1. SciScore for 10.1101/2021.06.07.21258375: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Following recruitment via email, potential participants were guided through an online informed consent process and completed an online questionnaire.
    IRB: Participants: Human subjects’ procedures were approved by the South Dakota State University Institutional Review Board prior to the start of the study, were in compliance with relevant laws and institutional guidelines, and were in accordance with the ethical standards of the Declaration of Helsinki.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Participants’ serum was tested for antibodies against SARS-CoV-2.
    SARS-CoV-2
    suggested: None
    Fluorescent microsphere immune assay (FMIA): A quantitative assessment of serum IgG, IgA and IgM antibodies against the SARS-CoV-2 nucleocapsid protein (NCP) was performed using a fluorescent microsphere immunoassay (FMIA) testing platform.
    SARS-CoV-2 nucleocapsid protein
    suggested: None
    Serum binding IgG, IgA and IgM antibody isotypes were detected using a polyisotypic, anti-human, biotinylated secondary antibody (Invitrogen, Carlsbad, CA) followed by a fluorescent (streptavidin-phycoerythrin) reporter (Invitrogen, Carlsbad, CA) that was added to sample and control wells.
    IgM
    suggested: None
    anti-human ,
    suggested: None
    Anti-NCP antibodies were quantified through a dual-laser instrument (Bio-Rad Bio-Plex 200) as previously described16.
    Anti-NCP
    suggested: None
    Transduced cells were sorted by flow cytometry 72 h post-transduction based on ACE2 expression detected with anti-hACE2 Alexa fluor 488 conjugated antibodies (Catalog# Fab9332G, clone# 535919, R&D Systems, Minneapolis, MN)
    anti-hACE2
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    After a 1-h incubation, trypsinized Vero 76 cells were added to the 96-well dilution plate, then incubated at 37°C for 48 h.
    Vero 76
    suggested: None
    After sorting, a population was generated in which 99.3% of the cells expressed ACE2 compared to the parental 293T cells which had no detectable ACE2 expression.
    293T
    suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
    Briefly, 3.5* 103 ACE2 293T cells were plated on white 96-well cell culture treated plates (Falcon, Waltham, MA) in DMEM supplemented with 10% FBS one day prior to infection with the pseudovirus.
    ACE2 293T
    suggested: None
    Recombinant DNA
    SentencesResources
    Briefly, the full length (1257 bp) coding sequence corresponding to the Wuhan-Hu-1, nucleoprotein gene (Genbank MN908947.3) was chemically synthesized and cloned into the bacterial expression plasmid pET-28a (EMD Millipore/Novagen, Billerica, MA)
    pET-28a
    suggested: RRID:Addgene_44242)
    Neutralization assay of SARS-CoV-2 Spike-pseudotyped particles (SARS-CoV-2pp): To mimic the infection condition of human cells, 293T cells were generated, which stably express human ACE2 by lentiviral transduction with pLENTI-hACE2-HygR (a gift from Raffaele De Francesco; Addgene plasmid# 155296)
    pLENTI-hACE2-HygR
    suggested: None
    For the purpose of Spike pseudovirus production, the vector pCMV14-3X-Flag-SARS-CoV-2 S was used, a gift from Zhaohui Qian lab (Addgene plasmid #145780)20 that carries a codon-optimized cDNA that encodes SARS-CoV2-S glycoprotein (Wuhan 2019) with C-terminal 19 amino acid deletion.
    pCMV14-3X-Flag-SARS-CoV-2
    suggested: RRID:Addgene_145780)
    Site directed mutagenesis was performed, confirmed by sequencing to make the D614G mutation in spike and named it pCMV-SD614G.
    pCMV-SD614G
    suggested: None
    Spike pseudovirus particles containing a Luciferase reporter gene were produced in 293T cells by co-transfection of packaging plasmid psAPX2 which was a gift from Didier Trono (Addgene plasmid# 12260), transfer plasmid pLenti-CMV V5-LUC (W567-1) which was gift from Eric Campeau (Addgene plasmid# 21474)21 and envelop plasmid pCMV-SD614G in 293T cells using TransIT-Lenti transfection reagent (Mirus Bio, Madison, WI).
    psAPX2
    suggested: None
    pLenti-CMV
    suggested: None

    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: We detected the following sentences addressing limitations in the study:
    A limitation of the study was the potential for participant bias as individuals who suspected they were exposed to SARS-CoV-2 may have been more likely to continue the study. This coincides with the fact that most participants reported having direct contact with either a suspected or a confirmed COVID-19 case (71.4%) in Phase 3. This exposure rate is likely higher than that among the general population given the estimated case rates for each county were below 9% at the time of this study. The study began with 336 participants with 101 individuals lost to follow-up prior to the final blood draw. The retention rate for blood draws over the course of the study was 69.9% with 74.7% of those with a final blood draw also completing the final questionnaire. In summary, serological testing will continue to be an important metric for understanding the true number of individuals who have been exposed to the SARS-CoV-2 virus and will be an essential tool for understanding the scope to which COVID-19 has spread in rural populations.

    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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