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García-Crespo C, de Ávila AI, Gallego I, Soria ME, Durán-Pastor A, Somovilla P, Martínez-González B, Muñoz-Flores J, Mínguez P, Salar-Vidal L, Esteban-Muñoz M, Cañar-Camacho E, Ferrer-Orta C, Zuñiga S, Sola I, Enjuanes L, Esteban J, Fernández-Roblas R, Gadea I, Gómez J, Verdaguer N, Domingo E, Perales C. Synergism between remdesivir and ribavirin leads to SARS-CoV-2 extinction in cell culture. Br J Pharmacol 2024. [PMID: 38616133 DOI: 10.1111/bph.16344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND AND PURPOSE There is a need for effective anti-COVID-19 treatments, mainly for individuals at risk of severe disease such as the elderly and the immunosuppressed. Drug repositioning has proved effective in identifying drugs that can find a new application for the control of coronavirus disease, in particular COVID-19. The purpose of the present study was to find synergistic antiviral combinations for COVID-19 based on lethal mutagenesis. EXPERIMENTAL APPROACH The effect of combinations of remdesivir and ribavirin on the infectivity of SARS-CoV-2 in cell culture has been tested. Viral populations were monitored by ultra-deep sequencing, and the decrease of infectivity as a result of the treatment was measured. KEY RESULTS Remdesivir and ribavirin exerted a synergistic inhibitory activity against SARS-CoV-2, quantified both by CompuSyn (Chou-Talalay method) and Synergy Finder (ZIP-score model). In serial passage experiments, virus extinction was readily achieved with remdesivir-ribavirin combinations at concentrations well below their cytotoxic 50 value, but not with the drugs used individually. Deep sequencing of treated viral populations showed that remdesivir, ribavirin, and their combinations evoked significant increases of the number of viral mutations and haplotypes, as well as modification of diversity indices that characterize viral quasi-species. CONCLUSION AND IMPLICATIONS SARS-CoV-2 extinction can be achieved by synergistic combination treatments based on lethal mutagenesis. In addition, the results offer prospects of triple drug treatments for effective SARS-CoV-2 suppression.
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Affiliation(s)
- Carlos García-Crespo
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain
| | - Isabel Gallego
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain
| | - María Eugenia Soria
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Antoni Durán-Pastor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Pilar Somovilla
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
| | - Brenda Martínez-González
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | | | - Pablo Mínguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Llanos Salar-Vidal
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Mario Esteban-Muñoz
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Elizabeth Cañar-Camacho
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Cristina Ferrer-Orta
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Barcelona, Spain
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Ricardo Fernández-Roblas
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Jordi Gómez
- Instituto de Parasitología y Biomedicina 'López-Neyra' (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, Granada, Spain
| | - Nuria Verdaguer
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Barcelona, Spain
| | - Esteban Domingo
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain
| | - Celia Perales
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
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2
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Aranda-Abreu GE, Carreón-Rodriguez A, Zuñiga S, Pozo D. Editorial: SARS-CoV-2 in neurodegenerative diseases. Front Neurosci 2024; 18:1360234. [PMID: 38292446 PMCID: PMC10824960 DOI: 10.3389/fnins.2024.1360234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024] Open
Affiliation(s)
| | | | - Sonia Zuñiga
- National Center for Biotechnology, Spanish National Research Council (CSIC), Madrid, Spain
| | - David Pozo
- Department of Medical Biochemistry, Molecular Biology and Immunology, Faculty of Medicine, University of Seville, Seville, Spain
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Wang L, Guzman M, Muñoz-Santos D, Honrubia JM, Ripoll-Gomez J, Delgado R, Sola I, Enjuanes L, Zuñiga S. Cell type dependent stability and virulence of a recombinant SARS-CoV-2, and engineering of a propagation deficient RNA replicon to analyze virus RNA synthesis. Front Cell Infect Microbiol 2023; 13:1268227. [PMID: 37942479 PMCID: PMC10628495 DOI: 10.3389/fcimb.2023.1268227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Engineering of reverse genetics systems for newly emerged viruses allows viral genome manipulation, being an essential tool for the study of virus life cycle, virus-host interactions and pathogenesis, as well as for the development of effective antiviral strategies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent human coronavirus that has caused the coronavirus disease (COVID-19) pandemic. The engineering of a full-length infectious cDNA clone and a fluorescent replicon of SARS-CoV-2 Wuhan-Hu-1, using a bacterial artificial chromosome, is reported. Viral growth and genetic stability in eleven cell lines were analyzed, showing that both VeroE6 cells overexpressing transmembrane serin protease 2 (TMPRSS2) and human lung derived cells resulted in the optimization of a cell system to preserve SARS-CoV-2 genetic stability. The recombinant SARS-CoV-2 virus and a point mutant expressing the D614G spike protein variant were virulent in a mouse model. The RNA replicon was propagation-defective, allowing its use in BSL-2 conditions to analyze viral RNA synthesis. The SARS-CoV-2 reverse genetics systems developed constitute a useful tool for studying the molecular biology of the virus, the development of genetically defined vaccines and to establish systems for antiviral compounds screening.
