A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in mice

  1. Tianyang Mao
  2. Benjamin Israelow
  3. Carolina Lucas
  4. Chantal B.F. Vogels
  5. Maria Luisa Gomez-Calvo
  6. Olga Fedorova
  7. Mallery I. Breban
  8. Bridget L. Menasche
  9. Huiping Dong
  10. Melissa Linehan
  11. Yale SARS-CoV-2 Genome Surveillance Initiative
  12. Tara Alpert
  13. F. Brito Anderson
  14. Rebecca Earnest
  15. Joseph R. Fauver
  16. Chaney C. Kalinich
  17. Ketty Munyenyembe
  18. Isabel M. Ott
  19. Mary E. Petrone
  20. Jessica Rothman
  21. Anne E. Watkins
  22. Craig B. Wilen
  23. Marie L. Landry
  24. Nathan D. Grubaugh
  25. Anna M. Pyle
  26. Akiko Iwasaki

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Abstract

As SARS-CoV-2 continues to cause morbidity and mortality around the world, there is an urgent need for the development of effective medical countermeasures. Here, we assessed the antiviral capacity of a minimal RIG-I agonist, stem-loop RNA 14 (SLR14), in viral control, disease prevention, post-infection therapy, and cross-variant protection in mouse models of SARS-CoV-2 infection. A single dose of SLR14 prevented viral infection in the lower respiratory tract and development of severe disease in a type I interferon (IFN-I)–dependent manner. SLR14 demonstrated remarkable prophylactic protective capacity against lethal SARS-CoV-2 infection and retained considerable efficacy as a therapeutic agent. In immunodeficient mice carrying chronic SARS-CoV-2 infection, SLR14 elicited near-sterilizing innate immunity in the absence of the adaptive immune system. In the context of infection with variants of concern (VOCs), SLR14 conferred broad protection against emerging VOCs. These findings demonstrate the therapeutic potential of SLR14 as a host-directed, broad-spectrum antiviral for early post-exposure treatment and treatment of chronically infected immunosuppressed patients.

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  1. Version published to 10.1084/jem.20211818
  2. ScreenIT

    SciScore for 10.1101/2021.06.16.448754: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethics: The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples conducted in this study is not research involving human subjects (IRB Protocol ID: 2000028599).
    IACUC: All procedures used in this study (sex-matched, age-matched) complied with federal guidelines and the institutional policies of the Yale School of Medicine Animal Care and Use Committee.
    Euthanasia Agents: Animals were anaesthetized using a mixture of ketamine (50 mg/kg) and xylazine (5 mg/kg), injected intraperitoneally.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Antibodies for flow cytometry: Anti-mouse antibodies used in this study, together with vendors and dilutions, are listed as follows: FITC anti-mCD11c (N418) (1:400) (BioLegend), PerCP-Cy5.5 anti-mLy6C (HK1.4) (1:400) (BioLegend),
    Anti-mouse
    suggested: None
    anti-mCD11c
    suggested: None
    anti-mLy6C
    suggested: None
    Following L a wash, cells were blocked with anti-mouse CD16/32 antibodies (BioXCell) for 30 min at 4 °C.
    anti-mouse CD16/32
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    For determination of infectious titer, plaque assays were performed using lung homogenates in Vero E6 cells cultured with MEM supplemented with NaHCO3, 4% FBS, and 0.6% Avicel RC-581.
    Vero E6
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    Mice: B6.Cg-Tg(K18-ACE2)2Prlmn/J (K18-hACE2), B6(Cg)-Ifnar1tm1.2Ees/J (Ifnar1−/−), B6.129S7-Rag1tm1Mom/J (B6J Rag1−/−), and C.129S7(B6)-Rag1tm1Mom/J (BALB/c Rag1−/−) mice were purchased from the Jackson Laboratories and were subsequently bred and housed at Yale University.
    B6.Cg-Tg(K18-ACE2)2Prlmn/J (K18-hACE2)
    suggested: None
    B6.129S7-Rag1tm1Mom/J
    suggested: RRID:IMSR_JAX:002216)
    B6J Rag1−/−
    suggested: None
    C.129S7(B6)-Rag1tm1Mom/J
    suggested: RRID:IMSR_JAX:003145)
    BALB/c
    suggested: RRID:IMSR_ORNL:BALB/cRl)
    Rag1−/−
    suggested: None
    Rag2−/− mice were generously gifted from R. Flavell (Yale University).
    Rag2−/−
    suggested: None
    Software and Algorithms
    SentencesResources
    Ethics: The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples conducted in this study is not research involving human subjects (IRB Protocol ID: 2000028599).
    Human Research Protection Program
    suggested: None
    0) (BD Biosciences), and Pacific Blue anti-mI-A/I-E (M5/114.15.2) (1:400) (BioLegend).
    BD Biosciences
    suggested: (BD Biosciences, RRID:SCR_013311)
    Data were analysed using FlowJo software version 10.6 software (Tree Star).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    All statistical tests were calculated using GraphPad Prism (GraphPad software).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    Results from OddPub: Thank you for sharing your data.

    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.

    Results from scite Reference Check: We found no unreliable references.

    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.

  3. Version published to 10.1101/2021.06.16.448754v1 on bioRxiv