | | - Andreas Jekle
- Aligos Therapeutics, Inc., South San Francisco, California, USA
| | | | | | - Julian A Symons
- Aligos Therapeutics, Inc., South San Francisco, California, USA
| | | | - Patrick Chaltin
- CISTIM Leuven vzw, Leuven, Belgium
- Centre for Drug Design and Discovery (CD3), KU Leuven, Leuven, Belgium
| | | | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology & Transplantation, Rega Institute, Laboratory of Virology & Chemotherapy, Leuven, Belgium
- Global Virus Network (GVN), Baltimore, Maryland, USA
| | - Jerome Deval
- Aligos Therapeutics, Inc., South San Francisco, California, USA
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33
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Dumenil T, Le TT, Rawle DJ, Yan K, Tang B, Nguyen W, Bishop C, Suhrbier A. Warmer ambient air temperatures reduce nasal turbinate and brain infection, but increase lung inflammation in the K18-hACE2 mouse model of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160163. [PMID: 36395835 PMCID: PMC9659553 DOI: 10.1016/j.scitotenv.2022.160163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Warmer climatic conditions have been associated with fewer COVID-19 cases. Herein we infected K18-hACE2 mice housed at the standard animal house temperature of ∼22 °C, or at ∼31 °C, which is considered to be thermoneutral for mice. On day 2 post infection, RNA-Seq analyses showed no significant differential gene expression lung in lungs of mice housed at the two temperatures, with almost identical viral loads and type I interferon responses. There was also no significant difference in viral loads in lungs on day 5, but RNA-Seq and histology analyses showed clearly elevated inflammatory signatures and infiltrates. Thermoneutrality thus promoted lung inflammation. On day 2 post infection mice housed at 31 °C showed reduced viral loads in nasal turbinates, consistent with increased mucociliary clearance at the warmer ambient temperature. These mice also had reduced virus levels in the brain, and an ensuing amelioration of weight loss and a delay in mortality. Warmer air temperatures may thus reduce infection of the upper respiratory track and the olfactory epithelium, resulting in reduced brain infection. Potential relevance for anosmia and neurological sequelae in COVID-19 patients is discussed.
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Affiliation(s)
- Troy Dumenil
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Thuy T Le
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Daniel J Rawle
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Kexin Yan
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Bing Tang
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Wilson Nguyen
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Cameron Bishop
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Andreas Suhrbier
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; Australian Infectious Disease Research Centre, GVN Center of Excellence, Brisbane, Queensland 4029, 4072, Australia.
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34
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Characterization of a Vesicular Stomatitis Virus-Vectored Recombinant Virus Bearing Spike Protein of SARS-CoV-2 Delta Variant. Microorganisms 2023; 11:microorganisms11020431. [PMID: 36838396 PMCID: PMC9960918 DOI: 10.3390/microorganisms11020431] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
The frequent emergence of SARS-CoV-2 variants thwarts the prophylactic and therapeutic countermeasures confronting COVID-19. Among them, the Delta variant attracts widespread attention due to its high pathogenicity and fatality rate compared with other variants. However, with the emergence of new variants, studies on Delta variants have been gradually weakened and ignored. In this study, a replication-competent recombinant virus carrying the S protein of the SARS-CoV-2 Delta variant was established based on the vesicular stomatitis virus (VSV), which presented a safe alternative model for studying the Delta variant. The recombinant virus showed a replication advantage in Vero E6 cells, and the viral titers reach 107.3 TCID50/mL at 36 h post-inoculation. In the VSV-vectored recombinant platform, the spike proteins of the Delta variant mediated higher fusion activity and syncytium formation than the wild-type strain. Notably, the recombinant virus was avirulent in BALB/c mice, Syrian hamsters, 3-day ICR suckling mice, and IFNAR/GR-/- mice. It induced protective neutralizing antibodies in rodents, and protected the Syrian hamsters against the SARS-CoV-2 Delta variant infection. Meanwhile, the eGFP reporter of recombinant virus enabled the visual assay of neutralizing antibodies. Therefore, the recombinant virus could be a safe and convenient surrogate tool for authentic SARS-CoV-2. This efficient and reliable model has significant potential for research on viral-host interactions, epidemiological investigation of serum-neutralizing antibodies, and vaccine development.
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35
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Dillard JA, Martinez SA, Dearing JJ, Montgomery SA, Baxter AK. Animal Models for the Study of SARS-CoV-2-Induced Respiratory Disease and Pathology. Comp Med 2023; 73:72-90. [PMID: 36229170 PMCID: PMC9948904 DOI: 10.30802/aalas-cm-22-000089] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Emergence of the betacoronavirus SARS-CoV-2 has resulted in a historic pandemic, with millions of deaths worldwide. An unprecedented effort has been made by the medical, scientific, and public health communities to rapidly develop and implement vaccines and therapeutics to prevent and reduce hospitalizations and deaths. Although SARS-CoV-2 infection can lead to disease in many organ systems, the respiratory system is its main target, with pneumonia and acute respiratory distress syndrome as the hallmark features of severe disease. The large number of patients who have contracted COVID-19 infections since 2019 has permitted a detailed characterization of the clinical and pathologic features of the disease in humans. However, continued progress in the development of effective preventatives and therapies requires a deeper understanding of the pathogenesis of infection. Studies using animal models are necessary to complement in vitro findings and human clinical data. Multiple animal species have been evaluated as potential models for studying the respiratory disease caused by SARSCoV-2 infection. Knowing the similarities and differences between animal and human responses to infection is critical for effective translation of animal data into human medicine. This review provides a detailed summary of the respiratory disease and associated pathology induced by SARS-CoV-2 infection in humans and compares them with the disease that develops in 3 commonly used models: NHP, hamsters, and mice. The effective use of animals to study SARS-CoV-2-induced respiratory disease will enhance our understanding of SARS-CoV-2 pathogenesis, allow the development of novel preventatives and therapeutics, and aid in the preparation for the next emerging virus with pandemic potential.