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Affiliation(s)
- Li Wang
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - María Guzman
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Diego Muñoz-Santos
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Jose Manuel Honrubia
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Jorge Ripoll-Gomez
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Rafael Delgado
- Laboratory of Molecular Microbiology, Instituto de Investigación Hospital 12 de Octubre (Imas12), Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
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4
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Alhammad YM, Parthasarathy S, Ghimire R, Kerr CM, O’Connor JJ, Pfannenstiel JJ, Chanda D, Miller CA, Baumlin N, Salathe M, Unckless RL, Zuñiga S, Enjuanes L, More S, Channappanavar R, Fehr AR. SARS-CoV-2 Mac1 is required for IFN antagonism and efficient virus replication in cell culture and in mice. Proc Natl Acad Sci U S A 2023; 120:e2302083120. [PMID: 37607224 PMCID: PMC10468617 DOI: 10.1073/pnas.2302083120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/30/2023] [Indexed: 08/24/2023] Open
Abstract
Several coronavirus (CoV) encoded proteins are being evaluated as targets for antiviral therapies for COVID-19. Included in these drug targets is the conserved macrodomain, or Mac1, an ADP-ribosylhydrolase and ADP-ribose binding protein encoded as a small domain at the N terminus of nonstructural protein 3. Utilizing point mutant recombinant viruses, Mac1 was shown to be critical for both murine hepatitis virus (MHV) and severe acute respiratory syndrome (SARS)-CoV virulence. However, as a potential drug target, it is imperative to understand how a complete Mac1 deletion impacts the replication and pathogenesis of different CoVs. To this end, we created recombinant bacterial artificial chromosomes (BACs) containing complete Mac1 deletions (ΔMac1) in MHV, MERS-CoV, and SARS-CoV-2. While we were unable to recover infectious virus from MHV or MERS-CoV ΔMac1 BACs, SARS-CoV-2 ΔMac1 was readily recovered from BAC transfection, indicating a stark difference in the requirement for Mac1 between different CoVs. Furthermore, SARS-CoV-2 ΔMac1 replicated at or near wild-type levels in multiple cell lines susceptible to infection. However, in a mouse model of severe infection, ΔMac1 was quickly cleared causing minimal pathology without any morbidity. ΔMac1 SARS-CoV-2 induced increased levels of interferon (IFN) and IFN-stimulated gene expression in cell culture and mice, indicating that Mac1 blocks IFN responses which may contribute to its attenuation. ΔMac1 infection also led to a stark reduction in inflammatory monocytes and neutrophils. These results demonstrate that Mac1 only minimally impacts SARS-CoV-2 replication, unlike MHV and MERS-CoV, but is required for SARS-CoV-2 pathogenesis and is a unique antiviral drug target.
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Affiliation(s)
- Yousef M. Alhammad
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66047
| | | | - Roshan Ghimire
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK74078
| | - Catherine M. Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66047
| | - Joseph J. O’Connor
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66047
| | | | - Debarati Chanda
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK74078
| | - Caden A. Miller
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK74078
| | - Nathalie Baumlin
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS66160
| | - Matthias Salathe
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS66160
| | - Robert L. Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66047
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology, National Center of Biotechnology, Madrid28049, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center of Biotechnology, Madrid28049, Spain
| | - Sunil More
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK74078
| | | | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66047
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5
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Hussein M, Andrade dos Ramos Z, Vink MA, Kroon P, Yu Z, Enjuanes L, Zuñiga S, Berkhout B, Herrera-Carrillo E. Efficient CRISPR-Cas13d-Based Antiviral Strategy to Combat SARS-CoV-2. Viruses 2023; 15:v15030686. [PMID: 36992394 PMCID: PMC10051389 DOI: 10.3390/v15030686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
The current SARS-CoV-2 pandemic forms a major global health burden. Although protective vaccines are available, concerns remain as new virus variants continue to appear. CRISPR-based gene-editing approaches offer an attractive therapeutic strategy as the CRISPR-RNA (crRNA) can be adjusted rapidly to accommodate a new viral genome sequence. This study aimed at using the RNA-targeting CRISPR-Cas13d system to attack highly conserved sequences in the viral RNA genome, thereby preparing for future zoonotic outbreaks of other coronaviruses. We designed 29 crRNAs targeting highly conserved sequences along the complete SARS-CoV-2 genome. Several crRNAs demonstrated efficient silencing of a reporter with the matching viral target sequence and efficient inhibition of a SARS-CoV-2 replicon. The crRNAs that suppress SARS-CoV-2 were also able to suppress SARS-CoV, thus demonstrating the breadth of this antiviral strategy. Strikingly, we observed that only crRNAs directed against the plus-genomic RNA demonstrated antiviral activity in the replicon assay, in contrast to those that bind the minus-genomic RNA, the replication intermediate. These results point to a major difference in the vulnerability and biology of the +RNA versus −RNA strands of the SARS-CoV-2 genome and provide important insights for the design of RNA-targeting antivirals.
