1. SciScore for 10.1101/2022.01.12.22269023: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Convalescent COVID-19 plasma donor selection and lymphocyte isolation: Convalescent COVID-19 plasma donors were prospectively enrolled onto an institutional review board-approved protocol (Clinical Trials Registration, NCT04360278)19 and provided written informed consent for the study.
    Consent: Convalescent COVID-19 plasma donor selection and lymphocyte isolation: Convalescent COVID-19 plasma donors were prospectively enrolled onto an institutional review board-approved protocol (Clinical Trials Registration, NCT04360278)19 and provided written informed consent for the study.
    IACUC: Prophylactic and therapeutic studies in the hamster model: The preclinical hamster studies were approved by the NIAID Animal Care and Use Committee.
    Euthanasia Agents: Animals were euthanized by CO2 inhalation prior to necropsy.
    Sex as a biological variableIn the prophylactic study, 80 male Syrian hamsters, aged 8-9 weeks, were randomly divided into groups of 10 animals each, bled for baseline serology and inoculated intraperitoneally with 0.5 mL of NE12, NA8, or IgG1 control at 12 mg/kg or 4 mg/kg, diluted to the concentration of 2.4 mg/mL or 0.8 mg/mL in PBS.
    RandomizationSingle colonies were randomly picked from the third cycle output and screening of specific binders was performed, using phage ELISA against S-2P, with a BSA coated-plate as a negative control.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    The plates were washed, and the secondary conjugated antibody (anti-His-HRP, anti-human Fab-HRP, or anti-M13-HRP) was added and incubated for 1 h at room temperature.
    anti-His-HRP
    suggested: None
    anti-M13-HRP
    suggested: None
    Following incubation for 2 h at room temperature, the plate was washed, and a secondary anti-human Fab-HRP antibody (Jackson ImmunoResearch) was added for 1 h at room temperature.
    anti-human Fab-HRP
    suggested: (SouthernBiotech Cat# 2085-05, RRID:AB_2795788)
    An in house- produced anti-poliovirus IgG antibody was used as a negative control43.
    anti-poliovirus IgG
    suggested: None
    Following incubation for 2 h at room temperature, the plates were washed, and a secondary anti-human IgG Fc-HRP antibody (Jackson ImmunoResearch) was added and incubated for 1 h at room temperature.
    anti-human IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    The mixture was then incubated with 104 ACE-2-expressing 293T cells (293T-hACE2.
    293T
    suggested: None
    The SARS-CoV-2 stocks were titrated in Vero E6 cells by determination of the 50% tissue culture infectious dose (TCID50) as previously described46.
    Vero E6
    suggested: None
    Recombinant DNA
    SentencesResources
    The restriction enzyme digested light chain fragments from one donor or pooled from 5 donors were then cloned into the pComb 3H vector by electroporation42.
    pComb 3H
    suggested: None
    One liter of 293 Freestyle cells at concentration of about 0.9 million cells per ml was transfected with 1 mg of S-2P plasmid, pre-mixed with 1 ml of 293fectin™ Transfection Reagent.
    S-2P
    suggested: None
    B.1.1.529/Omicron; luciferase (pHR’ CMV Luc), a lentivirus backbone (pCMV ΔR8.2), and human transmembrane protease serine 2 (TMPRSS2) at a ratio of 1:20:20:0.3 into HEK293T/17 cells (ATCC) using the transfection reagent LiFect293™.
    pCMV ΔR8.2
    suggested: None
    Software and Algorithms
    SentencesResources
    Live virus neutralization assay used in COVID-19 convalescent patients: Neutralization of live virus by patient plasmas was tested using a fluorescence reduction neutralization assay (FRNA) with SARS-CoV-2 [2019-nCoV/USA-WA1-A12/2020 (WA-1) from the US Centers for Disease Control and Prevention, Atlanta, GA, USA] at the NIH-NIAID Integrated Research Facility at Fort Detrick, MD, USA, as previously reported39.
    SARS-CoV-2
    suggested: (SARS-CoV-2-Sequences, RRID:SCR_018319)
    The data were plotted, and dose-response curves with and without inhibition with RBD were generated using Prism software (Graphpad Software, Inc.
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    Analyses were performed using Prism 9 (GraphPad Software)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    The following steps were performed using Relion 3.1.051, unless otherwise stated.
    Relion
    suggested: (RELION, RRID:SCR_016274)
    Local resolution was determined with ResMap 1.1.454.
    ResMap
    suggested: None

    Results from OddPub: Thank you for sharing your data.


    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
    NCT04360278Active, not recruitingPlasma Collection From Convalescent and/or Immunized Donors …


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


    Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 32, 33, 29 and 31. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.


    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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