1. SciScore for 10.1101/2022.01.12.476120: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The study was approved by the Institutional Review Board of Vanderbilt University Medical Center and specimens were obtained after written informed consent.
    Consent: The study was approved by the Institutional Review Board of Vanderbilt University Medical Center and specimens were obtained after written informed consent.
    IACUC: The protocols were approved by the Institutional Animal Care and Use Committee at the Washington University School of Medicine (assurance number A3381–01).
    Sex as a biological variableEight to nine week-old mice of both sexes were inoculated with 103 PFU of SARS-CoV-2 by an intranasal route.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationContamination: Mycoplasma testing of Expi293F and ExpiCHO cultures was performed monthly using a PCR- based mycoplasma detection kit (ATCC, 30-1012K).

    Table 2: Resources

    Antibodies
    SentencesResources
    In brief, synthesized antibody-encoding DNA (∼2 μg per transfection) was added to OptiPro serum free medium (OptiPro SFM), incubated with ExpiFectamine CHO Reagent and added to 800 µL of ExpiCHO cell cultures into 96-deep-well blocks using a ViaFlo 384 liquid handler (Integra Biosciences).
    antibody-encoding DNA
    suggested: None
    Antibody binding was detected with anti-IgG Alexa-Fluor-647-labelled secondary antibodies.
    anti-IgG Alexa-Fluor-647-labelled secondary antibodies .
    suggested: None
    The plates were incubated sequentially with 1 μg/mL of rCR3022 anti-S antibody or a murine anti-SARS-CoV-2 mAb, SARS2-16 (hybridoma supernatant diluted 1:6,000 to a final concentration of ∼20 ng/mL) and then HRP-conjugated goat anti-human IgG (Sigma-Aldrich, A6029) in PBS supplemented with 0.1% (w/v) saponin (Sigma) and 0.1% BSA.
    anti-S
    suggested: None
    anti-SARS-CoV-2
    suggested: None
    anti-human IgG
    suggested: (Sigma-Aldrich Cat# A6029, RRID:AB_258272)
    Serum antibody competition binding ELISAs with biotinylated reference mAbs: mAb COV2-3434 was biotinylated using NHS-PEG4-biotin (Thermo Fisher Scientific, cat# A39259) according to manufacturer protocol.
    NHS-PEG4-biotin
    suggested: None
    Competition ELISA of mAbs, related to Figure 4 Competition ELISA of mAbs with previously mapped antibodies COV2-2130, COV2-2196, COV2-2676, COV2-2489, r4A8 or rCR3022.
    COV2-2489
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Cell lines: Vero (ATCC, CCL-81), HEK293 (ATCC, CRL-1573) and HEK293T (ATCC, CRL-3216) cells were maintained at 37°C in 5% CO2 in Dulbecco’s minimal essential medium (DMEM) containing 10% (v/v) heat-inactivated fetal bovine serum (FBS), 10 mM HEPES pH 7.3, 1 mM sodium pyruvate, 1× non-essential amino acids and 100 U/mL of penicillin–streptomycin.
    HEK293
    suggested: None
    HEK293T
    suggested: None
    Vero-furin cells were obtained from T. Pierson (NIAID, NIH) and have been described previously (45) Vero-hACE2-TMPRSS2 cells were a gift of A. Creanga and B. Graham (Vaccine Research Center, NIH)
    Vero-hACE2-TMPRSS2
    suggested: None
    The antibody-virus complexes were added to Vero E6 cell-culture monolayers in 96-well plates for 1 h at 37°C.
    Vero E6
    suggested: None
    A suspension of 18,000 Vero-E6 cells in 50 μL of cell culture medium was seeded in each well, and the plate was placed on the analyzer.
    Vero-E6
    suggested: None
    Triplicate wells containing virus only (maximal CPE in the absence of mAb) and wells containing only Vero cells in medium (no-CPE wells) were included as controls.
    Vero
    suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
    Mice (8 to 9 weeks old) were inoculated with 1 × 104 focus forming units of SARS-CoV-2 (viral titer was determined on Vero-TMPRSS2-ACE2 cells) via the intranasal route.
    Vero-TMPRSS2-ACE2
    suggested: None
    A plasmid encoding cDNA for each spike protein mutant was transfected into HEK-293T cells and allowed to express for 22 h.
    HEK-293T
    suggested: None
    Briefly, lung homogenates were serially diluted and added to Vero+TMPRSS2+hACE2 cell monolayers in 12-well plates.
    Vero+TMPRSS2+hACE2
    suggested: None
    B. Neutralization of VSV-S by COV2-3434 was measured in the absence or presence of 25 μM biliverdin in Vero-CCL81 cells.
    Vero-CCL81
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    Heterozygous K18-hACE c57BL/6J mice (strain: 2B6.Cg-Tg(K18-ACE2)2Prlmn/J) were obtained from Jackson Laboratory (034860).
    K18-hACE c57BL/6J
    suggested: None
    Female heterozygous K18-hACE C57BL/6J mice were housed in groups of up to 5 mice per cage at 18 to 24°C ambient temperatures and 40 to 60% humidity.
    C57BL/6J
    suggested: None
    Eight-week-old female K18-hACE2 transgenic mice were inoculated by the intranasal route with 104 FFU of SARS-CoV-2 (WA1/2020 D614G).
    K18-hACE2
    suggested: RRID:IMSR_GPT:T037657)
    Software and Algorithms
    SentencesResources
    ) sequencing core laboratory at an appropriate target concentration for 10X Genomics library preparation and subsequent sequence analysis.
    Genomics
    suggested: (UTHSCSA Genomics Core, RRID:SCR_012239)
    Half maximal inhibitory concentration (IC50) values were determined by nonlinear regression analysis (with a variable slope) using Prism software.
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    Briefly, 50 μL of cell culture medium (DMEM supplemented with 2% FBS) was added to each well of a 96-well E-plate using a ViaFlo384 liquid handler (Integra Biosciences) to obtain background reading.
    Integra Biosciences
    suggested: None
    Expressed protein was incubate with BioLock (IBA Lifesciences) and then isolated by Strep affinity chromatography on StrepTrap HP columns (GE Healthcare).
    BioLock
    suggested: None
    Image processing was performed using the cryoSPARC (Punjani et al., 2017) software package.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)
    For each plate, background signal (signal from wells that were not coated with antigen) was subtracted and values were normalized to no-competition controls (signal from wells that had no competing serum or mAb) Four-parameter dose-response/inhibition curves were fit to the normalized data using Prism software (GraphPad) v8.1.1.
    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.

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