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Affiliation(s)
- Mouraya Hussein
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Zaria Andrade dos Ramos
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Monique A. Vink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Pascal Kroon
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Zhenghao Yu
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Correspondence:
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6
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Wang L, Guzmán M, Sola I, Enjuanes L, Zuñiga S. Cytoplasmic ribonucleoprotein complexes, RNA helicases and coronavirus infection. Front Virol 2022. [DOI: 10.3389/fviro.2022.1078454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA metabolism in the eukaryotic cell includes the formation of ribonucleoprotein complexes (RNPs) that, depending on their protein components, have a different function. Cytoplasmic RNPs, such as stress granules (SGs) or P-bodies (PBs) are quite relevant during infections modulating viral and cellular RNA expression and as key players in the host cell antiviral response. RNA helicases are abundant components of RNPs and could have a significant effect on viral infection. This review focuses in the role that RNPs and RNA helicases have during coronavirus (CoVs) infection. CoVs are emerging highly pathogenic viruses with a large single-stranded RNA genome. During CoV infection, a complex network of RNA-protein interactions in different RNP structures is established. In general, RNA helicases and RNPs have an antiviral function, but there is limited knowledge on whether the viral protein interactions with cell components are mediators of this antiviral effect or are part of the CoV antiviral counteraction mechanism. Additional data is needed to elucidate the role of these RNA-protein interactions during CoV infection and their potential contribution to viral replication or pathogenesis.
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7
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Varona JF, Landete P, Lopez-Martin JA, Estrada V, Paredes R, Guisado-Vasco P, Fernandez de Orueta L, Torralba M, Fortun J, Vates R, Barberan J, Clotet B, Ancochea J, Carnevali D, Cabello N, Porras L, Gijon P, Monereo A, Abad D, Zuñiga S, Sola I, Rodon J, Vergara-Alert J, Izquierdo-Useros N, Fudio S, Pontes MJ, de Rivas B, Giron de Velasco P, Nieto A, Gomez J, Aviles P, Lubomirov R, Belgrano A, Sopesen B, White KM, Rosales R, Yildiz S, Reuschl AK, Thorne LG, Jolly C, Towers GJ, Zuliani-Alvarez L, Bouhaddou M, Obernier K, McGovern BL, Rodriguez ML, Enjuanes L, Fernandez-Sousa JM, Krogan NJ, Jimeno JM, Garcia-Sastre A. Preclinical and randomized phase I studies of plitidepsin in adults hospitalized with COVID-19. Life Sci Alliance 2022; 5:e202101200. [PMID: 35012962 PMCID: PMC8761492 DOI: 10.26508/lsa.202101200] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/24/2021] [Accepted: 12/28/2021] [Indexed: 12/16/2022] Open
Abstract
Plitidepsin, a marine-derived cyclic-peptide, inhibits SARS-CoV-2 replication at nanomolar concentrations by targeting the host protein eukaryotic translation elongation factor 1A. Here, we show that plitidepsin distributes preferentially to lung over plasma, with similar potency against across several SARS-CoV-2 variants in preclinical studies. Simultaneously, in this randomized, parallel, open-label, proof-of-concept study (NCT04382066) conducted in 10 Spanish hospitals between May and November 2020, 46 adult hospitalized patients with confirmed SARS-CoV-2 infection received either 1.5 mg (n = 15), 2.0 mg (n = 16), or 2.5 mg (n = 15) plitidepsin once daily for 3 d. The primary objective was safety; viral load kinetics, mortality, need for increased respiratory support, and dose selection were secondary end points. One patient withdrew consent before starting procedures; 45 initiated treatment; one withdrew because of hypersensitivity. Two Grade 3 treatment-related adverse events were observed (hypersensitivity and diarrhea). Treatment-related adverse events affecting more than 5% of patients were nausea (42.2%), vomiting (15.6%), and diarrhea (6.7%). Mean viral load reductions from baseline were 1.35, 2.35, 3.25, and 3.85 log10 at days 4, 7, 15, and 31. Nonmechanical invasive ventilation was required in 8 of 44 evaluable patients (16.0%); six patients required intensive care support (13.6%), and three patients (6.7%) died (COVID-19-related). Plitidepsin has a favorable safety profile in patients with COVID-19.