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Key Words
- ace2, angiotensin-converting enzyme 2
- agm, african green monkey
- ali, acute lung injury
- ards, acute respiratory distress syndrome
- balf, bronchoalveolar lavage fluid
- cards, covid-19-associated acute respiratory distress syndrome
- dad, diffuse alveolar damage
- dpi, days postinfection
- ggo, ground glass opacities
- s, spike glycoprotein
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Affiliation(s)
- Jacob A Dillard
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sabian A Martinez
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Justin J Dearing
- Biological and Biomedical Sciences Program, Office of Graduate Education, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Stephanie A Montgomery
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Andvictoria K Baxter
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina;,
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36
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Li Q, Vijaykumar K, Phillips SE, Hussain SS, Huynh NV, Fernandez-Petty CM, Lever JEP, Foote JB, Ren J, Campos-Gómez J, Daya FA, Hubbs NW, Kim H, Onuoha E, Boitet ER, Fu L, Leung HM, Yu L, Detchemendy TW, Schaefers LT, Tipper JL, Edwards LJ, Leal SM, Harrod KS, Tearney GJ, Rowe SM. Mucociliary transport deficiency and disease progression in Syrian hamsters with SARS-CoV-2 infection. JCI Insight 2023; 8:e163962. [PMID: 36625345 PMCID: PMC9870055 DOI: 10.1172/jci.insight.163962] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/16/2022] [Indexed: 01/10/2023] Open
Abstract
Substantial clinical evidence supports the notion that ciliary function in the airways is important in COVID-19 pathogenesis. Although ciliary damage has been observed in both in vitro and in vivo models, the extent or nature of impairment of mucociliary transport (MCT) in in vivo models remains unknown. We hypothesize that SARS-CoV-2 infection results in MCT deficiency in the airways of golden Syrian hamsters that precedes pathological injury in lung parenchyma. Micro-optical coherence tomography was used to quantitate functional changes in the MCT apparatus. Both genomic and subgenomic viral RNA pathological and physiological changes were monitored in parallel. We show that SARS-CoV-2 infection caused a 67% decrease in MCT rate as early as 2 days postinfection (dpi) in hamsters, principally due to 79% diminished airway coverage of motile cilia. Correlating quantitation of physiological, virological, and pathological changes reveals steadily descending infection from the upper airways to lower airways to lung parenchyma within 7 dpi. Our results indicate that functional deficits of the MCT apparatus are a key aspect of COVID-19 pathogenesis, may extend viral retention, and could pose a risk factor for secondary infection. Clinically, monitoring abnormal ciliated cell function may indicate disease progression. Therapies directed toward the MCT apparatus deserve further investigation.
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Affiliation(s)
- Qian Li
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | | | - Scott E. Phillips
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | - Shah S. Hussain
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | | | | | | | | | | | | | - Farah Abou Daya
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | - Nathaniel W. Hubbs
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | - Harrison Kim
- Gregory Fleming James Cystic Fibrosis Research Center
- Department of Radiology, and
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ezinwanne Onuoha
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Evan R. Boitet
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | - Lianwu Fu
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | - Hui Min Leung
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Linhui Yu
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Levi T. Schaefers
- Department of Microbiology
- Department of Anesthesiology and Perioperative Medicine
| | | | | | - Sixto M. Leal
- Department of Microbiology
- Department of Anesthesiology and Perioperative Medicine
| | | | - Guillermo J. Tearney
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven M. Rowe
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
- Department of Pediatrics
- Department of Cell Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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37
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Gao S, Song L, Xu H, Fikatas A, Oeyen M, De Jonghe S, Zhao F, Jing L, Jochmans D, Vangeel L, Cheng Y, Kang D, Neyts J, Herdewijn P, Schols D, Zhan P, Liu X. Identification of Polyphenol Derivatives as Novel SARS-CoV-2 and DENV Non-Nucleoside RdRp Inhibitors. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010160. [PMID: 36615354 PMCID: PMC9822497 DOI: 10.3390/molecules28010160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
The Coronavirus Disease 2019 (COVID-19) and dengue fever (DF) pandemics both remain to be significant public health concerns in the foreseeable future. Anti-SARS-CoV-2 drugs and vaccines are both indispensable to eliminate the epidemic situation. Here, two piperazine-based polyphenol derivatives DF-47 and DF-51 were identified as potential inhibitors directly blocking the active site of SARS-CoV-2 and DENV RdRp. Data through RdRp inhibition screening of an in-house library and in vitro antiviral study selected DF-47 and DF-51 as effective inhibitors of SARS-CoV-2/DENV polymerase. Moreover, in silico simulation revealed stable binding modes between the DF-47/DF-51 and SARS-CoV-2/DENV RdRp, respectively, including chelating with Mg2+ near polymerase active site. This work discovered the inhibitory effect of two polyphenols on distinct viral RdRp, which are expected to be developed into broad-spectrum, non-nucleoside RdRp inhibitors with new scaffold.
