Adjuvanting a subunit SARS-CoV-2 nanoparticle vaccine to induce protective immunity in non-human primates

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   ScreenIT

   Feb 14, 2021

   SciScore for 10.1101/2021.02.10.430696: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: Animals were housed and maintained as per National Institutes of Health (NIH) guidelines at the New Iberia Research Center (NIRC) of the University of Louisiana at Lafayette in accordance with the rules and regulations of the Committee on the Care and Use of Laboratory Animal Resources.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Animal subjects and experimentation: Thirty-three male rhesus macaques (Macaca mulatta) of Indian origin, aged 3 - 9 years were assigned to the study (Supplementary Table 1).
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   In wells with …

   SciScore for 10.1101/2021.02.10.430696: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: Animals were housed and maintained as per National Institutes of Health (NIH) guidelines at the New Iberia Research Center (NIRC) of the University of Louisiana at Lafayette in accordance with the rules and regulations of the Committee on the Care and Use of Laboratory Animal Resources.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Animal subjects and experimentation: Thirty-three male rhesus macaques (Macaca mulatta) of Indian origin, aged 3 - 9 years were assigned to the study (Supplementary Table 1).
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   In wells with anti-human IgG capture antibody, human IgG control (SinoBiological, #HG1K) was serially diluted from 0.5-500 ng/mL in TBST in triplicate and 50 μL of each dilution incubated for 1 h.	anti-human IgG suggested: None
   The antibody-virus mixture was added to VeroE6 cell (C1008, ATCC, #CRL-1586	C1008 suggested: None
   assay: Antibodies blocking the binding of SARS-CoV-2 Spike RBD to the angiotensin-converting enzyme 2 (ACE2) were detected with a V-PLEX SARS-CoV-2 Panel 2 (ACE2) Kit (Meso Scale Diagnostics) according to the manufacturer’s instructions.	ACE2 suggested: None
   Luminex Isotype and FcR Binding Assay: To determine relative concentrations of antigen-specific antibody isotypes and Fc receptor binding activity, a Luminex isotype assay was performed as previously described39.	antigen-specific suggested: None
   Mouse-anti-rhesus antibody detectors were then added for each antibody isotype (IgG1, IgG2, IgG3, IgG4, IgA, NIH Nonhuman Primate Reagent Resource supported by AI126683 and OD010976).	IgG1 , IgG2 suggested: None IgG3 , IgG4 suggested: None
   Tertiary anti-mouse-IgG detector antibodies conjugated to PE were then added.	anti-mouse-IgG detector suggested: None
   Systems serology: To quantify antibody functionality of plasma samples, bead-based assays were used to measure antibody-dependent cellular phagocytosis (ADCP), antibody-dependent neutrophil phagocytosis (ADNP) and antibody-dependent complement deposition (ADCD), as previously described40-43.	antibody-dependent neutrophil phagocytosis ( ADNP suggested: None antibody-dependent complement deposition ( ADCD) suggested: None
   SARS-CoV-2 spike protein (Hexapro antigen from Erica Ollmann Saphire, La Jallo for Immunology) was coupled to fluorescent streptavidin beads (Thermo Fisher) and incubated with sera samples to allow antibody binding to occur.	SARS-CoV-2 spike protein ( Hexapro antigen from Erica Ollmann Saphire , La Jallo for Immunology ) suggested: None SARS-CoV-2 spike protein ( Hexapro antigen from Erica Ollmann Saphire , suggested: None
   After phagocytosis of immune complexes, neutrophils were stained with an anti-CD66b Pacific Blue detection antibody (Biolegend) prior to flow cytometry.	anti-CD66b suggested: None
   For quantification of antibody-dependent NK cell activation, diluted plasma samples were incubated in Nunc MaxiSorp plates (Thermo Fisher Scientific) coated with antigen.	antigen . suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Anti-S binding ELISA: SARS-CoV-2 Spike protein was produced in HEK293T cells (Atum, Newark, CA)	HEK293T suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
   For neutralization assays, HEK-hACE2 cells were cultured in DMEM with 10% FBS (Hyclone) and 1% PenStrep with 8% CO2 in a 37°C incubator on poly-lysine (sigma) 96 well plates.	HEK-hACE2 suggested: None
   Pseudovirions were produced in HEK293T/17 cells by co-transfection of a lentivirus backbone plasmid, a Spike-expressing plasmid, and a firefly Luc reporter gene plasmid.	HEK293T/17 suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)
   The furin cleavage site, a site with frequent culture adaptation in Vero E6 cells, harbored no polymorphisms at greater than 1% of sequence reads in this stock.	Vero E6 suggested: RRID:CVCL_XD71)
   For ADCP, cultured human monocytes (THP-1 cell line) were incubated with immune complexes, during which phagocytosis occurred.	THP-1 suggested: CLS Cat# 300356/p804_THP-1, RRID:CVCL_0006)
   Software and Algorithms
   Sentences	Resources
   Animals were housed and maintained as per National Institutes of Health (NIH) guidelines at the New Iberia Research Center (NIRC) of the University of Louisiana at Lafayette in accordance with the rules and regulations of the Committee on the Care and Use of Laboratory Animal Resources.	NIRC suggested: None
   Alum (Alhydrogel 2%) was purchased from Croda Healthcare (Batch #0001610348).	Croda Healthcare suggested: None
   Plates were immediately read at 450 nm on a SpectraMax M5 plate reader (Molecular Devices) and data plotted and fit in Prism (GraphPad) using nonlinear regression sigmoidal, 4PL, X is log(concentration) to determine EC50 values from curve fits.	Prism suggested: (PRISM, RRID:SCR_005375) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   All flow cytometry data were analyzed using Flowjo software v10 (TreeStar Inc.)	Flowjo suggested: (FlowJo, RRID:SCR_008520)
   Before analysis, the PET images were Gaussian smoothed in OsiriX and smoothing was applied to raw data with a 3 x 3 matrix size and a matrix normalization value of 24.	OsiriX suggested: None
   PET quantification values were organized in Microsoft Excel.	Microsoft Excel suggested: (Microsoft Excel, RRID:SCR_016137)
   All the statistical analyses were performed using GraphPad Prism v.9.0.0 or R version 3.6.1.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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   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).

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   Results from scite Reference Check: We found no unreliable references.

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   Version published to 10.1101/2021.02.10.430696 on bioRxiv

   Feb 11, 2021