Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America

  1. Carlos Franco-Muñoz
  2. Diego A. Álvarez-Díaz
  3. Katherine Laiton-Donato
  4. Magdalena Wiesner
  5. Patricia Escandón
  6. José A. Usme-Ciro
  7. Nicolás D. Franco-Sierra
  8. Astrid C. Flórez-Sánchez
  9. Sergio Gómez-Rangel
  10. Luz D. Rodríguez-Calderon
  11. Juliana Barbosa-Ramirez
  12. Erika Ospitia-Baez
  13. Diana M. Walteros
  14. Martha L. Ospina-Martinez
  15. Marcela Mercado-Reyes

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Abstract

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  1. Version published to 10.1016/j.meegid.2020.104557
  2. Version published to 10.1101/2020.06.02.20120782v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.06.02.20120782: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: The INS is authorized to use the biological material for research purposes, without informed consent, which includes the anonymous disclosure of results.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    2.4 Sequence Analysis: Reads were mapped to the Wuhan-Hu-1 reference genome (NC_045512.2) using BWA (Li et al., 2020) and BBmap (brian-jgi, 2020); then, assembled sequences were submitted to GISAID.
    BWA
    suggested: (BWA, RRID:SCR_010910)
    BBmap
    suggested: (BBmap, RRID:SCR_016965)
    Substitution matrices of nucleotides and amino acids of S and N proteins were generated from a multiple sequence alignment with the reference genome against the 43 assembled Colombian SARS-CoV-2 genomes (Table 1) using the Muscle algorithm (Edgar, 2004) in MEGA X (Kumar et al., 2016).
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    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.

  4. Version published to 10.1101/2020.06.02.20120782v1 on medRxiv