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Affiliation(s)
- Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Shenzhen Research Institute of Shandong University, A301 Virtual University Park in South District of Shenzhen, Shenzhen 518057, China
| | - Letian Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Hongtao Xu
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- Correspondence: (H.X.); (D.S.); (P.Z.); (X.L.)
| | - Antonios Fikatas
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Merel Oeyen
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Fabao Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Lanlan Jing
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Laura Vangeel
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Yusen Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- Correspondence: (H.X.); (D.S.); (P.Z.); (X.L.)
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Correspondence: (H.X.); (D.S.); (P.Z.); (X.L.)
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Correspondence: (H.X.); (D.S.); (P.Z.); (X.L.)
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Animal Models to Test SARS-CoV-2 Vaccines: Which Ones Are in Use and Future Expectations. Pathogens 2022; 12:pathogens12010020. [PMID: 36678369 PMCID: PMC9861368 DOI: 10.3390/pathogens12010020] [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: 09/22/2022] [Revised: 11/04/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
Since late 2019 and early 2020, with the emergence of the COVID-19 pandemic, scientists are rushing to develop treatment and prevention methods to combat SARS-CoV-2. Among these are vaccines. In view of this, the use of animals as experimental models, both to investigate the immunopathology of the disease and to evaluate the efficacy and safety of vaccines, is mandatory. This work aims to describe, through recent scientific articles found in reliable databases, the animal models used for the in vivo testing of COVID-19 vaccines, demonstrating some possibilities of more advantageous/gold-standard models for SARS-CoV-2 vaccines. The majority of the studies use rodents and primates. Meanwhile, the most adequate model to be used as the gold standard for in vivo tests of COVID-19 vaccines is not yet conclusive. Promising options are being discussed as new tests are being carried out and new SARS-CoV-2 variants are emerging.
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Abdelnabi R, Maes P, de Jonghe S, Weynand B, Neyts J. Combination of the parent analogue of remdesivir (GS-441524) and molnupiravir results in a markedly potent antiviral effect in SARS-CoV-2 infected Syrian hamsters. Front Pharmacol 2022; 13:1072202. [PMID: 36605401 PMCID: PMC9807602 DOI: 10.3389/fphar.2022.1072202] [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: 10/17/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Remdesivir was the first antiviral drug to be approved for the treatment of severe COVID-19; followed by molnupiravir (another prodrug of a nucleoside analogue) and the protease inhibitor nirmatrelvir. Combination of antiviral drugs may result in improved potency and help to avoid or delay the development of resistant variants. We set out to explore the combined antiviral potency of GS-441524 (the parent nucleoside of remdesivir) and molnupiravir against SARS-CoV-2. In SARS-CoV-2 (BA.5) infected A549-Dual™ hACE2-TMPRSS2 cells, the combination resulted in an overall additive antiviral effect with a synergism at certain concentrations. Next, the combined effect was explored in Syrian hamsters infected with SARS-CoV-2 (Beta, B.1.351); treatment was started at the time of infection and continued twice daily for four consecutive days. At day 4 post-infection, GS-441524 (50 mg/kg, oral BID) and molnupiravir (150 mg/kg, oral BID) as monotherapy reduced infectious viral loads by 0.5 and 1.6 log10, respectively, compared to the vehicle control. When GS-441524 (50 mg/kg, BID) and molnupiravir (150 mg/kg, BID) were combined, infectious virus was no longer detectable in the lungs of 7 out of 10 of the treated hamsters (4.0 log10 reduction) and titers in the other animals were reduced by ∼2 log10. The combined antiviral activity of molnupiravir which acts by inducing lethal mutagenesis and GS-441524, which acts as a chain termination appears to be highly effective in reducing SARS-CoV-2 replication/infectivity. The unexpected potent antiviral effect of the combination warrants further exploration as a potential treatment for COVID-19.
