An intranasal lentiviral booster broadens immune recognition of SARS-CoV-2 variants and reinforces the waning mRNA vaccine-induced immunity that it targets to lung mucosa

  1. Benjamin Vesin
  2. Jodie Lopez
  3. Amandine Noirat
  4. Pierre Authié
  5. Ingrid Fert
  6. Fabien Le Chevalier
  7. Fanny Moncoq
  8. Kirill Nemirov
  9. Catherine Blanc
  10. Cyril Planchais
  11. Hugo Mouquet
  12. Françoise Guinet
  13. David Hardy
  14. Christiane Gerke
  15. François Anna
  16. Maryline Bourgine
  17. Laleh Majiessi
  18. Pierre Charneau

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Abstract

As the COVID-19 pandemic continues and new SARS-CoV-2 variants of concern emerge, the adaptive immunity initially induced by the first-generation COVID-19 vaccines wains and needs to be strengthened and broadened in specificity. Vaccination by the nasal route induces mucosal humoral and cellular immunity at the entry point of SARS-CoV-2 into the host organism and has been shown to be the most effective for reducing viral transmission. The lentiviral vaccination vector (LV) is particularly suitable for this route of immunization because it is non-cytopathic, non-replicative and scarcely inflammatory. Here, to set up an optimized cross-protective intranasal booster against COVID-19, we generated an LV encoding stabilized Spike of SARS-CoV-2 Beta variant (LV::S Beta-2P ). mRNA vaccine–primed and -boosted mice, with waning primary humoral immunity at 4 months post-vaccination, were boosted intranasally with LV::S Beta-2P . Strong boost effect was detected on cross-sero-neutralizing activity and systemic T-cell immunity. In addition, mucosal anti-Spike IgG and IgA, lung resident B cells, and effector memory and resident T cells were efficiently induced, correlating with complete pulmonary protection against the SARS-CoV-2 Delta variant, demonstrating the suitability of the LV::S Beta-2P vaccine candidate as an intranasal booster against COVID-19.

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    SciScore for 10.1101/2022.01.30.478159: (What is this?)

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

    Table 1: Rigor

    EthicsIACUC: Ethical approval of animal experimentation: Experimentation on animals was performed in accordance with the European and French guidelines (Directive 86/609/CEE and Decree 87-848 of 19 October 1987) subsequent to approval by the Institut Pasteur Safety, Animal Care and Use Committee, protocol agreement delivered by local ethical committee (CETEA #DAP20007, CETEA #DAP200058) and Ministry of High Education and Research APAFIS#24627-2020031117362508 v1, APAFIS#28755-2020122110238379 v1.
    Sex as a biological variableMice immunization and SARS-CoV-2 infection: Female C57BL/6JRj mice were purchased from Janvier (Le Genest Saint Isle, France), housed in individually-ventilated cages under specific pathogen-free conditions at the Institut Pasteur animal facilities and used at the age of 7 wks.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Analysis of humoral and systemic T-cell immunity: Anti-SCoV-2 IgG and IgA antibody titers were determined by ELISA by use of recombinant stabilized SCoV-2 or RBD fragment for coating.
    Anti-SCoV-2 IgG
    suggested: None
    IgA
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    Mice immunization and SARS-CoV-2 infection: Female C57BL/6JRj mice were purchased from Janvier (Le Genest Saint Isle, France), housed in individually-ventilated cages under specific pathogen-free conditions at the Institut Pasteur animal facilities and used at the age of 7 wks.
    C57BL/6JRj
    suggested: RRID:MGI:2670020)
    Recombinant DNA
    SentencesResources
    Construction and production of vaccinal LV::SBeta-2P: First, a codon-optimized sequence of Spike from the Ancestral, D614G, Alpha, Beta or Gamma VOCs were synthetized and inserted into the pMK-RQ_S-2019-nCoV_S501YV2 plasmid.
    pMK-RQ_S-2019-nCoV_S501YV2
    suggested: None
    The S sequence was then extracted by BamHI/XhoI digestion to be ligated into the pFlap lentiviral plasmid between the BamHI and XhoI restriction sites, located between the native human ieCMV promoter and the mutated atg starting codon of Woodchuck Posttranscriptional Regulatory Element (WPRE) sequence (Figure S5).
    pFlap
    suggested: None
    Various pFlap-ieCMV-S-WPREm or pFlap-ieCMV-S2P-WPREm plasmids were amplified and used to produce non-integrative vaccinal LV, as described elsewhere [2,6].
    pFlap-ieCMV-S2P-WPREm
    suggested: None
    Software and Algorithms
    SentencesResources
    Lung Brm were studied by surface staining with a mixture of PerCP Vio700-anti-IgM (130-106-012, Miltenyi), and PerCP Vio700-anti-IgD (130-103-797, Miltenyi), APC-H7-anti-CD19 (560143, BD Biosciences), PE-anti-CD38 (102708, BioLegend Europe BV), PE-Cy7-anti-CD62L (ab25569, AbCam), BV711-anti-CD69 (740664, BD Biosciences), BV421-anti-CD73 (127217, BioLegend Europe BV), FITC-anti-CD80 (104705, BioLegend Europe BV and yellow Live/Dead (Invitrogen).
    BD Biosciences
    suggested: (BD Biosciences, RRID:SCR_013311)
    Samples were acquired in an Attune NxT cytometer (Invitrogen) and data analyzed by FlowJo software (Treestar, OR, USA).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Slides were scanned using the AxioScan Z1 (Zeiss) system and images were analyzed with the Zen 2.6 software.
    Zen
    suggested: None

    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.

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  2. Version published to 10.1101/2022.01.30.478159v1 on bioRxiv