Severe Acute Respiratory Syndrome Coronavirus 2 in Farmed Mink ( Neovison vison ), Poland

  1. Lukasz Rabalski
  2. Maciej Kosinski
  3. Teemu Smura
  4. Kirsi Aaltonen
  5. Ravi Kant
  6. Tarja Sironen
  7. Bogusław Szewczyk
  8. Maciej Grzybek

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Abstract

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  1. Version published to 10.3201/eid2709.210286
  2. ScreenIT

    SciScore for 10.1101/2020.12.24.422670: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIACUC: No permit from Local Bioethical Committee for Animal Experimentation was obtained because animals were culled by the owner for production of pelts.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    At Gdansk two independent protocols were used for SARS-CoV-2 genome sequencing: Illumina RNA prep with enrichment for respiratory virus oligos panel V2 followed by Illumina MiniSeq medium output run that produced 150-nucleotide paired-end reads, and ARTICv3 amplicon generation followed by Oxford Nanopore Technology MinION run (Quick 2020).
    MinION
    suggested: (MinION, RRID:SCR_017985)
    The fasta files generated by the Illumina procedure were further analysed in Kraken2 software to classify every read to reference database containing viral and American mink genomes (Wood et al., 2019).
    Kraken2
    suggested: None
    Sequencing was conducted using MiSeq V3 reagent kit with 250 bp reads.
    MiSeq
    suggested: (A5-miseq, RRID:SCR_012148)
    Raw sequence reads were trimmed and low quality (quality score <30) and short (<50 nt) sequences removed using Trimmomatic (Bolger et al., 2014).
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    The trimmed sequence reads were assembled against SARS-CoV-2 reference sequence (NC_045512.2) using BWA-MEM algorithm (Li 2013) implemented in SAMTools version 1.8 (Li et al., 2009). 2.7.
    BWA-MEM
    suggested: (Sniffles, RRID:SCR_017619)
    SAMTools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    In short: the Augur toolkit v10.1.1 was used for phylogenetic analysis and Auspice v2.10.1 for visualisation.
    Augur
    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 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.

  3. Version published to 10.1101/2020.12.24.422670v1 on bioRxiv