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Affiliation(s)
- Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
- The VirusBank Platform, Leuven, Belgium
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
- Zoonotic Infectious Diseases Unit, Leuven, Belgium
| | - Steven de Jonghe
- KU Leuven Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Birgit Weynand
- Division of Translational Cell and Tissue Research, KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
- The VirusBank Platform, Leuven, Belgium
- Global Virus Network, GVN, Baltimore, MD, United States
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40
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Kehrer T, Cupic A, Ye C, Yildiz S, Bouhhadou M, Crossland NA, Barrall E, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena N, Aslam S, Saqi A, Marin A, Rutkowska M, Ummadi MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.18.512708. [PMID: 36299428 PMCID: PMC9603824 DOI: 10.1101/2022.10.18.512708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We and others have previously shown that the SARS-CoV-2 accessory protein ORF6 is a powerful antagonist of the interferon (IFN) signaling pathway by directly interacting with Nup98-Rae1 at the nuclear pore complex (NPC) and disrupting bidirectional nucleo-cytoplasmic trafficking. In this study, we further assessed the role of ORF6 during infection using recombinant SARS-CoV-2 viruses carrying either a deletion or a well characterized M58R loss-of-function mutation in ORF6. We show that ORF6 plays a key role in the antagonism of IFN signaling and in viral pathogenesis by interfering with karyopherin(importin)-mediated nuclear import during SARS-CoV-2 infection both in vitro , and in the Syrian golden hamster model in vivo . In addition, we found that ORF6-Nup98 interaction also contributes to inhibition of cellular mRNA export during SARS-CoV-2 infection. As a result, ORF6 expression significantly remodels the host cell proteome upon infection. Importantly, we also unravel a previously unrecognized function of ORF6 in the modulation of viral protein expression, which is independent of its function at the nuclear pore. Lastly, we characterized the ORF6 D61L mutation that recently emerged in Omicron BA.2 and BA.4 and demonstrated that it is able to disrupt ORF6 protein functions at the NPC and to impair SARS-CoV-2 innate immune evasion strategies. Importantly, the now more abundant Omicron BA.5 lacks this loss-of-function polymorphism in ORF6. Altogether, our findings not only further highlight the key role of ORF6 in the antagonism of the antiviral innate immune response, but also emphasize the importance of studying the role of non-spike mutations to better understand the mechanisms governing differential pathogenicity and immune evasion strategies of SARS-CoV-2 and its evolving variants. ONE SENTENCE SUMMARY SARS-CoV-2 ORF6 subverts bidirectional nucleo-cytoplasmic trafficking to inhibit host gene expression and contribute to viral pathogenesis.
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41
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Park YJ, Pinto D, Walls AC, Liu Z, De Marco A, Benigni F, Zatta F, Silacci-Fregni C, Bassi J, Sprouse KR, Addetia A, Bowen JE, Stewart C, Giurdanella M, Saliba C, Guarino B, Schmid MA, Franko NM, Logue JK, Dang HV, Hauser K, di Iulio J, Rivera W, Schnell G, Rajesh A, Zhou J, Farhat N, Kaiser H, Montiel-Ruiz M, Noack J, Lempp FA, Janer J, Abdelnabi R, Maes P, Ferrari P, Ceschi A, Giannini O, de Melo GD, Kergoat L, Bourhy H, Neyts J, Soriaga L, Purcell LA, Snell G, Whelan SPJ, Lanzavecchia A, Virgin HW, Piccoli L, Chu HY, Pizzuto MS, Corti D, Veesler D. Imprinted antibody responses against SARS-CoV-2 Omicron sublineages. Science 2022; 378:619-627. [PMID: 36264829 DOI: 10.1126/science.adc9127] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters elicit plasma-neutralizing antibodies against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5, and that breakthrough infections, but not vaccination alone, induce neutralizing antibodies in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1, BA.2, and BA.4/5 receptor-binding domains, whereas Omicron primary infections elicit B cells of narrow specificity up to 6 months after infection. Although most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant-neutralizing antibody that is a strong candidate for clinical development.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Dora Pinto
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anna De Marco
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabrizia Zatta
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Jessica Bassi
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Christian Saliba
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Michael A Schmid
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicholas M Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Jennifer K Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Ha V Dang
- Vir Biotechnology, San Francisco, CA, USA
| | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA, USA
| | | | | | | | | | | | - Javier Janer
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Piet Maes
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Guilherme Dias de Melo
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | - Lauriane Kergoat
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | | | | | | | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Luca Piccoli
- Humabs Biomed SA, Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | | | - 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
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42
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Updated vaccine protects against SARS-CoV-2 variants including Omicron (B.1.1.529) and prevents transmission in hamsters. Nat Commun 2022; 13:6644. [PMID: 36333374 PMCID: PMC9636174 DOI: 10.1038/s41467-022-34439-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Current COVID-19 vaccines are based on prototypic spike sequences from ancestral 2019 SARS-CoV-2 strains. However, the ongoing pandemic is fueled by variants of concern (VOC) escaping vaccine-mediated protection. Here we demonstrate how immunization in hamsters using prototypic spike expressed from yellow fever 17D (YF17D) as vector blocks ancestral virus (B lineage) and VOC Alpha (B.1.1.7) yet fails to fully protect from Beta (B.1.351). However, the same YF17D vectored vaccine candidate with an evolved antigen induced considerably improved neutralizing antibody responses against VOCs Beta, Gamma (P.1) and the recently predominant Omicron (B.1.1.529), while maintaining immunogenicity against ancestral virus and VOC Delta (B.1.617.2). Thus vaccinated animals resisted challenge by all VOCs, including vigorous high titre exposure to the most difficult to cover Beta, Delta and Omicron variants, eliminating detectable virus and markedly improving lung pathology. Finally, vaccinated hamsters did not transmit Delta variant to non-vaccinated cage mates. Overall, our data illustrate how current first-generation COVID-19 vaccines may need to be updated to maintain efficacy against emerging VOCs and their spread at community level.
