An intranasally administrated SARS-CoV-2 beta variant subunit booster vaccine prevents beta variant replication in rhesus macaques

  1. Yongjun Sui
  2. Jianping Li
  3. Hanne Andersen
  4. Roushu Zhang
  5. Sunaina K Prabhu
  6. Tanya Hoang
  7. David Venzon
  8. Anthony Cook
  9. Renita Brown
  10. Elyse Teow
  11. Jason Velasco
  12. Laurent Pessaint
  13. Ian N Moore
  14. Laurel Lagenaur
  15. Jim Talton
  16. Matthew W Breed
  17. Josh Kramer
  18. Kevin W Bock
  19. Mahnaz Minai
  20. Bianca M Nagata
  21. Hyoyoung Choo-Wosoba
  22. Mark G Lewis
  23. Lai-Xi Wang
  24. Jay A Berzofsky

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Abstract

Emergence of SARS-CoV-2 variants and waning of vaccine/infection-induced immunity pose threats to curbing the COVID-19 pandemic. Effective, safe, and convenient booster vaccines are in need. We hypothesized that a variant-modified mucosal booster vaccine might induce local immunity to prevent SARS-CoV-2 infection at the port of entry. The beta-variant is one of the hardest to cross-neutralize. Herein, we assessed the protective efficacy of an intranasal booster composed of beta variant-spike protein S1 with IL-15 and TLR agonists in previously immunized macaques. The macaques were first vaccinated with Wuhan strain S1 with the same adjuvant. A total of 1 year later, negligibly detectable SARS-CoV-2-specific antibody remained. Nevertheless, the booster induced vigorous humoral immunity including serum- and bronchoalveolar lavage (BAL)-IgG, secretory nasal- and BAL-IgA, and neutralizing antibody against the original strain and/or beta variant. Beta-variant S1-specific CD4+ and CD8+ T cell responses were also elicited in PBMC and BAL. Following SARS-CoV-2 beta variant challenge, the vaccinated group demonstrated significant protection against viral replication in the upper and lower respiratory tracts, with almost full protection in the nasal cavity. The fact that one intranasal beta-variant booster administrated 1 year after the first vaccination provoked protective immunity against beta variant infections may inform future SARS-CoV-2 booster design and administration timing.

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  1. Version published to 10.1093/pnasnexus/pgac091
  2. ScreenIT

    SciScore for 10.1101/2021.10.19.464990: (What is this?)

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

    Table 1: Rigor

    EthicsIACUC: Animal Protocol No. VB-037 was approved by the NCI Animal Care and Use Committee (ACUC) to conduct the study.
    Sex as a biological variableAnimals: 10 Indian-origin adult male rhesus macaques (Macaca mulatta), 3-8 years old, were enrolled in the study.
    Randomizationnot detected.
    BlindingBriefly, hematoxylin and eosin (H&E) sections were examined under light microscopy and scored by a board-certified veterinary pathologist, who was blind to the groups.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    ELISA assay to detect S1-specific antibody responses: The BAL samples were concentrated using Amicon Ultra centrifugal filter units (10kDa cutoff, Millipore Sigma), and the total IgG and IgA were determined using the Rhesus Monkey IgG-UNLB (Southern Biotech), and the Monkey IgA ELISA development kit (HRP) (MabTech) respectively, following the manufacturer’s protocol as described before 20.
    total IgG
    suggested: None
    For IgG and IgA binding assay, Goat Anti-Monkey IgG (alpha-chain specific)-HRP conjugate (1:5,000 dilutions, Alpha Diagnostic) and were used, respectively, as a secondary antibody.
    Anti-Monkey IgG (alpha-chain
    suggested: None
    Original BAL samples or nasal swab flow-through from vaccinated and naïve animals were added in duplicate to the plates, followed by adding mouse anti-rhesus J chain [CA1L_33e1_A1a3] antibody (1:1000 dilutions, NIH nonhuman primate reagent resource), and Goat anti-mouse IgG-HRP conjugate (1:10,000 dilutions, R&D Systems).
    anti-rhesus J chain [CA1L_33e1_A1a3
    suggested: None
    anti-mouse IgG-HRP
    suggested: None
    Cells were stained with viability dye (Invitrogen) and the following antibody mixtures: PE-Cy7-CD3, BV605-CD4, APC-Cy7-CD8, Alexa Fluor® 700-CD45 were from BD Biosciences, FITC-CD28, Pe-Cy5-CD95, BV711-TNFα, IFNγ-PE or - PerCP, Alexa Fluor® 647-IL4, BV785-IL2, BV421-IL-17A, BV785-CD14, BV421-CD16 were from Biolegend; PE-IL13 was from Miltenyi Biotech.
    BV785-CD14
    suggested: None
    A rabbit polyclonal SARS-CoV-2 antibody (GeneTex) was used immunohistochemically to stain for the presence of SARS-CoV-2 virus antigen.
    SARS-CoV-2 virus antigen.
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Vero E6 cells (ATCC, cat. no. CRL-1586), and 30 pfu challenge titers of SARS-CoV-2 virus USA-WA1/2020 strain or Vero TMPRSS2 cells (obtained from Dr. Adrian Creanga and Barney Graham, VRC, NIAID, Bethesda, MD) and same titer of the beta variant (B.1.351, SRA strain) was used to test the PRNT titers against the WA or beta variant of SARS-CoV-2 44.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Vero TMPRSS2
    suggested: None
    The challenge stock was grown in Calu-3 cells and was deep sequenced, which confirmed the expected sequence identity with no mutations in the Spike protein greater than >2.5% frequency and no mutations elsewhere in the virus at >13% frequency.
    Calu-3
    suggested: BCRJ Cat# 0264, RRID:CVCL_0609)
    Software and Algorithms
    SentencesResources
    Area under the curve, endpoint titer, and ID50 values were calculated by GraphPad Prism 8 software with sigmoidal nonlinear regression.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Data acquisition and analyses were performed using an LSRII flow cytometer with 4 lasers (BD Bioscience) and FlowJo software (Becton Dickinson).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistical analysis: Prism version 8 (Graph Pad) was used for statistical analyses.
    Prism
    suggested: (PRISM, RRID:SCR_005375)

    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.

  3. Version published to 10.1101/2021.10.19.464990 on bioRxiv