Engineered ACE2 counteracts vaccine-evading SARS-CoV-2 Omicron variant

  1. Nariko Ikemura
  2. Shunta Taminishi
  3. Tohru Inaba
  4. Takao Arimori
  5. Daisuke Motooka
  6. Kazutaka Katoh
  7. Yuhei Kirita
  8. Yusuke Higuchi
  9. Songling Li
  10. Tatsuya Suzuki
  11. Yumi Itoh
  12. Yuki Ozaki
  13. Shota Nakamura
  14. Satoaki Matoba
  15. Daron M Standley
  16. Toru Okamoto
  17. Junichi Takagi
  18. Atsushi Hoshino

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

The novel SARS-CoV-2 variant, Omicron (B.1.1.529) contains an unusually high number of mutations (>30) in the spike protein, raising concerns of escape from vaccines, convalescent sera and therapeutic drugs. Here we analyze the alteration of neutralizing titer with Omicron pseudovirus. Sera obtained 3 months after double BNT162b2 vaccination exhibit approximately 18-fold lower neutralization titers against Omicron than parental virus. Convalescent sera from Alpha and Delta patients allow similar levels of breakthrough by Omicron. Domain-wise analysis using chimeric spike revealed that this efficient evasion was primarily achieved by mutations clustered in the receptor-binding domain, but that multiple mutations in the N-terminal domain contributed as well. Omicron escapes a therapeutic cocktail of imdevimab and casirivimab, whereas sotrovimab, which targets a conserved region to avoid viral mutation, remains effective. The ACE2 decoy is another virus-neutralizing drug modality that is free, at least in theory, from complete escape. Deep mutational analysis demonstrated that, indeed, engineered ACE2 prevented escape for each single-residue mutation in the receptor-binding domain, similar to immunized sera. Engineered ACE2 neutralized Omicron comparable to Wuhan and also showed a therapeutic effect against Omicron infection in hamsters and human ACE2 transgenic mice. Like previous SARS-CoV-2 variants, some sarbecoviruses showed high sensitivity against engineered ACE2, confirming the therapeutic value against diverse variants, including those that are yet to emerge.

One Sentence Summary

Omicron, carrying ∼30 mutations in the spike, exhibits effective immune evasion but remains highly susceptible to blockade by engineered ACE2.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2021.12.22.473804: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethics statement: Blood samples were obtained from hospitalized adults with PCR-confirmed SARS-CoV-2 infection and vaccinated individuals who were enrolled in a prospective cohort study approved by the Clinical Research Review Committee in Kyoto Prefectural University of medicine (ERB-C-1810-2, ERB-C-1949-1).
    Consent: All human subjects provided written informed consent.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationContamination: All the cell lines were routinely tested negative for mycoplasma contamination.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Cell culture: Lenti-X 293T cells (Clontech) and its derivative, 293T/ACE2 cells were cultured at 37 °C with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM, WAKO) containing 10% fetal bovine serum (Gibco) and penicillin/streptomycin (100 U/ml, Invitrogen).
    293T
    suggested: None
    The 293T/ACE2 cells were seeded at 10,000 cells per well in 96-well plate.
    293T/ACE2
    suggested: RRID:CVCL_YZ65)
    HiBit value-matched Pseudovirus and three-fold dilution series of serum or therapeutic agents were incubated for 1 hr, then this mixture was administered to ACE2/293T cells.
    ACE2/293T
    suggested: None
    Recombinant DNA
    SentencesResources
    Synthesized oligo was extended by overlap PCR and cloned into pcDNA4TO HMM38-HA-full length S plasmid.
    pcDNA4TO
    suggested: None
    Expi293F cells at 2 × 106/ml were transfected with a mixture of 3 ng of library plasmid with 1.5 μg of pMSCV as a junk plasmid using ExpiFectamine (Thermo Fisher Scientific).
    pMSCV
    suggested: RRID:Addgene_12570)
    Software and Algorithms
    SentencesResources
    The assay of each serum was performed in triplicate, and the 50% neutralization titer was calculated using Prism 9 (GraphPad Software).
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Statistical analysis: Neutralization measurements were done in technical triplicates and relative luciferase units were converted to percent neutralization and plotted with a non-linear regression model to determine IC50/ID50 values using GraphPad PRISM software (version 9.0.0).
    GraphPad PRISM
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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.

    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.

  2. Version published to 10.1101/2021.12.22.473804 on bioRxiv