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Wang S, Xu L, Mu T, Qin M, Zhao P, Xie L, Du L, Wu Y, Legrand N, Mouchain K, Fichet G, Liu Y, Yin W, Zhao J, Ji M, Gong B, Klein M, Wu K. Intranasal delivery of a chimpanzee adenovirus vector expressing a pre-fusion spike (BV-AdCoV-1) protects golden Syrian hamsters against SARS-CoV-2 infection. Front Cell Infect Microbiol 2022; 12:979641. [PMID: 36405962 PMCID: PMC9671113 DOI: 10.3389/fcimb.2022.979641] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 08/08/2023] Open
Abstract
We evaluated the immunogenicity and protective ability of a chimpanzee replication-deficient adenovirus vectored COVID-19 vaccine (BV-AdCoV-1) expressing a stabilized pre-fusion SARS-CoV-2 spike glycoprotein in golden Syrian hamsters. Intranasal administration of BV-AdCoV-1 elicited strong humoral and cellular immunity in the animals. Furthermore, vaccination prevented weight loss, reduced SARS-CoV-2 infectious virus titers in the lungs as well as lung pathology and provided protection against SARS-CoV-2 live challenge. In addition, there was no vaccine-induced enhanced disease nor immunopathological exacerbation in BV-AdCoV-1-vaccinated animals. Furthermore, the vaccine induced cross-neutralizing antibody responses against the ancestral strain and the B.1.617.2, Omicron(BA.1), Omicron(BA.2.75) and Omicron(BA.4/5) variants of concern. These results demonstrate that BV-AdCoV-1 is potentially a promising candidate vaccine to prevent SARS-CoV-2 infection, and to curtail pandemic spread in humans.
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Affiliation(s)
- Shen Wang
- Regularoty and Medical Affairs Department, Wuhan BravoVax Co., Ltd., Wuhan, China
| | - Long Xu
- Project Management Department, Wuhan BravoVax Co., Ltd., Wuhan, China
| | - Ting Mu
- Innovative Discovery Department, Wuhan BravoVax Co., Ltd., Wuhan, China
| | - Mian Qin
- Project Management Department, Wuhan BravoVax Co., Ltd., Wuhan, China
| | - Ping Zhao
- Test Development Department, Wuhan BravoVax Co., Ltd., Wuhan, China
| | - Liang Xie
- Innovative Discovery Department, Wuhan BravoVax Co., Ltd., Wuhan, China
| | - Linsen Du
- China Office, Voisin Consulting Life Sciences, Shanghai, China
| | - Yue Wu
- Test Development Department, Wuhan BravoVax Co., Ltd., Wuhan, China
| | - Nicolas Legrand
- In Vivo Sciences Department, Oncodesign, Centre François Hyafil, Villebon-sur-Yvette, France
| | - Karine Mouchain
- DMPK & Bioanalytical Sciences Department, Oncodesign, Centre François Hyafil, Villebon-sur-Yvette, France
| | - Guillaume Fichet
- In Vitro Sciences Department, Oncodesign, Centre François Hyafil, Villebon-sur-Yvette, France
| | - Yi Liu
- Project Management Department, Wuhan BravoVax Co., Ltd., Wuhan, China
- State Key Laboratory of Biocatalysts and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Wenhao Yin
- Project Management Department, Wuhan BravoVax Co., Ltd., Wuhan, China
| | - Jin Zhao
- Test Development Department, Wuhan BravoVax Co., Ltd., Wuhan, China
| | - Min Ji
- Regularoty and Medical Affairs Department, Wuhan BravoVax Co., Ltd., Wuhan, China
| | - Bo Gong
- Regularoty and Medical Affairs Department, Wuhan BravoVax Co., Ltd., Wuhan, China
| | - Michel Klein
- Executive Office, Wuhan BravoVax Co., Ltd., Wuhan, China
- Executive Office, Shanghai BravoBio Co., Ltd., Shanghai, China
| | - Ke Wu
- Executive Office, Wuhan BravoVax Co., Ltd., Wuhan, China
- Executive Office, Shanghai BravoBio Co., Ltd., Shanghai, China
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44
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Martinez-Gualda B, Graus M, Camps A, Vanhulle E, Saul S, Azari S, Nhu Tran DH, Vangeel L, Chiu W, Neyts J, Schols D, Einav S, Vermeire K, De Jonghe S. Synthesis and evaluation of 3-alkynyl-5-aryl-7-aza-indoles as broad-spectrum antiviral agents. Front Chem 2022; 10:1058229. [PMID: 36385995 PMCID: PMC9643853 DOI: 10.3389/fchem.2022.1058229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
RNA viral infections, including those caused by respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Venezuelan Equine encephalitis virus (VEEV), pose a major global health challenge. Here, we report the synthesis and screening of a series of pyrrolo[2,3-b]pyridines targeting RSV, SARS-CoV-2 and/or VEEV. From this campaign, a series of lead compounds was generated that demonstrated antiviral activity in the low single-digit micromolar range against the various viruses and did not show cytotoxicity. These findings highlight the potential of 3-alkynyl-5-aryl-7-aza-indoles as a promising chemotype for the development of broad-spectrum antiviral agents.
