Vaccine protection against the SARS-CoV-2 Omicron variant in macaques

  1. Abishek Chandrashekar
  2. Jingyou Yu
  3. Katherine McMahan
  4. Catherine Jacob-Dolan
  5. Jinyan Liu
  6. Xuan He
  7. David Hope
  8. Tochi Anioke
  9. Julia Barrett
  10. Benjamin Chung
  11. Nicole P. Hachmann
  12. Michelle Lifton
  13. Jessica Miller
  14. Olivia Powers
  15. Michaela Sciacca
  16. Daniel Sellers
  17. Mazuba Siamatu
  18. Nehalee Surve
  19. Haley VanWyk
  20. Huahua Wan
  21. Cindy Wu
  22. Laurent Pessaint
  23. Daniel Valentin
  24. Alex Van Ry
  25. Jeanne Muench
  26. Mona Boursiquot
  27. Anthony Cook
  28. Jason Velasco
  29. Elyse Teow
  30. Adrianus C.M. Boon
  31. Mehul S. Suthar
  32. Neharika Jain
  33. Amanda J. Martinot
  34. Mark G. Lewis
  35. Hanne Andersen
  36. Dan H. Barouch

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Abstract

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  1. Version published to 10.1016/j.cell.2022.03.024
  2. ScreenIT

