Ad26.COV2.S Prevents SARS-CoV-2 Induced Pathways of Inflammation and Thrombosis in Hamsters

  1. Malika Aid
  2. Samuel J. Vidal
  3. Cesar Piedra-Mora
  4. Sarah Ducat
  5. Chi N. Chan
  6. Stephen Bondoc
  7. Alessandro Colarusso
  8. Carly E. Starke
  9. Michael Nekorchuk
  10. Kathleen Busman-Sahay
  11. Jacob D. Estes
  12. Amanda J. Martinot
  13. Dan H. Barouch

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Abstract

Syrian golden hamsters exhibit features of severe disease after SARS-CoV-2 challenge and are therefore useful models of COVID-19 pathogenesis and prevention with vaccines. Recent studies have shown that SARS-CoV-2 infection stimulates type I interferon, myeloid, and inflammatory signatures similar to human disease, and that weight loss can be prevented with vaccines. However, the impact of vaccination on transcriptional programs associated with COVID-19 pathogenesis and protective adaptive immune responses is unknown. Here we show that SARS-CoV-2 challenge in hamsters stimulates antiviral, myeloid, and inflammatory programs as well as signatures of complement and thrombosis associated with human COVID-19. Notably, single dose immunization with Ad26.COV2.S, an adenovirus serotype 26 vector (Ad26)-based vaccine expressing a stabilized SARS-CoV-2 spike protein, prevents the upregulation of these pathways such that the gene expression profiles of vaccinated hamsters are comparable to uninfected animals. Finally, we show that Ad26.COV2.S vaccination induces T and B cell signatures that correlate with binding and neutralizing antibody responses. These data provide further insights into the mechanisms of Ad26.COV2.S based protection against severe COVID-19 in hamsters.

Author Summary

In this study, we show that vaccination with Ad26.COV2.S protected SARS-CoV-2 challenged hamsters from developing severe COVID-19 disease by attenuating excessive proinflammatory responses, such as IL-6 and IL-1, macrophages and neutrophils signaling. Ad26 vaccination also prevented the upregulation of pathways associated with thrombosis such coagulation and clotting cascades associated with infection, and the transcriptomic profiles of vaccinated animals were largely comparable to control uninfected hamsters. In contrast, SARS-CoV-2 challenged unvaccinated hamsters showed significant increase of these proinflammatory and prothrombotic pathways and significant weight loss compared to vaccinated hamsters.

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  1. ScreenIT

    SciScore for 10.1101/2021.09.30.462514: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: All animal studies were conducted in compliance with all relevant local, state and federal regulations and were approved by the Bioqual Institutional Animal Care and Use Committee.
    IACUC: All animal studies were conducted in compliance with all relevant local, state and federal regulations and were approved by the Bioqual Institutional Animal Care and Use Committee.
    Sex as a biological variableAnimals and study design: Seventy male and female Syrian golden hamsters (Envigo), 10–12 weeks old, were randomly allocated to groups.
    RandomizationAnimals and study design: Seventy male and female Syrian golden hamsters (Envigo), 10–12 weeks old, were randomly allocated to groups.
    BlindingAll immunologic and virologic assays were performed blinded.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Primary rabbit anti-Iba-1 antibody (Wako; 019-19741 at 1:500) was applied for 30 minutes followed by rabbit Mach-2 HRP-Polymer (BioCare; RHRP520L) for 30 minutes then counterstained with hematoxylin followed by bluing using 0.25% ammonia water.
    anti-Iba-1
    suggested: (FUJIFILM Wako Shibayagi Cat# 016-20001, RRID:AB_839506)
    Staining for MPO and Mx1 IHC was performed as previously described using a Biocare intelliPATH autostainer, with all antibodies being incubated for 1 h at room temperature.
    Mx1
    suggested: None
    Software and Algorithms
    SentencesResources
    RNA quality was assessed using an Agilent Bioanalyzer and ten nanograms of total RNA used as input for library preparation using the SMARTer Stranded Total RNA-Seq V2 Pico Input Mammalian kit (Takara Bio) according to the manufacturer’s instructions.
    Agilent Bioanalyzer
    suggested: None
    Differential expression at the gene level were performed by DESeq2 implemented in the DESeq2 R package.
    DESeq2
    suggested: (DESeq, RRID:SCR_000154)
    analyses: Gene set enrichment analysis and a compendium of databases of biological and immunological pathways were used to test the longitudinal enrichment of pathways and transcription factors (TFs) signatures at 4 dpi in vaccinated, sham and control hamster groups.
    Gene set enrichment analysis
    suggested: (Gene Set Enrichment Analysis, RRID:SCR_003199)
    Genes were pre-ranked by fold change from the highest to the lowest and GSEA was used to assess the enrichment of selected gene sets.
    GSEA
    suggested: (SeqGSEA, RRID:SCR_005724)
    Thrombosis signatures were compiled from the MSigDB curated C2 gene sets, IPA ingenuity pathway analysis (https://targetexplorer.ingenuity.com) and were manually curated in-house by checking the individual function of each gene using GeneCard data base (https://www.genecards.org/).
    ingenuity pathway analysis
    suggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)
    Functional analysis of statistically significant gene and protein changes was performed using Ingenuity Pathways Knowledge Base (IPA; Ingenuity Systems).
    Ingenuity Pathways Knowledge Base
    suggested: (Ingenuity Pathways Knowledge Base, RRID:SCR_008117)
    Quantification and statistical analysis: Quality of RNA-Seq raw reads was examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and reads were aligned using STAR v2.7.3.
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    STAR
    suggested: (STAR, RRID:SCR_004463)
    For data annotation and presentation, we used a collection of tools including Cytoscape version 3.6.0 (https://cytoscape.org)
    Cytoscape
    suggested: (Cytoscape, RRID:SCR_003032)
    https://cytoscape.org
    suggested: (CluePedia Cytoscape plugin, RRID:SCR_015784)
    , GeneMANIA version 3.3.1 (http://genemania.org) and Genecards (https://www.genecards.org).
    GeneMANIA
    suggested: (GeneMANIA, RRID:SCR_005709)
    All statistical analyses were performed using the R statistical software 3.5.1.
    R statistical
    suggested: (R Project for Statistical Computing, RRID:SCR_001905)

    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 10.1101/2021.09.30.462514v1 on bioRxiv