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45
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Daems M, Liesenborghs L, Boudewijns R, Simmonds SJ, Kraisin S, Van Wauwe J, Cuijpers I, Raman J, Geuens N, Buyten TV, Lox M, Verhamme P, Van Linthout S, Martinod K, Heymans S, Tschöpe C, Neyts J, Jones EAV. SARS-CoV-2 infection causes prolonged cardiomyocyte swelling and inhibition of HIF1α translocation in an animal model COVID-19. Front Cardiovasc Med 2022; 9:964512. [PMID: 36324747 PMCID: PMC9618878 DOI: 10.3389/fcvm.2022.964512] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Recovered COVID-19 patients often display cardiac dysfunction, even after a mild infection. Most current histological results come from patients that are hospitalized and therefore represent more severe outcomes than most COVID-19 patients face. To overcome this limitation, we investigated the cardiac effects of SARS-CoV-2 infection in a hamster model. SARS-CoV-2 infected hamsters developed diastolic dysfunction after recovering from COVID-19. Histologically, increased cardiomyocyte size was present at the peak of viral load and remained at all time points investigated. As this increase is too rapid for hypertrophic remodeling, we found instead that the heart was oedemic. Moreover, cardiomyocyte swelling is associated with the presence of ischemia. Fibrin-rich microthrombi and pericyte loss were observed at the peak of viral load, resulting in increased HIF1α in cardiomyocytes. Surprisingly, SARS-CoV-2 infection inhibited the translocation of HIF1α to the nucleus both in hamster hearts, in cultured cardiomyocytes, as well as in an epithelial cell line. We propose that the observed diastolic dysfunction is the consequence of cardiac oedema, downstream of microvascular cardiac ischemia. Additionally, our data suggest that inhibition of HIF1α translocation could contribute to an exaggerated response upon SARS-CoV-2 infection.
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Affiliation(s)
- Margo Daems
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Laurens Liesenborghs
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Robbert Boudewijns
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Sirima Kraisin
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Jore Van Wauwe
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Ilona Cuijpers
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
| | - Jana Raman
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Nadèche Geuens
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Tina Van Buyten
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marleen Lox
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Peter Verhamme
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Sophie Van Linthout
- Virchow Clinic, Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - University Medicine Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
| | - Kimberly Martinod
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Stephane Heymans
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
| | - Carsten Tschöpe
- Virchow Clinic, Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - University Medicine Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- Department of Cardiology and Pneumology, Charité - University Medicine Berlin, Berlin, Germany
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Elizabeth A. V. Jones
- Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
- *Correspondence: Elizabeth A. V. Jones
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Cooper MS, Zhang L, Ibrahim M, Zhang K, Sun X, Röske J, Göhl M, Brönstrup M, Cowell JK, Sauerhering L, Becker S, Vangeel L, Jochmans D, Neyts J, Rox K, Marsh GP, Maple HJ, Hilgenfeld R. Diastereomeric Resolution Yields Highly Potent Inhibitor of SARS-CoV-2 Main Protease. J Med Chem 2022; 65:13328-13342. [PMID: 36179320 PMCID: PMC9574927 DOI: 10.1021/acs.jmedchem.2c01131] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Indexed: 12/02/2022]
Abstract
SARS-CoV-2 is the causative agent behind the COVID-19 pandemic. The main protease (Mpro, 3CLpro) of SARS-CoV-2 is a key enzyme that processes polyproteins translated from the viral RNA. Mpro is therefore an attractive target for the design of inhibitors that block viral replication. We report the diastereomeric resolution of the previously designed SARS-CoV-2 Mpro α-ketoamide inhibitor 13b. The pure (S,S,S)-diastereomer, 13b-K, displays an IC50 of 120 nM against the Mpro and EC50 values of 0.8-3.4 μM for antiviral activity in different cell types. Crystal structures have been elucidated for the Mpro complexes with each of the major diastereomers, the active (S,S,S)-13b (13b-K), and the nearly inactive (R,S,S)-13b (13b-H); results for the latter reveal a novel binding mode. Pharmacokinetic studies show good levels of 13b-K after inhalative as well as after peroral administration. The active inhibitor (13b-K) is a promising candidate for further development as an antiviral treatment for COVID-19.
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Affiliation(s)
- Mark S. Cooper
- Bio-Techne
(Tocris), The Watkins
Building, Atlantic Road, Bristol, BS11 9QD, U.K.
| | - Linlin Zhang
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Mohamed Ibrahim
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Kaixuan Zhang
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Judith Röske
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Matthias Göhl
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research (HZI), 38124 Braunschweig, Germany
| | - Mark Brönstrup
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research (HZI), 38124 Braunschweig, Germany
- German
Center for Infection Research (DZIF), Partner
Site Braunschweig-Hannover, 38124 Braunschweig, Germany
| | - Justin K. Cowell
- Bio-Techne
(Tocris), The Watkins
Building, Atlantic Road, Bristol, BS11 9QD, U.K.
