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RESEARCH ARTICLE

Synergism between remdesivir and ribavirin leads to SARS-CoV-2 extinction in cell culture

Carlos García-Crespo

Carlos García-Crespo

Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain

Contribution: Data curation (lead), Formal analysis (equal), ​Investigation (equal), Methodology (lead), Software (equal), Writing - review & editing (lead)

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Ana Isabel de Ávila

Ana Isabel de Ávila

Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain

Contribution: Data curation (equal), Formal analysis (equal), ​Investigation (equal), Methodology (equal), Writing - review & editing (equal)

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Isabel Gallego

Isabel Gallego

Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain

Contribution: Data curation (equal), Formal analysis (equal), ​Investigation (equal), Methodology (equal)

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María Eugenia Soria

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

Contribution: Data curation (equal), Formal analysis (equal), ​Investigation (equal), Methodology (equal)

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Antoni Durán-Pastor

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

Contribution: Data curation (equal), Formal analysis (equal), ​Investigation (equal), Methodology (equal)

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Pilar Somovilla

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

Contribution: Data curation (equal), Formal analysis (equal), ​Investigation (equal), Methodology (equal)

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Brenda Martínez-González

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

Contribution: Data curation (equal), Formal analysis (equal), ​Investigation (equal), Methodology (equal)

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Javier Muñoz-Flores

Javier Muñoz-Flores

GMS Management Solutions S.L., Torre Picasso, Madrid, Spain

Contribution: Formal analysis (equal), Methodology (equal)

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Pablo Mínguez

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

Contribution: Formal analysis (equal), Methodology (equal), Software (equal)

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Llanos Salar-Vidal

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

Contribution: ​Investigation (equal), Methodology (equal)

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Mario Esteban-Muñoz

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

Contribution: ​Investigation (equal), Methodology (equal)

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Elizabeth Cañar-Camacho

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

Contribution: ​Investigation (equal), Methodology (equal)

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Cristina Ferrer-Orta

Cristina Ferrer-Orta

Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Barcelona, Spain

Contribution: Formal analysis (equal), ​Investigation (equal), Methodology (equal)

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Sonia Zuñiga

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

Contribution: ​Investigation (equal), Supervision (equal), Writing - review & editing (equal)

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Isabel Sola

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

Contribution: ​Investigation (equal), Supervision (equal), Writing - review & editing (equal)

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Luis Enjuanes

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

Contribution: ​Investigation (equal), Supervision (equal), Writing - review & editing (equal)

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Jaime Esteban

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

Contribution: ​Investigation (equal), Supervision (equal), Writing - review & editing (equal)

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Ricardo Fernández-Roblas

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

Contribution: ​Investigation (equal), Supervision (equal), Writing - review & editing (equal)

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Ignacio Gadea

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

Contribution: ​Investigation (equal), Supervision (equal), Writing - review & editing (equal)

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Jordi Gómez

Jordi Gómez

Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, Granada, Spain

Contribution: ​Investigation (equal), Supervision (equal), Writing - review & editing (equal)

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Nuria Verdaguer

Nuria Verdaguer

Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Barcelona, Spain

Contribution: ​Investigation (equal), Supervision (equal), Writing - review & editing (equal)

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Esteban Domingo

Corresponding Author

Esteban Domingo

Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain

Correspondence

Esteban Domingo, Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain.

Email: [email protected]

Celia Perales, Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain.

Email: [email protected]

Contribution: Formal analysis (equal), Funding acquisition (equal), ​Investigation (equal), Project administration (equal), Supervision (equal), Writing - original draft (lead)

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Celia Perales

Corresponding Author

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

Correspondence

Esteban Domingo, Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Campus de Cantoblanco, Madrid, Spain.

Email: [email protected]

Celia Perales, Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain.

Email: [email protected]

Contribution: Conceptualization (lead), Funding acquisition (equal), ​Investigation (lead), Project administration (lead), Supervision (equal), Validation (equal), Writing - original draft (equal)

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First published: 14 April 2024

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.

CONFLICT OF INTEREST STATEMENT

The authors declare no conflict of interest.

DATA AVAILABILITY STATEMENT

The files for the SARS-CoV-2 sequences included in the present study are available at ENA under accession no. PRJEB66908 and PRJEB56440.