Interferon alpha-based combinations suppress SARS-CoV-2 infection in vitro and in vivo

  1. Aleksandr Ianevski
  2. Rouan Yao
  3. Eva Zusinaite
  4. Laura Sandra Lello
  5. Sainan Wang
  6. Eunji Jo
  7. Jaewon Yang
  8. Erlend Ravlo
  9. Wei Wang
  10. Hilde Lysvand
  11. Kirsti Løseth
  12. Valentyn Oksenych
  13. Tanel Tenson
  14. Marc P. Windisch
  15. Minna Poranen
  16. Anni I. Nieminen
  17. Svein Arne Nordbø
  18. Mona Høysæter Fenstad
  19. Gunnveig Grødeland
  20. Pål Aukrust
  21. Marius Trøseid
  22. Anu Kantele
  23. Astra Vitkauskiene
  24. Nicolas Legrand
  25. Andres Merits
  26. Magnar Bjørås
  27. Denis E. Kainov

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

There is an urgent need for new antivirals with powerful therapeutic potential and tolerable side effects. In the present study, we found that recombinant human interferon-alpha (IFNa) triggers intrinsic and extrinsic cellular antiviral responses, as well as reduces replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro. Although IFNa alone was insufficient to completely abolish SARS-CoV-2 replication, combinations of IFNa with remdesivir or other antiviral agents (EIDD-2801, camostat, cycloheximide, or convalescent serum) showed strong synergy and effectively inhibited SARS-CoV-2 infection in human lung epithelial Calu-3 cells. Furthermore, we showed that the IFNa-remdesivir combination suppressed virus replication in human lung organoids, and that its single prophylactic dose attenuated SARS-CoV-2 infection in lungs of Syrian hamsters. Transcriptome and metabolomic analyses showed that the combination of IFNa-remdesivir suppressed virus-mediated changes in infected cells, although it affected the homeostasis of uninfected cells. We also demonstrated synergistic antiviral activity of IFNa2a-based combinations against other virus infections in vitro. Altogether, our results indicate that IFNa2a-based combination therapies can achieve higher efficacy while requiring lower dosage compared to monotherapies, making them attractive targets for further pre-clinical and clinical development.

Article activity feed

  1. Version published to 10.1101/2021.01.05.425331v5 on bioRxiv
  2. Version published to 10.1101/2021.01.05.425331v4 on bioRxiv
  3. Version published to 10.1101/2021.01.05.425331v3 on bioRxiv
  4. Version published to 10.1101/2021.01.05.425331v2 on bioRxiv
  5. ScreenIT

    SciScore for 10.1101/2021.01.05.425331: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power AnalysisSubsequently, samples were sonicated for 3 cycle (60 s, power = 60 and frequency = 37), vortexed for 2 min and centrifuged at 4 °C, 14000 rpm for 10 min.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    The propagation of human non-small cell lung cancer Calu-3, human adenocarcinoma alveolar basal epithelial A549, African green monkey kidney Vero-E6, T-cell like ACH-2 cells, which possess a single integrated copy of the provirus HIV-1 strain LAI (NIH AIDS Reagent Program), and human cervical cancer derived TZM-bl, which express firefly luciferase under control of HIV-1 long terminal repeat (LTR) promoter allowing quantitation of the viral infection (tat-protein expression by integrated HIV-1 provirus) using firefly luciferase assay, have been described in our previous studies [22, 40–43].
    ACH-2
    suggested: NIH-ARP Cat# 349-443, RRID:CVCL_0138)
    For testing compound toxicity and efficacy against FluAV, approximately 4 × 104 A549 cells were seeded in each well of a 96-well plate.
    A549
    suggested: None
    Drug Combination Test and Synergy Calculations: Calu-3, A549 or TZM-bl cells were treated with different concentrations of two drugs and infected with SARS-CoV-2-mCherry (moi = 0.01), FluAV (moi = 0.5), HIV-1 (corresponding to 300 ng/mL of HIV-1 p24) or mock.
    TZM-bl
    suggested: None
    Gene Expression Analysis: Calu-3 cells were treated with 1 μg/ml IFNa2a or vehicle control.
    Calu-3
    suggested: KCLB Cat# 30055, RRID:CVCL_0609)
    Software and Algorithms
    SentencesResources
    The propagation of human non-small cell lung cancer Calu-3, human adenocarcinoma alveolar basal epithelial A549, African green monkey kidney Vero-E6, T-cell like ACH-2 cells, which possess a single integrated copy of the provirus HIV-1 strain LAI (NIH AIDS Reagent Program), and human cervical cancer derived TZM-bl, which express firefly luciferase under control of HIV-1 long terminal repeat (LTR) promoter allowing quantitation of the viral infection (tat-protein expression by integrated HIV-1 provirus) using firefly luciferase assay, have been described in our previous studies [22, 40–43].
    NIH AIDS Reagent Program
    suggested: (National Center for Research Resources - Primate Resources, RRID:SCR_006863)
    The half-maximal cytotoxic concentration (CC50) for each compound was calculated based on viability/death curves obtained on mock-infected cells after non-linear regression analysis with a variable slope using GraphPad Prism software version 7.0a.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    The expected responses were calculated based on the ZIP reference model using SynergyFinder version 2 [49, 50].
    SynergyFinder
    suggested: (SynergyFinder, RRID:SCR_019318)
    Reads were aligned using the Bowtie 2 software package version 2.4.2 to the NCBI reference sequence for SARS-CoV-2 (NC_045512.2) and to the human GRCh38 genome.
    Bowtie 2
    suggested: (Bowtie 2, RRID:SCR_016368)
    The number of mapped and unmapped reads that aligned to each gene were obtained with the featureCounts function from Rsubread R-package version 2.10.
    featureCounts
    suggested: (featureCounts, RRID:SCR_012919)
    Rsubread
    suggested: (Rsubread, RRID:SCR_016945)
    The heatmaps were generated using the pheatmap package (https://cran.r-project.org/web/packages/pheatmap/index.html) based on log2-transformed profiling data.
    pheatmap
    suggested: (pheatmap, RRID:SCR_016418)
    Instrument control was operated with Xcalibur 4.1.31.9 software (Thermo Fischer Scientific, Waltham, MA, USA)
    Xcalibur
    suggested: (Thermo Xcalibur, RRID:SCR_014593)
    After integration of QC data with TraceFinder 4.1, each detected metabolite was checked and %RSD were calculated, while the acceptance limit was set to ≤ 20%.
    TraceFinder
    suggested: None

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  6. Version published to 10.1101/2021.01.05.425331v1 on bioRxiv