Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France

  1. Grégory Quéromès
  2. Grégory Destras
  3. Antonin Bal
  4. Hadrien Regue
  5. Gwendolyne Burfin
  6. Solenne Brun
  7. Rémi Fanget
  8. Florence Morfin
  9. Martine Valette
  10. Sophie Trouillet-Assant
  11. Bruno Lina
  12. Emilie Frobert
  13. Laurence Josset

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Abstract

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  1. Version published to 10.1080/22221751.2021.1872351
  2. ScreenIT

    SciScore for 10.1101/2020.08.07.241653: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study was presented by the ethics committee of the Hospices Civils de Lyon (HCL), Lyon, France and registered on the HCL database of RIPHN studies (AGORA N°41).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Virus replication kinetics: Replication kinetics was performed on both confluent buffalo green monkey (BGM) (BioWhittaker Europe) and human lung adenocarcinoma (Calu-3) cells (ATCC® HTB-55™,
    Calu-3
    suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)
    Software and Algorithms
    SentencesResources
    Phylogeny: Multiple sequence alignment was performed using the DECIPHER package in R (45).
    DECIPHER
    suggested: (DECIPHER, RRID:SCR_006552)
    Statistical analysis was performed by two-way ANOVA with Tukey multiple comparisons between both factors of comparison (virus strain and cell line) on GraphPad Prism (software version 8.4.3).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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.

  3. ScreenIT

    SciScore for 10.1101/2020.08.07.241653: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementThis study was presented by the ethics committee of the Hospices Civils de 256 Lyon (HCL), Lyon, France and registered on the HCL database of RIPHN studies (AGORA N°41).Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variablenot detected.Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    237 Virus replication kinetics 238 Replication kinetics was performed on both confluent buffalo green monkey (BGM) (BioWhittaker 239 Europe) and human lung adenocarcinoma (Calu-3) cells (ATCC® HTB-55™,
    Calu-3
    suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)
    Software and Algorithms
    SentencesResources
    228 Phylogeny 229 Multiple sequence alignment was performed using the DECIPHER package in R (45).
    DECIPHER
    suggested: (DECIPHER, RRID:SCR_006552)
    Statistical analysis was 245 performed by two-way ANOVA with Tukey multiple comparisons between both factors of comparison 246 (virus strain and cell line) on GraphPad Prism (software version 8.4.3).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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 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.

    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.

  4. Version published to 10.1101/2020.08.07.241653 on bioRxiv