Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV-2

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Abstract

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  1. SciScore for 10.1101/2020.10.14.20212795: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Patient samples ethics statement: Human samples from patients were collected under University of California San Diego’s Human Research Protection Program protocol number 200470 for negatives (PI: Lauge Farnaes), and under a waiver of consent from clinical samples from San Diego County for positives (PI: Kristian Andersen), as part of the SEARCH Alliance activities.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Bioinformatic scripts can be found in File S1.
    Bioinformatic
    suggested: (QFAB Bioinformatics, RRID:SCR_012513)
    The synthetic targets were chosen based on sequence homology identified using NCBI BLAST searches against gRNA-T and gRNA-Z.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    We synthesized both the synthetic vRNA and gRNAs through in vitro transcription (IVT) using MEGAscript™ T7 Transcription Kit (Invitrogen™ #AM1334), followed by DNaseI digestion and purification using the MEGAclear™ Transcription Clean-Up Kit (Invitrogen™ #AM1908).
    MEGAscript™
    suggested: None
    To check for possible cross-reactivity with human transcripts, the probes were mapped to the human transcriptome (GRCh38, ENSEMBL release 99, ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/) comprising both coding and non-coding RNAs using bowtie 1.2.3 allowing up to two mismatches (-v 2).
    bowtie
    suggested: (Bowtie, RRID:SCR_005476)
    Viral genes that are affected by each probe were identified using the intersect function of bedtools (Table S3).
    bedtools
    suggested: (BEDTools, RRID:SCR_006646)
    Patient samples ethics statement: Human samples from patients were collected under University of California San Diego’s Human Research Protection Program protocol number 200470 for negatives (PI: Lauge Farnaes), and under a waiver of consent from clinical samples from San Diego County for positives (PI: Kristian Andersen), as part of the SEARCH Alliance activities.
    Human Research Protection Program
    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: 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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).


    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.

    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.