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Affiliation(s)
- Jose F Varona
- Departamento de Medicina Interna, Hospital Universitario HM Monteprincipe, HM Hospitales, Madrid, Spain
- Facultad de Medicina, Universidad San Pablo-CEU, Madrid, Spain
| | - Pedro Landete
- Hospital Universitario La Princesa, Madrid, Spain
- Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Vicente Estrada
- Hospital Clínico San Carlos, Madrid, Spain
- Universidad Complutense de Madrid, Madrid, Spain
| | - Roger Paredes
- Infectious Diseases Department, IrsiCaixa AIDS Research Institute, Barcelona, Spain
- Hospital Germans Trias I Pujol, Barcelona, Spain
| | - Pablo Guisado-Vasco
- Hospital Universitario Quironsalud Madrid, Madrid, Spain
- Universidad Europea, Madrid, Spain
| | - Lucia Fernandez de Orueta
- Universidad Europea, Madrid, Spain
- Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain
| | - Miguel Torralba
- Health Sciences Faculty, University of Alcalá, Madrid, Spain
- Guadalajara University Hospital, Guadalajara, Spain
| | - Jesus Fortun
- Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Roberto Vates
- Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain
| | - Jose Barberan
- Departamento de Medicina Interna, Hospital Universitario HM Monteprincipe, HM Hospitales, Madrid, Spain
- Facultad de Medicina, Universidad San Pablo-CEU, Madrid, Spain
| | - Bonaventura Clotet
- Infectious Diseases Department, IrsiCaixa AIDS Research Institute, Barcelona, Spain
- Hospital Germans Trias I Pujol, Barcelona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Universitat de Vic, Universitat Central de Catalunya, Barcelona, Spain
| | - Julio Ancochea
- Hospital Universitario La Princesa, Madrid, Spain
- Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Daniel Carnevali
- Hospital Universitario Quironsalud Madrid, Madrid, Spain
- Universidad Europea, Madrid, Spain
| | - Noemi Cabello
- Infectious Diseases Department, Clinico San Carlos University Hospital, Madrid, Spain
| | - Lourdes Porras
- Internal Medicine, Hospital General de Ciudad Real, Ciudad Real, Spain
| | - Paloma Gijon
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Alfonso Monereo
- Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain
| | - Daniel Abad
- Universidad Europea, Madrid, Spain
- Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Jordi Rodon
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, Bellaterra, Spain
| | - Julia Vergara-Alert
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, Bellaterra, Spain
| | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Barcelona, Spain
- Germans Trias I Pujol Research Institute (IGTP), Badalona, Spain
| | | | | | | | | | | | | | | | | | | | - Belen Sopesen
- Virology and Inflammation Unit, PharmaMar, SA, Madrid, Spain
- Sylentis, SAU, Madrid, Spain
- Biocross, SL, Valladolid, Spain
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Soner Yildiz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - Lorena Zuliani-Alvarez
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J David Gladstone Institutes, San Francisco, CA, USA
- QBI, Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J David Gladstone Institutes, San Francisco, CA, USA
- QBI, Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J David Gladstone Institutes, San Francisco, CA, USA
- QBI, Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Briana L McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | | | - Nevan J Krogan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J David Gladstone Institutes, San Francisco, CA, USA
- QBI, Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Jose M Jimeno
- Virology and Inflammation Unit, PharmaMar, SA, Madrid, Spain
| | - Adolfo Garcia-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tish Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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8
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Tarazona N, Martín-Arana J, Tébar-Martínez R, Gimeno-Valiente F, Gambardella V, Alvaro MH, Martínez-Ciarpaglini C, Alfaro-Cervello C, Cabeza-Segura M, García-Micó B, Moragón S, Tapia M, Carbonell-Asins J, Rentero-Garrido P, Zuñiga S, Roselló S, Fleitas T, Castillo J, Perez DR, Cervantes A. 464P Exome sequencing of ctDNA portrays the mutational landscape of patients with relapsing colon cancer and indicates new actionable targets. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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9
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van der Gaag K, Hoogenboom J, Busscher L, Benschop C, Zuñiga S, Sijen T. The impact of FDSTools noise correction on the analysis of data from the Forenseq™ DNA Signature Prep Kit. Forensic Science International: Genetics Supplement Series 2019. [DOI: 10.1016/j.fsigss.2019.10.181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Tarazona N, Gimeno-Valiente F, Gambardella V, Zuñiga S, Rentero-Garrido P, Huerta M, Roselló S, Martinez-Ciarpaglini C, Carbonell-Asins JA, Carrasco F, Ferrer-Martínez A, Bruixola G, Fleitas T, Martín J, Tébar-Martínez R, Moro D, Castillo J, Espí A, Roda D, Cervantes A. Targeted next-generation sequencing of circulating-tumor DNA for tracking minimal residual disease in localized colon cancer. Ann Oncol 2019; 30:1804-1812. [PMID: 31562764 DOI: 10.1093/annonc/mdz390] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND A high percentage of patients diagnosed with localized colon cancer (CC) will relapse after curative treatment. Although pathological staging currently guides our treatment decisions, there are no biomarkers determining minimal residual disease (MRD) and patients are at risk of being undertreated or even overtreated with chemotherapy in this setting. Circulating-tumor DNA (ctDNA) can to be a useful tool to better detect risk of relapse. PATIENTS AND METHODS One hundred and fifty patients diagnosed with localized CC were prospectively enrolled in our study. Tumor tissue from those patients was sequenced by a custom-targeted next-generation sequencing (NGS) panel to characterize somatic mutations. A minimum variant allele frequency (VAF) of 5% was applied for variant filtering. Orthogonal droplet digital PCR (ddPCR) validation was carried out. We selected known variants with higher VAF to track ctDNA in the plasma samples by ddPCR. RESULTS NGS found known pathological mutations in 132 (88%) primary tumors. ddPCR showed high concordance with NGS (r = 0.77) for VAF in primary tumors. Detection of ctDNA after surgery and in serial plasma samples during follow-up were associated with poorer disease-free survival (DFS) [hazard ratio (HR), 17.56; log-rank P = 0.0014 and HR, 11.33; log-rank P = 0.0001, respectively]. Tracking at least two variants in plasma increased the ability to identify MRD to 87.5%. ctDNA was the only significantly independent predictor of DFS in multivariable analysis. In patients treated with adjuvant chemotherapy, presence of ctDNA after therapy was associated with early relapse (HR 10.02; log-rank P < 0.0001). Detection of ctDNA at follow-up preceded radiological recurrence with a median lead time of 11.5 months. CONCLUSIONS Plasma postoperative ctDNA detected MRD and identified patients at high risk of relapse in localized CC. Mutation tracking with more than one variant in serial plasma samples improved our accuracy in predicting MRD.
