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  1. SciScore for 10.1101/2021.11.25.470011: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The study and corresponding experiments were approved by the local ethics committee (S64089) and all patients gave their written informed consent.
    Consent: The study and corresponding experiments were approved by the local ethics committee (S64089) and all patients gave their written informed consent.
    Euthanasia Agents: At day 4 post-infection, animals were euthanized by intraperitoneal injection of 500 μL Dolethal (200 mg/mL sodium pentobarbital, Vétoquinol SA).
    Sex as a biological variableFemale Syrian hamsters (Mesocricetus auratus) were purchased from Janvier Laboratories and kept per two in individually ventilated isolator cages (IsoCage N Bio-containment System, Tecniplast) at 21°C, 55% humidity and 12:12 day/night cycles.
    RandomizationNo randomization methods were used and confounders were not controlled, though all caretakers and technicians were blinded to group allocation in the animal facility and to sample numbers for analysis (qPCR, titration, and histology).
    BlindingNo randomization methods were used and confounders were not controlled, though all caretakers and technicians were blinded to group allocation in the animal facility and to sample numbers for analysis (qPCR, titration, and histology).
    Power AnalysisGroup size was calculated based on the independent t-test with an effect size of 2.0 and a power of 80% (effect size = delta mean/SD = 1 log10 decrease in viral RNA/0.5 log10), resulting in 5-6 animals/group.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    His-tag labeled SARS-CoV-2 RBD (The Native Antigen Company) was biotinylated with the EZ-Link Sulfo-NHS-LC-Biotin kit (Thermofisher Scientific) according to the manufacturer’s protocol, corresponding to 1-3 biotin groups per antibody molecule.
    Sulfo-NHS-LC-Biotin
    suggested: None
    After the 60 minutes incubation, B cells were washed with FACS buffer and stained with PerCP-cy5.5 anti-human CD19 antibody (Biolegend, 363016)
    anti-human CD19
    suggested: (BioLegend Cat# 363016, RRID:AB_2564207)
    FITC anti-human CD3 antibody (Biolegend, 300306) and PE streptavidin (Biolegend, 405203) for 25 minutes on ice.
    anti-human CD3
    suggested: (BioLegend Cat# 300306, RRID:AB_314042)
    As a positive and negative control, an anti-SARS-CoV-2 RBD mAb (40150-D004, Sino Biological) and anti-SARS-CoV-2 nucleocapsid antibody (MBS2563841, MyBioSource) were used, respectively.
    anti-SARS-CoV-2
    suggested: None
    anti-SARS-CoV-2 nucleocapsid antibody ( MBS2563841
    suggested: None
    First, mouse anti-human IgG (Fc) antibody (Human Antibody Capture Kit, Cytiva) was immobilized on a CM5 chip according to manufacturer instructions.
    anti-human IgG
    suggested: None
    Monoclonal antibody neutralization assays: a. Production of S-pseudotyped virus and serum neutralization test (SARS2, SARS1, MERS, 229E): VSV S-pseudotypes were generated as described previously56.
    SARS2
    suggested: None
    Two hours later, the medium was replaced by medium containing anti-VSV-G antibody (I1-hybridoma, ATCC CRL-2700) to neutralize residual VSV-G input.
    anti-VSV-G
    suggested: None
    In brief, serial dilutions of antibodies were mixed separately with live SARS-CoV-2 Wuhan, alpha, beta and gamma virus strains, incubated at 37 °C for 1h, and added to the monolayer of Vero E6 cells.
    1h
    suggested: None
    Antibody protein treatments (anti-SARS-CoV-2 mAbs or human IgG1 isotype control Trastuzumab/Herceptin® (Roche)) were initiated 24 hours post infection by intraperitoneal injection.
    human IgG1
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Briefly, HEK-293T cells (SARS-CoV, SARS-CoV-2 and MERS-S) or BHK-21J cells (229E) were transfected with the respective S protein expression plasmids, and one day later infected (MOI = 2) with GFP-encoding VSVΔG backbone virus (purchased from Kerafast).
    HEK-293T
    suggested: None
    BHK-21J
    suggested: None
    To quantify nAbs, serial dilutions of serum samples were incubated for 1 hour at 37 °C with an equal volume of S pseudotyped VSV particles and inoculated on Vero E6 cells (SARS-CoV and SARS-CoV-2) or Huh-7 cells (229E and MERS-S) for 18 hours.
    Huh-7
    suggested: None
    Shortly, 104 VeroE6 cells/well were seeded in 96-well plates one day prior to the titration and inoculated with 10–fold serial dilutions of virus solutions and cultured for 3 days at 37°C.
    VeroE6
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Infectious virus was isolated by serial passaging on Huh7 and Vero E6 cells58; passage 6 virus was used for the study described here.
    Huh7
    suggested: None
    Recombinant DNA
    SentencesResources
    Intramuscular pDNA electroporation: 3B8 was delivered in vivo, encoded in the CMV-driven pcDNA3.4 vectors, as an equimolar mixture of the 3B8 heavy and light chain plasmids (jointly referred to as ‘p3B8’).
    pcDNA3.4
    suggested: RRID:Addgene_131198)
    Software and Algorithms
    SentencesResources
    Analysis was performed using Graphpad Prism 9.0 (Graphpad Software). b.
    Graphpad
    suggested: (GraphPad, RRID:SCR_000306)
    Epitope binning graphs were made in Microsoft Excel and clustering was done with ClustVis web tool (
    Microsoft Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)
    ClustVis
    suggested: (ClustVis, RRID:SCR_017133)
    Neutralization IC50 values were determined by normalizing the serum neutralization dilution curve to a virus (100%) and cell control (0%) and fitting in Graphpad Prism (GraphPad Software, Inc.). b.
    Graphpad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Both strains were subjected to sequencing on a MinION platform (Oxford pore) directly from the nasopharyngeal swabs
    MinION
    suggested: (MinION, RRID:SCR_017985)

    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: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT03831503Active, not recruitingA Study of INO-A002 in Healthy Dengue Virus-naive Adults


    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.

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