| | - Lucie Sauerhering
- Institute
of Virology, University of Marburg, 35043 Marburg, Germany
| | - Stephan Becker
- Institute
of Virology, University of Marburg, 35043 Marburg, Germany
- German Center
for Infection Research (DZIF), Marburg-Gießen-Langen
Site, 35043 Marburg, Germany
| | - Laura Vangeel
- Rega
Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, B-3000 Leuven, Belgium
| | - Dirk Jochmans
- Rega
Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, B-3000 Leuven, Belgium
| | - Johan Neyts
- Rega
Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, B-3000 Leuven, Belgium
| | - Katharina Rox
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research (HZI), 38124 Braunschweig, Germany
- German
Center for Infection Research (DZIF), Partner
Site Braunschweig-Hannover, 38124 Braunschweig, Germany
| | - Graham P. Marsh
- Bio-Techne
(Tocris), The Watkins
Building, Atlantic Road, Bristol, BS11 9QD, U.K.
| | - Hannah J. Maple
- Bio-Techne
(Tocris), The Watkins
Building, Atlantic Road, Bristol, BS11 9QD, U.K.
| | - Rolf Hilgenfeld
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German
Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems
Site, University of Lübeck, 23562 Lübeck, Germany
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47
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COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data. Biomolecules 2022; 12:biom12101446. [PMID: 36291657 PMCID: PMC9599684 DOI: 10.3390/biom12101446] [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: 09/02/2022] [Revised: 10/01/2022] [Accepted: 10/02/2022] [Indexed: 11/17/2022] Open
Abstract
Host genetics affect both the susceptibility and response to viral infection. Searching for host genes that contribute to COVID-19, the Host Genetics Initiative (HGI) was formed to investigate the genetic factors involved in COVID-19 via genome-wide association studies (GWAS). The GWAS suffer from limited statistical power and in general, only a few genes can pass the conventional significance thresholds. This statistical limitation may be overcome by boosting weak association signals through integrating independent functional information such as molecular interactions. Additionally, the boosted results can be evaluated by various independent data for further connections to COVID-19. We present COVID-GWAB, a web-based tool to boost original GWAS signals from COVID-19 patients by taking the signals of the interactome neighbors. COVID-GWAB takes summary statistics from the COVID-19 HGI or user input data and reprioritizes candidate host genes for COVID-19 using HumanNet, a co-functional human gene network. The current version of COVID-GWAB provides the pre-processed data of releases 5, 6, and 7 of the HGI. Additionally, COVID-GWAB provides web interfaces for a summary of augmented GWAS signals, prediction evaluations by appearance frequency in COVID-19 literature, single-cell transcriptome data, and associated pathways. The web server also enables browsing the candidate gene networks.
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48
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Frere JJ, Serafini RA, Pryce KD, Zazhytska M, Oishi K, Golynker I, Panis M, Zimering J, Horiuchi S, Hoagland DA, Møller R, Ruiz A, Kodra A, Overdevest JB, Canoll PD, Borczuk AC, Chandar V, Bram Y, Schwartz R, Lomvardas S, Zachariou V, tenOever BR. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery. Sci Transl Med 2022; 14:eabq3059. [PMID: 35857629 PMCID: PMC9210449 DOI: 10.1126/scitranslmed.abq3059] [Citation(s) in RCA: 114] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/27/2022] [Indexed: 12/14/2022]
Abstract
The host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can result in prolonged pathologies collectively referred to as post-acute sequalae of COVID-19 (PASC) or long COVID. To better understand the mechanism underlying long COVID biology, we compared the short- and long-term systemic responses in the golden hamster after either SARS-CoV-2 or influenza A virus (IAV) infection. Results demonstrated that SARS-CoV-2 exceeded IAV in its capacity to cause permanent injury to the lung and kidney and uniquely affected the olfactory bulb (OB) and olfactory epithelium (OE). Despite a lack of detectable infectious virus, the OB and OE demonstrated myeloid and T cell activation, proinflammatory cytokine production, and an interferon response that correlated with behavioral changes extending a month after viral clearance. These sustained transcriptional changes could also be corroborated from tissue isolated from individuals who recovered from COVID-19. These data highlight a molecular mechanism for persistent COVID-19 symptomology and provide a small animal model to explore future therapeutics.