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Affiliation(s)
- N Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain
| | - F Gimeno-Valiente
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain
| | - V Gambardella
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain
| | - S Zuñiga
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Precision Medicine Unit, Valencia, Spain; Bioinformatics and Biostatistics Unit, Valencia, Spain
| | - P Rentero-Garrido
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Precision Medicine Unit, Valencia, Spain
| | - M Huerta
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain
| | - S Roselló
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain
| | - C Martinez-Ciarpaglini
- Instituto de Salud Carlos III, CIBERONC, Madrid, Spain; Departments of Pathology, Valencia, Spain
| | - J A Carbonell-Asins
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Precision Medicine Unit, Valencia, Spain; Bioinformatics and Biostatistics Unit, Valencia, Spain
| | - F Carrasco
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain; Precision Medicine Unit, Valencia, Spain
| | - A Ferrer-Martínez
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain; Precision Medicine Unit, Valencia, Spain
| | - G Bruixola
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain
| | - T Fleitas
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain
| | - J Martín
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain; Bioinformatics and Biostatistics Unit, Valencia, Spain
| | - R Tébar-Martínez
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Precision Medicine Unit, Valencia, Spain
| | - D Moro
- Departments of Surgery, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - J Castillo
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain
| | - A Espí
- Departments of Surgery, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - D Roda
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain
| | - A Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain.
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11
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Cejalvo J, Moragon S, Ortega B, Hernando C, Martínez M, Gambardella V, Tarazona Llavero N, Roda D, Burgues O, Alonso E, Simón S, Poveda J, Rentero P, Zuñiga S, Bermejo B, Lluch A, Cervantes A. Clinical application of mutational analysis in breast cancer patients: The relevance of PIK3CA analysis for precision medicine. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz242.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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12
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Llavero NT, Gimeno-Valiente F, Gambardella V, Huerta M, Keranen SR, Bruixola G, Fontana E, Ciarpaglini CM, Zuñiga S, Rentero P, Fleitas T, Papaccio F, Moro D, Pla V, Nyamundanda G, Castillo J, Sadanadam A, Espí A, Roda D, Cervantes A. Mutation tracking in circulating tumour DNA (ctDNA) detects minimal residual disease (MRD) in patients with localized colorectal cancer (CRC) and identifies those at high risk of recurrence regardless of stage, lack of CDX2 expression and CMS subtype. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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13
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Pascual-Iglesias A, Sanchez CM, Penzes Z, Sola I, Enjuanes L, Zuñiga S. Recombinant Chimeric Transmissible Gastroenteritis Virus (TGEV) - Porcine Epidemic Diarrhea Virus (PEDV) Virus Provides Protection against Virulent PEDV. Viruses 2019; 11:v11080682. [PMID: 31349683 PMCID: PMC6723174 DOI: 10.3390/v11080682] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is an enteric coronavirus causing high morbidity and mortality in porcine herds worldwide. Although both inactivated and live attenuated vaccines have been extensively used, the emergence of highly virulent strains and the recurrent outbreaks even in vaccinated farms highlight the need of effective vaccines. Engineering of genetically defined live attenuated vaccines is a rational approach for novel vaccine development. In this line, we engineered an attenuated virus based on the transmissible gastroenteritis virus (TGEV) genome, expressing a chimeric spike protein from a virulent United States (US) PEDV strain. This virus (rTGEV-RS-SPEDV) was attenuated in highly-sensitive five-day-old piglets, as infected animals did not lose weight and none of them died. In addition, the virus caused very minor tissue damage compared with a virulent virus. The rTGEV-RS-SPEDV vaccine candidate was also attenuated in three-week-old animals that were used to evaluate the protection conferred by this virus, compared with the protection induced by infection with a virulent PEDV US strain (PEDV-NVSL). The rTGEV-RS-SPEDV virus protected against challenge with a virulent PEDV strain, reducing challenge virus titers in jejunum and leading to undetectable challenge virus RNA levels in feces. The rTGEV-RS-SPEDV virus induced a humoral immune response specific for PEDV, including neutralizing antibodies. Altogether, the data indicated that rTGEV-RS-SPEDV is a promising vaccine candidate against virulent PEDV infection.
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Affiliation(s)
- Alejandro Pascual-Iglesias
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, 28049 Madrid, Spain
| | - Carlos M Sanchez
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, 28049 Madrid, Spain
| | - Zoltan Penzes
- Ceva Animal Health, Ceva-Phylaxia, Szallas u. 5, 1107 Budapest, Hungary
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, 28049 Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, 28049 Madrid, Spain.
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, 28049 Madrid, Spain.
