SARS-CoV-2 Omicron is specifically restricted in its replication in human lung tissue, compared to other variants of concern

  1. Or Alfi
  2. Marah Hamdan
  3. Ori Wald
  4. Arkadi Yakirevitch
  5. Ori Wandel
  6. Esther Oiknine-Djian
  7. Ben Gvili
  8. Hadas Knoller
  9. Noa Rozendorn
  10. Hadar Golan
  11. Sheera Adar
  12. Olesya Vorontsov
  13. Michal Mandelboim
  14. Zichria Zakay-Rones
  15. Menachem Oberbaum
  16. Amos Panet
  17. Dana G. Wolf

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Abstract

SARS-CoV-2 Omicron variant has been characterized by decreased clinical severity, raising the question of whether early variant-specific interactions within the mucosal surfaces of the respiratory tract could mediate its attenuated pathogenicity. Here, we employed ex vivo infection of native human nasal and lung tissues to investigate the local-mucosal susceptibility and innate immune response to Omicron, compared to Delta and earlier SARS-CoV-2 variants of concern (VOC). We show that the replication of Omicron in lung tissues is highly restricted compared to other VOC, whereas it remains relatively unchanged in nasal tissues. Mechanistically, Omicron induced a much stronger antiviral interferon response in infected tissues compared to Delta and earlier VOC - a difference which was most striking in the lung tissues, where the innate immune response to all other SARS-CoV-2 VOC was blunted. Our data provide new insights to the reduced lung involvement and clinical severity of Omicron.

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  1. ScreenIT

    SciScore for 10.1101/2022.03.31.486531: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The study was approved by the Hadassah Medical Center (#0296-20-HMO) and the Sheba Medical Center (#2832-15-SMC) Institutional Review Boards.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    The following primary antibodies were used: α-E-Cadherin (Mouse monoclonal, 1:100, Abcam, ab1416; for the detection of epithelial cells), α-SARS-CoV-2 Nucleocapsid (Rabbit monoclonal, 1:500, Abcam, ab271180).
    α-E-Cadherin
    suggested: None
    α-SARS-CoV-2 Nucleocapsid
    suggested: None
    The following secondary antibodies were used: Donkey anti-Mouse IgG pre-adsorbed, Alexa Fluor® 568 (1:250, Abcam, Cat# ab175700), Goat anti-Rabbit IgG Highly Cross-Adsorbed Alexa Fluor Plus 647 (1:250, Thermo Fisher Scientific, Cat# A32733).
    anti-Mouse IgG
    suggested: (DSHB Cat# LEP100 IgG, RRID:AB_528124)
    anti-Rabbit IgG
    suggested: (Biorbyt Cat# orb14385, RRID:AB_10735740)
    Experimental Models: Cell Lines
    SentencesResources
    Cells and viruses: Simian kidney Vero E6 (ATCC CRL-1586), Calu-3 (ATCC HTB-55), Madin-Darby Canine Kidney (MDCK, ATCC CCL-34™) cells and H1299-ACE2 overexpressed cells (kindly provided by Dr. Alex Sigal)1 were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Biological Industries, Beit Haemek, Israel), supplemented with 10% fetal bovine serum, 2 mM L-Glutamine, 10 IU/ml Penicillin, and 10 μg/ml streptomycin (Biological Industries, Beit Haemek, Israel).
    E6
    suggested: None
    Calu-3
    suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)
    Influenza virus A(H1N1) pdm09 (NIBRG-121xp, Cat# 09/268; obtained from NIBSC, UK) was propagated in MDCK cells.
    MDCK
    suggested: CLS Cat# 602280/p823_MDCK_(NBL-2, RRID:CVCL_0422)
    The virus titers of cleared infected cells- and tissue supernatants were determined by a standard plaque assay on H1299-ACE2 cells (SARS-CoV-2) or MDCK cells (influenza virus).
    H1299-ACE2
    suggested: None
    Software and Algorithms
    SentencesResources
    Whole-mount tissues were visualized using a Nikon A1R confocal microscope and were analyzed using NIS Elements software (Nikon).
    NIS Elements
    suggested: (NIS-Elements, RRID:SCR_014329)
    Statistical analysis: All data, presented as means ± standard errors of the mean (SEM), were analyzed using paired, two-tailed t test in GraphPad Prism 9 software (GraphPad Software Inc., San Diego CA).
    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: We detected the following sentences addressing limitations in the study:
    Our study has several limitations. Native respiratory tissues in organ culture are relatively short-lived (up to 7 days in culture). Thus, our ex vivo infection models mirror early events of infection and do not address the late phase of viral transmission or the combined effects of the local and systemic immune responses. Nonetheless, our studies recapitulate SARS-CoV-2 infection and innate immune response within the authentic multicellular complexity of both the upper and the lower human respiratory tract, containing tissue-specific compositions of cell types, including immune cells, and extracellular matrix. To date, we are not aware of studies that have examined the distinctive innate tissue responses to Omicron as related to its altered replication phenotype in the lower respiratory tract. Such data are critical to better understand and address the evolution of SARS-CoV-2 into a less virulent human-tropic virus. In summary, our studies in native human nasal and lung tissues infected ex vivo reveal a significantly enhanced interferon response to Omicron, compared to precedent SARS-CoV-2 VOC. The findings imply that the early induction of antiviral ISG, which was most prominent in lung tissues, could play a part in the restricted replication and pathology of Omicron in the lungs. They provide insights for the attenuated pathogenicity of Omicron, and for further studies of pathways involved in the enhanced mucosal innate immune responses to this newly evolving variant.

    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 10.1101/2022.03.31.486531 on bioRxiv