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Affiliation(s)
- Justin J. Frere
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | - Randal A. Serafini
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kerri D. Pryce
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Marianna Zazhytska
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027
| | - Kohei Oishi
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | - Ilona Golynker
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | - Maryline Panis
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | - Jeffrey Zimering
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Shu Horiuchi
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | | | - Rasmus Møller
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | - Anne Ruiz
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Albana Kodra
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027
| | - Jonathan B. Overdevest
- Department of Otolaryngology- Head and Neck Surgery, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Peter D. Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Alain C. Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021
| | - Vasuretha Chandar
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY 10021
| | - Yaron Bram
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY 10021
| | - Robert Schwartz
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY 10021
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027
| | - Venetia Zachariou
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Benjamin R. tenOever
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
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49
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Ravlo E, Evensen L, Sanson G, Hildonen S, Ianevski A, Skjervold PO, Ji P, Wang W, Kaarbø M, Kaynova GD, Kainov DE, Bjørås M. Antiviral Immunoglobulins of Chicken Egg Yolk for Potential Prevention of SARS-CoV-2 Infection. Viruses 2022; 14:v14102121. [PMID: 36298676 PMCID: PMC9609661 DOI: 10.3390/v14102121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 12/16/2022] Open
Abstract
Background: Some viruses cause outbreaks, which require immediate attention. Neutralizing antibodies could be developed for viral outbreak management. However, the development of monoclonal antibodies is often long, laborious, and unprofitable. Here, we report the development of chicken polyclonal neutralizing antibodies against SARS-CoV-2 infection. Methods: Layers were immunized twice with 14-day intervals using the purified receptor-binding domain (RBD) of the S protein of SARS-CoV-2/Wuhan or SARS-CoV-2/Omicron. Eggs were harvested 14 days after the second immunization. Polyclonal IgY antibodies were extracted. Binding of anti-RBD IgYs was analyzed by immunoblot and indirect ELISA. Furthermore, the neutralization capacity of anti-RBD IgYs was measured in Vero-E6 cells infected with SARS-CoV-2-mCherry/Wuhan and SARS-CoV-2/Omicron using fluorescence and/or cell viability assays. In addition, the effect of IgYs on the expression of SARS-CoV-2 and host cytokine genes in the lungs of Syrian Golden hamsters was examined using qRT-PCR. Results: Anti-RBD IgYs efficiently bound viral RBDs in situ, neutralized the virus variants in vitro, and lowered viral RNA amplification, with minimal alteration of virus-mediated immune gene expression in vivo. Conclusions: Altogether, our results indicate that chicken polyclonal IgYs can be attractive targets for further pre-clinical and clinical development for the rapid management of outbreaks of emerging and re-emerging viruses.
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Affiliation(s)
- Erlend Ravlo
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway
- Correspondence: (E.R.); (M.B.); Tel.: +47-73598474 (M.B.)
| | - Lasse Evensen
- Norimun AS, Felleskjøpet Agri SA, Postboks 469, 0105 Oslo, Norway
| | - Gorm Sanson
- Felleskjøpet Fôrutvikling AS, Nedre Ila 20, 7018 Trondheim, Norway
| | - Siri Hildonen
- Norimun AS, Felleskjøpet Agri SA, Postboks 469, 0105 Oslo, Norway
| | - Aleksandr Ianevski
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway
| | | | - Ping Ji
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway
| | - Wei Wang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway
| | - Mari Kaarbø
- Department of Microbiology, Oslo University Hospital, 0105 Oslo, Norway
| | | | - Denis E. Kainov
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
- Institute for Molecular Medicine Finland, University of Helsinki, 00014 Helsinki, Finland
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway
- Correspondence: (E.R.); (M.B.); Tel.: +47-73598474 (M.B.)
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50
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Clerbaux LA, Mayasich SA, Muñoz A, Soares H, Petrillo M, Albertini MC, Lanthier N, Grenga L, Amorim MJ. Gut as an Alternative Entry Route for SARS-CoV-2: Current Evidence and Uncertainties of Productive Enteric Infection in COVID-19. J Clin Med 2022; 11:5691. [PMID: 36233559 PMCID: PMC9573230 DOI: 10.3390/jcm11195691] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/17/2022] [Accepted: 09/20/2022] [Indexed: 12/15/2022] Open
Abstract
The gut has been proposed as a potential alternative entry route for SARS-CoV-2. This was mainly based on the high levels of SARS-CoV-2 receptor expressed in the gastrointestinal (GI) tract, the observations of GI disorders (such as diarrhea) in some COVID-19 patients and the detection of SARS-CoV-2 RNA in feces. However, the underlying mechanisms remain poorly understood. It has been proposed that SARS-CoV-2 can productively infect enterocytes, damaging the intestinal barrier and contributing to inflammatory response, which might lead to GI manifestations, including diarrhea. Here, we report a methodological approach to assess the evidence supporting the sequence of events driving SARS-CoV-2 enteric infection up to gut adverse outcomes. Exploring evidence permits to highlight knowledge gaps and current inconsistencies in the literature and to guide further research. Based on the current insights on SARS-CoV-2 intestinal infection and transmission, we then discuss the potential implication on clinical practice, including on long COVID. A better understanding of the GI implication in COVID-19 is still needed to improve disease management and could help identify innovative therapies or preventive actions targeting the GI tract.
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Affiliation(s)
| | - Sally A. Mayasich
- University of Wisconsin-Madison Aquatic Sciences Center at US EPA, Duluth, MN 55804, USA
| | - Amalia Muñoz
- European Commission, Joint Research Centre (JRC), 2440 Geel, Belgium
| | - Helena Soares
- Laboratory of Human Immunobiology and Pathogenesis, iNOVA4Health, Faculdade de Ciências Médicas—Nova Medical School, Universidade Nova de Lisboa, 1099-085 Lisbon, Portugal
| | | | | | - Nicolas Lanthier
- Laboratory of Hepatogastroenterology, Service d’Hépato-Gastroentérologie, Cliniques Universitaires Saint-Luc, UCLouvain, 1200 Brussels, Belgium
| | - Lucia Grenga
- Département Médicaments et Technologies pour la Santé, Commissariat à l’Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay, 91190 Paris, France
| | - Maria-Joao Amorim
- Instituto Gulbenkian de Ciência, 2780-156 Lisbon, Portugal
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa, 1649-023 Lisbon, Portugal
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