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Tarazona Llavero N, Fontana E, Gambardella V, Gimeno-Valiente F, Castillo J, Calon A, Martínez-Ciarpaglini C, Peiró-Chova L, Huerta M, Zuñiga S, Rentero-Garrido P, Montón-Bueno J, Roda D, Roselló S, Bellosillo B, Vivancos A, Nyamundana G, Montagut C, Sadanandam A, Cervantes A. A multi-omic analysis for prospective patient stratification in localised colorectal cancer (CRC). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy424.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Virus vaccines have to be immunogenic, sufficiently stable, safe, and suitable to induce long-lasting immunity. To meet these requirements, vaccine studies need to provide a comprehensive understanding of (i) the protective roles of antiviral B and T-cell-mediated immune responses, (ii) the complexity and plasticity of major viral antigens, and (iii) virus molecular biology and pathogenesis. There are many types of vaccines including subunit vaccines, whole-inactivated virus, vectored, and live-attenuated virus vaccines, each of which featuring specific advantages and limitations. While nonliving virus vaccines have clear advantages in being safe and stable, they may cause side effects and be less efficacious compared to live-attenuated virus vaccines. In most cases, the latter induce long-lasting immunity but they may require special safety measures to prevent reversion to highly virulent viruses following vaccination. The chapter summarizes the recent progress in the development of coronavirus (CoV) vaccines, focusing on two zoonotic CoVs, the severe acute respiratory syndrome CoV (SARS-CoV), and the Middle East respiratory syndrome CoV, both of which cause deadly disease and epidemics in humans. The development of attenuated virus vaccines to combat infections caused by highly pathogenic CoVs was largely based on the identification and characterization of viral virulence proteins that, for example, interfere with the innate and adaptive immune response or are involved in interactions with specific cell types, such as macrophages, dendritic and epithelial cells, and T lymphocytes, thereby modulating antiviral host responses and viral pathogenesis and potentially resulting in deleterious side effects following vaccination.
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Affiliation(s)
- L Enjuanes
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain.
| | - S Zuñiga
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - C Castaño-Rodriguez
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - J Gutierrez-Alvarez
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - J Canton
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - I Sola
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain.
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Abstract
Coronaviruses (CoVs) infect humans and many animal species, and are associated with respiratory, enteric, hepatic, and central nervous system diseases. The large size of the CoV genome and the instability of some CoV replicase gene sequences during its propagation in bacteria, represent serious obstacles for the development of reverse genetic systems similar to those used for smaller positive sense RNA viruses. To overcome these limitations, several alternatives to more conventional plasmid-based approaches have been established in the last 13 years. In this report, we briefly review and discuss the different reverse genetic systems developed for CoVs, paying special attention to the severe acute respiratory syndrome CoV (SARS-CoV).
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Affiliation(s)
- Fernando Almazán
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Silvia Marquez-Jurado
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Lucia Morales
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Martina Becares
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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Almazán F, Sola I, Zuñiga S, Marquez-Jurado S, Morales L, Becares M, Enjuanes L. Coronavirus reverse genetic systems: infectious clones and replicons. Virus Res 2014; 189:262-70. [PMID: 24930446 PMCID: PMC4727449 DOI: 10.1016/j.virusres.2014.05.026] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 01/09/2023]
Abstract
Coronaviruses (CoVs) infect humans and many animal species, and are associated with respiratory, enteric, hepatic, and central nervous system diseases. The large size of the CoV genome and the instability of some CoV replicase gene sequences during its propagation in bacteria, represent serious obstacles for the development of reverse genetic systems similar to those used for smaller positive sense RNA viruses. To overcome these limitations, several alternatives to more conventional plasmid-based approaches have been established in the last 13 years. In this report, we briefly review and discuss the different reverse genetic systems developed for CoVs, paying special attention to the severe acute respiratory syndrome CoV (SARS-CoV).
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Affiliation(s)
- Fernando Almazán
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Silvia Marquez-Jurado
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Lucia Morales
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Martina Becares
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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18
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Thuenemann EC, Lenzi P, Love AJ, Taliansky M, Bécares M, Zuñiga S, Enjuanes L, Zahmanova GG, Minkov IN, Matić S, Noris E, Meyers A, Hattingh A, Rybicki EP, Kiselev OI, Ravin NV, Eldarov MA, Skryabin KG, Lomonossoff GP. The use of transient expression systems for the rapid production of virus-like particles in plants. Curr Pharm Des 2014; 19:5564-73. [PMID: 23394559 DOI: 10.2174/1381612811319310011] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 01/31/2013] [Indexed: 11/22/2022]
Abstract
Advances in transient expression technologies have allowed the production of milligram quantities of proteins within a matter of days using only small amounts (tens of grams) of plant tissue. Among the proteins that have been produced using this approach are the structural proteins of viruses which are capable of forming virus-like particles (VLPs). As such particulate structures are potent stimulators of the immune system, they are excellent vaccine candidates both in their own right and as carriers of additional immunogenic sequences. VLPs of varying complexity derived from a variety of animal viruses have been successfully transiently expressed in plants and their immunological properties assessed. Generally, the plant-produced VLPs were found to have the expected antigenicity and immunogenicity. In several cases, including an M2e-based influenza vaccine candidate, the plant-expressed VLPs have been shown to be capable of stimulating protective immunity. These findings raise the prospect that low-cost plant-produced vaccines could be developed for both veterinary and human use.