    SciScore for 10.1101/2022.02.06.479285: (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).
    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 (IACUC).
    Sex as a biological variableAnimals, Vaccines, and Challenge Stock: 30 adult male and female cynomolgus macaques ages 4-12 years old were randomly allocated to 5 experimental groups (N=6/group; Fig. S1).
    RandomizationAnimals, Vaccines, and Challenge Stock: 30 adult male and female cynomolgus macaques ages 4-12 years old were randomly allocated to 5 experimental groups (N=6/group; Fig. S1).
    BlindingImmunologic and virologic assays were performed blinded.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Pseudovirus neutralizing antibody assay: The SARS-CoV-2 pseudoviruses expressing a luciferase reporter gene were used to measure pseudovirus neutralizing antibodies13.
    antibodies13
    suggested: None
    The plates were again washed 3 times and 50 μL of SULFO-Tagged anti-Human IgG detection antibody diluted to 1x in Diluent 100 was added to each well and incubated shaking at 700 rpm at room temperature for at least 1 h.
    anti-Human IgG
    suggested: (RevMAb Biosciences Cat# 31-1021-MK, RRID:AB_2783629)
    106 peripheral blood mononuclear cells well were re-suspended in 100 µL of R10 media supplemented with CD49d monoclonal antibody (1 µg/mL) and CD28 monoclonal antibody (1 µg/mL).
    CD49d
    suggested: (BD Biosciences Cat# 347690, RRID:AB_647457)
    The next day, the cells were washed twice with DPBS, stained with aqua live/dead dye for 10 mins and then stained with predetermined titers of monoclonal antibodies against CD279 (clone EH12.1, BB700), CD38 (clone OKT10, PE), CD28 (clone 28.2, PE CY5), CD4 (clone L200, BV510), CD95 (clone DX2, BUV737), CD8 (clone SK1, BUV805) for 30 min.
    CD279
    suggested: (Thermo Fisher Scientific Cat# EPX140-15803-901, RRID:AB_2576106)
    CD38
    suggested: (BD Biosciences Cat# 742074, RRID:AB_2871359)
    CD28
    suggested: (BD Biosciences Cat# 748474, RRID:AB_2872889)
    CD4
    suggested: None
    CD95
    suggested: (BD Biosciences Cat# 741968, RRID:AB_2871273)
    CD8
    suggested: None
    Cells were washed twice with 1X Perm Wash buffer (BD Perm/WashTM Buffer 10X in the CytoFix/CytoPerm Fixation/ Permeabilization kit diluted with MilliQ water and passed through 0.22µm filter) and stained with intracellularly with monoclonal antibodies against Ki67 (clone B56, FITC), CD69 (clone TP1.55.3, ECD), IL10 (clone JES3-9D7, PE CY7), IL13 (clone JES10-5A2, BV421), TNF-α (clone Mab11, BV650), IL4 (clone MP4-25D2, BV711), IFN-γ (clone B27; BUV395), CD45 (clone D058-1283, BUV615), IL2 (clone MQ1-17H12, APC), CD3 (clone SP34.2, Alexa 700)for 30 min.
    Ki67
    suggested: (Akoya Biosciences Cat# 4250019, RRID:AB_2895046)
    CD69
    suggested: (BD Biosciences Cat# 740220, RRID:AB_2739968)
    IL10
    suggested: (BD Biosciences Cat# 564083, RRID:AB_2738583)
    IL13
    suggested: (BD Biosciences Cat# 564288, RRID:AB_2738731)
    TNF-α
    suggested: None
    IL4
    suggested: (BD Biosciences Cat# 743163, RRID:AB_2741316)
    IFN-γ
    suggested: (BD Biosciences Cat# 563563, RRID:AB_2738277)
    IL2
    suggested: None
    After blocking, samples were stained with monoclonal antibodies against CD45 (clone D058-1283, brilliant ultraviolet (BUV) 805), CD3 (clone SP34.2, allophycocyanin (APC)-Cy7), CD7 (clone M-T701, Alexa Fluor700), CD123 (clone 6H6, Alexa Fluor 700), CD11c (clone 3.9, Alexa Fluor 700), CD19 (clone J3-119, phycoerythrin (PE)), CD20 (clone 2H7, PE-Cy5), IgD (IA6-2, PE), IgG (clone G18-145, BUV737), IgM (clone G20-127, BUV395), CD80 (clone L307.4, brilliant violet (BV) 786), CD95 (clone DX2, BV711), CD27 (clone M-T271, BUV563), CD21 (clone B-ly4, BV605), CD14 (clone M5E2, BV570).
    CD45
    suggested: (Creative Biomart Cat# DMABT-H22043, RRID:AB_11439556)
    CD3
    suggested: (GenWay Biotech Inc. Cat# GWB-48F4B7, RRID:AB_10522262)
    CD7
    suggested: (BD Biosciences Cat# 741824, RRID:AB_2871159)
    CD123
    suggested: (Thermo Fisher Scientific Cat# 56-1239-41, RRID:AB_2815247)
    CD11c
    suggested: (Nanostring Cat# 121300104, RRID:AB_2893077)
    CD19
    suggested: (GenWay Biotech Inc. Cat# GWB-B7A22E, RRID:AB_10528952)
    CD20
    suggested: (BD Biosciences Cat# 563781, RRID:AB_2744325)
    IgM
    suggested: (BD Biosciences Cat# 563903, RRID:AB_2721269)
    CD80
    suggested: (Thermo Fisher Scientific Cat# EPX140-15803-901, RRID:AB_2576106)
    CD27
    suggested: (BD Biosciences Cat# 748705, RRID:AB_2873109)
    CD21
    suggested: (BD Biosciences Cat# 740395, RRID:AB_2740125)
    CD14
    suggested: (BioLegend Cat# 301831, RRID:AB_10897803)
    For intracellular staining, cells were permeabilized using Caltag Fix & Perm (Thermo Fisher Scientific), then stained with monoclonal antibodies against Ki67 (clone B56, peridinin chlorophyll protein (PerCP)-Cy5.5) and Bcl6 (clone K112-91, PE-CF594).
    Bcl6
    suggested: None
    Primary mouse anti-SARS-CoV-nucleoprotein antibody (Sinobiological; 40143-MM05) at 1:1000, was applied for 60 min, followed by mouse Mach-2 HRP-Polymer (Biocare) for 30 min and then counterstained with hematoxylin followed by bluing using 0.25% ammonia water.
    anti-SARS-CoV-nucleoprotein
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    This challenge stock was generated in VeroE6-TMPRSS2 cells and had a titer of 2.3×109 TCID50/ml and 2.5×107 PFU/ml in VeroE6-TMPRSS2 cells and was fully sequenced (EPI_ISL_7171744; Mehul Suthar, Emory University).
    VeroE6-TMPRSS2
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    In brief, the packaging construct psPAX2 (AIDS Resource and Reagent Program), luciferase reporter plasmid pLenti-CMV Puro-Luc (Addgene) and spike protein expressing pcDNA3.1-SARS-CoV-2 SΔCT were co-transfected into HEK293T cells (ATCC CRL_3216) with lipofectamine 2000 (ThermoFisher Scientific).
    HEK293T
    suggested: ATCC Cat# CRL-3216, RRID:CVCL_0063)
    To determine the neutralization activity of human serum, HEK293T-hACE2 cells were seeded in 96-well tissue culture plates at a density of 2.0 × 104 cells per well overnight.
    HEK293T-hACE2
    suggested: RRID:CVCL_A7UK)
    Recombinant DNA
    SentencesResources
    In brief, the packaging construct psPAX2 (AIDS Resource and Reagent Program), luciferase reporter plasmid pLenti-CMV Puro-Luc (Addgene) and spike protein expressing pcDNA3.1-SARS-CoV-2 SΔCT were co-transfected into HEK293T cells (ATCC CRL_3216) with lipofectamine 2000 (ThermoFisher Scientific).
    psPAX2
    suggested: RRID:Addgene_12260)
    pLenti-CMV Puro-Luc
    suggested: None
    pcDNA3.1-SARS-CoV-2
    suggested: None
    The gene fragment was subsequently cloned into a pcDNA3.1+ expression plasmid using restriction site cloning (Integrated DNA Technologies).
    pcDNA3.1+
    suggested: RRID:Addgene_117272)
    Software and Algorithms
    SentencesResources
    Fixed cells were transferred to 96-well round bottom plate and analyzed by BD FACSymphony™ system.
    BD FACSymphony™
    suggested: None
    Subsequent analyses were performed using FlowJo software (BD Bioscience, v.9.9.6).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistical analysis: Descriptive statistics and logistic regression were performed using GraphPad Prism 8.4.3, (GraphPad Software, San Diego, California).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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 10.1101/2022.02.06.479285 on bioRxiv