Omicron variant of SARS-CoV-2 exhibits an increased resilience to the antiviral type I interferon response

  1. Lyudmila Shalamova
  2. Ulrike Felgenhauer
  3. Jochen Wilhelm
  4. Andreas R Schaubmar
  5. Kathrin Büttner
  6. Andreas Schoen
  7. Marek Widera
  8. Sandra Ciesek
  9. Friedemann Weber

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

The new variant of concern (VOC) of SARS-CoV-2, Omicron (B.1.1.529), is genetically very different from other VOCs. We compared Omicron with the preceding VOC Delta (B.1.617.2) and the wildtype (wt) strain (B.1) with respect to their interactions with the antiviral interferon (IFN-alpha/beta) response in infected cells. Our data indicate that IFN induction by Omicron is low and comparable to the wt, whereas Delta showed an increased IFN induction. However, Omicron exceeded both the wt and the Delta strain with respect to the ability to withstand the antiviral state imposed by IFN-alpha.

Article activity feed

  1. Version published to 10.1093/pnasnexus/pgac067
  2. ScreenIT

    SciScore for 10.1101/2022.01.20.476754: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationContamination: Of note, all cells and viruses were tested mycoplasma-negative.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Cells and viruses: Calu-3, Caco-2, Vero E6 and Vero E6-TMPRSS2 cells (kindly provided by Stefan Poehlmann, German Primate Center, Goettingen) were cultivated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum.
    Caco-2
    suggested: None
    SARS-CoV-2 strains “wildtype (wt)” (SARS-CoV-2/München-1.2/2020/984 (B.1) p.4; (16), (kindly provided by Christian Drosten, Charité, Berlin)), “VOC Delta” (SARS-CoV-2 B.1.617.2 (FFM-IND8424/2021) (17)) and “VOC Omicron” (SARS-CoV-2 B.1.1.529 (FFM- SIM0550/2021) (3)) were grown on Vero E6-TMPRSS2 cells (wt SARS-CoV-2) or Caco- 2 cells (VOCs Delta, Omicron), respectively and titrated on Vero E6 cells.
    Vero E6-TMPRSS2
    suggested: None
    Interferon induction analysis: Calu-3 cells were seeded into 24-well plates (7.5×10E4 per well) and infected 24 h later at an MOI of 1.
    Calu-3
    suggested: None
    At 24 h post-infection, cell supernatants were collected and titrated by plaque assay on Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)

    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.
    • No funding statement was detected.
    • 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 10.1101/2022.01.20.476754v1 on bioRxiv