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Affiliation(s)
- Eva C Thuenemann
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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Mateos-Gomez PA, Morales L, Zuñiga S, Enjuanes L, Sola I. Long-distance RNA-RNA interactions in the coronavirus genome form high-order structures promoting discontinuous RNA synthesis during transcription. J Virol 2013; 87:177-86. [PMID: 23055566 PMCID: PMC3536410 DOI: 10.1128/jvi.01782-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/04/2012] [Indexed: 02/06/2023] Open
Abstract
Coronavirus (CoV) transcription requires a high-frequency recombination process that links newly synthesized minus-strand subgenomic RNA copies to the leader region, which is present only once, at the 5' end of the genome. This discontinuous RNA synthesis step is based on the complementarity between the transcription-regulating sequences (TRSs) at the leader region and those preceding each gene in the nascent minus-strand RNA. Furthermore, the template switch requires the physical proximity of RNA genome domains located between 20,000 and 30,000 nucleotides apart. In this report, it is shown that the efficacy of this recombination step is promoted by novel additional long-distance RNA-RNA interactions between RNA motifs located close to the TRSs controlling the expression of each gene and their complementary sequences mapping close to the 5' end of the genome. These interactions would bring together the motifs involved in the recombination process. This finding indicates that the formation of high-order RNA structures in the CoV genome is necessary to control the expression of at least the viral N gene. The requirement of these long-distance interactions for transcription was shown by the engineering of CoV replicons in which the complementarity between the newly identified sequences was disrupted. Furthermore, disruption of complementarity in mutant viruses led to mutations that restored complementarity, wild-type transcription levels, and viral titers by passage in cell cultures. The relevance of these high-order structures for virus transcription is reinforced by the phylogenetic conservation of the involved RNA motifs in CoVs.
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Affiliation(s)
- Pedro A Mateos-Gomez
- Department of Molecular and Cell Biology, National Center of Biotechnology, Campus de la Universidad Autonoma de Madrid, Madrid, Spain
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Cruz JLG, Sola I, Becares M, Alberca B, Plana J, Enjuanes L, Zuñiga S. Coronavirus gene 7 counteracts host defenses and modulates virus virulence. PLoS Pathog 2011; 7:e1002090. [PMID: 21695242 PMCID: PMC3111541 DOI: 10.1371/journal.ppat.1002090] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 04/12/2011] [Indexed: 12/14/2022] Open
Abstract
Transmissible gastroenteritis virus (TGEV) genome contains three accessory genes: 3a, 3b and 7. Gene 7 is only present in members of coronavirus genus a1, and encodes a hydrophobic protein of 78 aa. To study gene 7 function, a recombinant TGEV virus lacking gene 7 was engineered (rTGEV-Δ7). Both the mutant and the parental (rTGEV-wt) viruses showed the same growth and viral RNA accumulation kinetics in tissue cultures. Nevertheless, cells infected with rTGEV-Δ7 virus showed an increased cytopathic effect caused by an enhanced apoptosis mediated by caspase activation. Macromolecular synthesis analysis showed that rTGEV-Δ7 virus infection led to host translational shut-off and increased cellular RNA degradation compared with rTGEV-wt infection. An increase of eukaryotic translation initiation factor 2 (eIF2α) phosphorylation and an enhanced nuclease, most likely RNase L, activity were observed in rTGEV-Δ7 virus infected cells. These results suggested that the removal of gene 7 promoted an intensified dsRNA-activated host antiviral response. In protein 7 a conserved sequence motif that potentially mediates binding to protein phosphatase 1 catalytic subunit (PP1c), a key regulator of the cell antiviral defenses, was identified. We postulated that TGEV protein 7 may counteract host antiviral response by its association with PP1c. In fact, pull-down assays demonstrated the interaction between TGEV protein 7, but not a protein 7 mutant lacking PP1c binding motif, with PP1. Moreover, the interaction between protein 7 and PP1 was required, during the infection, for eIF2α dephosphorylation and inhibition of cell RNA degradation. Inoculation of newborn piglets with rTGEV-Δ7 and rTGEV-wt viruses showed that rTGEV-Δ7 virus presented accelerated growth kinetics and pathology compared with the parental virus. Overall, the results indicated that gene 7 counteracted host cell defenses, and modified TGEV persistence increasing TGEV survival. Therefore, the acquisition of gene 7 by the TGEV genome most likely has provided a selective advantage to the virus.
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Affiliation(s)
- Jazmina L. G. Cruz
- Centro Nacional de Biotecnología, CNB, CSIC, Department of Molecular and Cell Biology, Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Isabel Sola
- Centro Nacional de Biotecnología, CNB, CSIC, Department of Molecular and Cell Biology, Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Martina Becares
- Centro Nacional de Biotecnología, CNB, CSIC, Department of Molecular and Cell Biology, Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | | | | | - Luis Enjuanes
- Centro Nacional de Biotecnología, CNB, CSIC, Department of Molecular and Cell Biology, Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- * E-mail:
| | - Sonia Zuñiga
- Centro Nacional de Biotecnología, CNB, CSIC, Department of Molecular and Cell Biology, Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
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Sola I, Mateos-Gomez PA, Almazan F, Zuñiga S, Enjuanes L. RNA-RNA and RNA-protein interactions in coronavirus replication and transcription. RNA Biol 2011; 8:237-48. [PMID: 21378501 PMCID: PMC3230552 DOI: 10.4161/rna.8.2.14991] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/17/2011] [Accepted: 01/19/2011] [Indexed: 02/07/2023] Open
Abstract
Coronavirus (CoV) RNA synthesis includes the replication of the viral genome, and the transcription of sgRNAs by a discontinuous mechanism. Both processes are regulated by RNA sequences such as the 5' and 3' untranslated regions (UTRs), and the transcription regulating sequences (TRSs) of the leader (TRS-L) and those preceding each gene (TRS-Bs). These distant RNA regulatory sequences interact with each other directly and probably through protein-RNA and protein-protein interactions involving viral and cellular proteins. By analogy to other plus-stranded RNA viruses, such as polioviruses, in which translation and replication switch involves a cellular factor (PCBP) and a viral protein (3CD) it is conceivable that in CoVs the switch between replication and transcription is also associated with the binding of proteins that are specifically recruited by the replication or transcription complexes. Complexes between RNA motifs such as TRS-L and the TRS-Bs located along the CoV genome are probably formed previously to the transcription start, and most likely promote template-switch of the nascent minus RNA to the TRS-L region. Many cellular proteins interacting with regulatory CoV RNA sequences are members of the heterogeneous nuclear ribonucleoprotein (hnRNP) family of RNA-binding proteins, involved in mRNA processing and transport, which shuttle between the nucleus and the cytoplasm. In the context of CoV RNA synthesis, these cellular ribonucleoproteins might also participate in RNA-protein complexes to bring into physical proximity TRS-L and distant TRS-B, as proposed for CoV discontinuous transcription. In this review, we summarize RNA-RNA and RNA-protein interactions that represent modest examples of complex quaternary RNA-protein structures required for the fine-tuning of virus replication. Design of chemically defined replication and transcription systems will help to clarify the nature and activity of these structures.
