Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene

  1. Paul D. Hartley
  2. Richard L. Tillett
  3. David P. AuCoin
  4. Joel R. Sevinsky
  5. Yanji Xu
  6. Andrew Gorzalski
  7. Mark Pandori
  8. Erin Buttery
  9. Holly Hansen
  10. Michael A. Picker
  11. Cyprian C. Rossetto
  12. Subhash C. Verma

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  1. ScreenIT

    SciScore for 10.1101/2020.08.21.20178863: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The data files are available at GISAID, NCBI under the https://www.ncbi.nlm.nih.gov/bioproject/657893 Computational analysis: Sequence pair libraries were trimmed using Trimmomatic, version 0.39 and adapter-clipping setting “2:30:10:2:keepBothReads” [15].
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Read pairs were aligned against the Wuhan reference genome (NC_045512.2) by Bowtie 2, version 2.3.5, local alignment [16].
    Bowtie
    suggested: (Bowtie, RRID:SCR_005476)
    PCR optical duplicates were removed via Picard MarkDuplicates [17].
    Picard
    suggested: (Picard, RRID:SCR_006525)
    Variants were called using Freebayes, version 1.0.2, with ploidy set to 1, minimum allele frequency 0.75, and minimum depth of 4 [18].
    Freebayes
    suggested: (FreeBayes, RRID:SCR_010761)
    High-quality variant sites were selected where site “QUAL > 20” using vcffilter, VCFlib version 1.0.0_rc2 [19].
    VCFlib
    suggested: (vcflib, RRID:SCR_001231)
    Plots and pie charts were generated using GraphPad Prism (version 8).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    nsp12 protein modeling: Sequence of nsp12 (RdRp) protein for SARS-CoV-2 (YP_009725307.0) was retrieved from NCBI protein database and 3D model was structured based on a previously published report (PDB ID: 6XEZ [24].
    NCBI
    suggested: (NCBI, RRID:SCR_006472)
    Mutational changes to residue 323 within nsp12 were performed using PyMol Molecular Graphics System (version 2.0, Schrödinger LLC).
    PyMol
    suggested: (PyMOL, RRID:SCR_000305)
    To determine any NCBI deposited sequences which contain the P323F variant, standard protein BLAST from the BLASTp suite was used to find nsp12 protein sequences which contained FSTVFPFTSFGP (P323F is bold and underlined) from full length SARS-CoV-2 genomes.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    BLASTp
    suggested: (BLASTP, RRID:SCR_001010)

    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: 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.

    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.

  2. Version published to 10.1016/j.jgg.2021.01.004
  3. Version published to 10.1101/2020.08.21.20178863 on medRxiv