Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine

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1. Version published to 10.1038/s41467-022-33985-4

   Oct 23, 2022
2. 

   Version published to 10.1101/2022.01.26.477915v2 on bioRxiv

   Feb 14, 2022
3. 

   ScreenIT

   Feb 1, 2022

   SciScore for 10.1101/2022.01.26.477915: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Animals and immunizations: The study protocol and all veterinarian procedures were approved by the Bioqual IACUC per a memorandum of understanding with the Duke IACUC, and were performed based on standard operating procedures.
   Sex as a biological variable	Male and female macaques per group were balanced when availability permitted.
   Randomization	not detected.
   Blinding	Samples were scored by a board-certified veterinary pathologist in a blinded manner.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: All cells were tested monthly for mycoplasma.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   ACE2 and neutralizing antibody blocking assay: ELISA plates were coated as stated above …

   SciScore for 10.1101/2022.01.26.477915: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Animals and immunizations: The study protocol and all veterinarian procedures were approved by the Bioqual IACUC per a memorandum of understanding with the Duke IACUC, and were performed based on standard operating procedures.
   Sex as a biological variable	Male and female macaques per group were balanced when availability permitted.
   Randomization	not detected.
   Blinding	Samples were scored by a board-certified veterinary pathologist in a blinded manner.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: All cells were tested monthly for mycoplasma.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   ACE2 and neutralizing antibody blocking assay: ELISA plates were coated as stated above with 2 μg/mL recombinant ACE-2 protein or neutralizing antibodies, then washed and blocked with 3% BSA in 1x PBS.	ACE2 suggested: None
   A peroxide block (Leica) was applied for 5 min to quench endogenous peroxidase activity prior to applying the SARS-CoV-2 antibody (1:2000, GeneTex, GTX135357).	SARS-CoV-2 suggested: (Leinco Technologies Cat# LT2000, RRID:AB_2893936) GTX135357 suggested: (GeneTex Cat# GTX135357, RRID:AB_2868464)
   Experimental Models: Cell Lines
   Sentences	Resources
   ACE2-Fc was expressed by transient transfection of Freestyle 293-F cells.	293-F suggested: RRID:CVCL_6642)
   Pseudovirions were produced in HEK 293T/17 cells (ATCC cat. no. CRL-11268) by transfection using Fugene 6 (Promega, Catalog #E2692).	HEK 293T/17 suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)
   Pseudovirions were produced by co-transfection of Lenti-X 293T cells with psPAX2(gag/pol),	293T suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)
   The supernatants were collected at 48 h after transfection and filtered through 0.45-μm membranes and titrated using HEK293T cells that express ACE2 and TMPRSS2 protein (293T-ACE2-TMPRSS2 cells).	HEK293T suggested: None
   For the neutralization assay, 50 μl of SARS-CoV-2 spike pseudovirions were pre-incubated with an equal volume of medium containing serum at varying dilutions at room temperature for 1 h, then virus-antibody mixtures were added to 293T-ACE2-TMPRSS2 cells in a 96-well plate.	293T-ACE2-TMPRSS2 suggested: None
   Briefly, target cells were either Vero E6 cells after a 2 day-infection with SARS-CoV-2 USA-WA1/2020 or 293T cells 2-days post transfection with a SARS-CoV-2 S protein (D614) expression plasmid.	Vero E6 suggested: RRID:CVCL_A7UJ)
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Mouse immunization and challenge: Eleven-month-old female BALB/c mice were purchased from Envigo (#047) and were used for the SARS-CoV, SARS-CoV-2 WA-1, SARS-CoV-2 B.1.351, and RsSHC014-CoV protection experiments.	BALB/c suggested: None
   Recombinant DNA
   Sentences	Resources
   Pseudovirions for 293T/ACE2 infection were produced by co-transfection with a lentiviral backbone (pCMV ΔR8.2) and firefly luciferase reporter gene (pHR’ CMV Luc) (Naldini et al., 1996)	pCMV ΔR8.2 suggested: None
   Pseudovirions were produced by co-transfection of Lenti-X 293T cells with psPAX2(gag/pol),	psPAX2 suggested: RRID:Addgene_12260)
   The recombinant pcDNA3.1 plasmid was linearized, transcribed using MEGAscript T7 Transcription Kit (ThermoFisher, catalog # AM1334), and purified with MEGAclear Transcription Clean-Up Kit (ThermoFisher, catalog # AM1908).	pcDNA3.1 suggested: RRID:Addgene_79663)
   Software and Algorithms
   Sentences	Resources
   All mutations were confirmed by full-length spike gene sequencing by Sanger Sequencing, using Sequencher and SnapGene for sequence analyses.	Sequencher suggested: (Sequencher, RRID:SCR_001528) SnapGene suggested: (SnapGene, RRID:SCR_015052)
   Data analysis was performed using FlowJo 10 software (BD Biosciences).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Images were analyzed by 2D class averages using standard protocols with Relion 3.0 (Zivanov et al., 2018).	Relion suggested: (RELION, RRID:SCR_016274)
   Statistics Analysis: Data were plotted using Prism GraphPad 8.0.	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Wilcoxon rank sum exact test was performed to compare differences between groups with p-value < 0.05 considered significant using SAS 9.4 (SAS Institute, Cary, NC).	SAS Institute suggested: (Statistical Analysis System, RRID:SCR_008567)

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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: We detected the following sentences addressing limitations in the study:

   Our study has several limitations. First, our study did not evaluate the durability of vaccine-induced immune responses and protection against SARS-CoV-2 variants. Second, we did not set up longer time intervals between the second and the third booster vaccination, to mimic 4-6 month boosting interval in humans. Lastly, we challenged the animals with WA-1 strain, the Beta variant and the Delta variant; future in vivo protection studies will be required upon availability of viral stocks of other SARS-CoV-2 variants such as the Omicron variant. Thus, our study demonstrates that scNP vaccines with SARS-CoV-2 spike or spike subunits confer potent protection in NHPs against WA-1, Beta and Delta variants, and that they induce neutralizing antibodies to all SARS-CoV-2 variants tested in vitro. These findings have important implications for development of the next generation of COVID-19 vaccines.

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   Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04915768	Recruiting	Evaluating the Safety and Immunogenicity of Stabilized CH505…
   NCT04177355	Recruiting	Evaluating the Safety and Immunogenicity of HIV-1 BG505 SOSI…

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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 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.

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

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   Read the original source
4. 

   Version published to 10.1101/2022.01.26.477915v1 on bioRxiv

   Jan 28, 2022