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Affiliation(s)
- Isabel Sola
- Department of Molecular and Cell Biology, CNB, CSIC, Cantoblanco, Madrid, Spain
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Abstract
Infection by different coronaviruses (CoVs) causes alterations in the transcriptional and translational patterns, cell cycle, cytoskeleton, and apoptosis pathways of the host cells. In addition, CoV infection may cause inflammation, alter immune and stress responses, and modify the coagulation pathways. The balance between the up- and downregulated genes could explain the pathogenesis caused by these viruses. We review specific aspects of CoV-host interactions. CoV genome replication takes place in the cytoplasm in a membrane-protected microenvironment and may control the cell machinery by locating some of their proteins in the host cell nucleus. CoVs initiate translation by cap-dependent and cap-independent mechanisms. CoV transcription involves a discontinuous RNA synthesis (template switching) during the extension of a negative copy of the subgenomic mRNAs. The requirement for base-pairing during transcription has been formally demonstrated in arteriviruses and CoVs. CoV N proteins have RNA chaperone activity that may help initiate template switching. Both viral and cellular proteins are required for replication and transcription, and the role of selected proteins is addressed.
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Affiliation(s)
- Luis Enjuanes
- Department of Molecular and Cell Biology, CNB, CSIC, 28049 Madrid, Spain.
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Almazán F, Dediego ML, Galán C, Escors D, Alvarez E, Ortego J, Sola I, Zuñiga S, Alonso S, Moreno JL, Nogales A, Capiscol C, Enjuanes L. Construction of a severe acute respiratory syndrome coronavirus infectious cDNA clone and a replicon to study coronavirus RNA synthesis. J Virol 2006; 80:10900-6. [PMID: 16928748 PMCID: PMC1641757 DOI: 10.1128/jvi.00385-06] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The engineering of a full-length infectious cDNA clone and a functional replicon of the severe acute respiratory syndrome coronavirus (SARS-CoV) Urbani strain as bacterial artificial chromosomes (BACs) is described in this study. In this system, the viral RNA was expressed in the cell nucleus under the control of the cytomegalovirus promoter and further amplified in the cytoplasm by the viral replicase. Both the infectious clone and the replicon were fully stable in Escherichia coli. Using the SARS-CoV replicon, we have shown that the recently described RNA-processing enzymes exoribonuclease, endoribonuclease, and 2'-O-ribose methyltransferase were essential for efficient coronavirus RNA synthesis. The SARS reverse genetic system developed as a BAC constitutes a useful tool for the study of fundamental viral processes and also for developing genetically defined vaccines.
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Affiliation(s)
- Fernando Almazán
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, CSIC, Darwin 3, Campus Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
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González-Martin G, Cattan C, Zuñiga S. Pharmacokinetics of lysine clonixinate in children in postoperative care. Int J Clin Pharmacol Ther 1996; 34:396-9. [PMID: 8880290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The pharmacokinetics of 2 doses of intravenous lysine clonixinate (4 and 6 mg x kg-1) were studied in 10 children (age 4-10 years) under postoperative care. A single dose of the drug was injected in a forearm vein. Blood samples were collected at regular intervals for 3 hours. Serum clonixin concentrations (expressed as clonixin) were analyzed using a high pressure liquid chromatography method. Pharmacokinetic values were estimated by a nonlinear computer program. The distribution volume was similar in both groups of children (1.288 +/- 0.829 1 and 1. 139 +/- 0.667 1, respectively). There were no differences between the values of total plasma clearance and the administered doses (0.026 +/- 0.017 ml x min-1 and 0.017 +/- 0.008 ml x min-1, t = 1.07, p = 0.76). The elimination half-life was longer in children who received 6 mg x kg-1 (44.26 +/- 6.34 min vs 38.63 +/- 10.93 min) but this difference was not statistically significant (t = 0.99, p < 0.34). The pharmacokinetic parameters calculated in these children were different from those found by other authors in adults and experimental animals.
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Affiliation(s)
- G González-Martin
- Department of Pharmacy, Faculty of Chemistry, Pontifical Catholic University of Chile, Santiago, Chile
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