Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia

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

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Abstract

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  1. Version published to 10.1016/j.meegid.2020.104390
  2. ScreenIT

    SciScore for 10.1101/2020.05.22.20107292: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: According to the national law 9/1979, decrees 786/1990 and 2323/2006, the INS is the reference lab and health authority of the national network of laboratories and in cases of public health emergency or those in which scientific research for public health purposes as required, the INS may 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
    Next generation sequencing: The complete SARS-CoV-2 genome sequence of 30 patients was obtained through NGS, ten genomes with Oxford Nanopore (Oxford Nanopore Technologies, Oxford, UK) and 20 genomes with lllumina MiSeq (lllumina, San Diego, CA, USA) technologies, following the artic.network “nCoV-2019 sequencing protocol” (Quick, 2020).
    Oxford Nanopore
    suggested: (Oxford Nanopore Technologies, RRID:SCR_003756)
    The genomes were assembled by mapping to the reference genome (NC_045512.2) using the BWA (Li et al., 2020) and BBmap (brian-jgi, 2020) software to generate a consensus genome by the two assembly tools.
    BWA
    suggested: (BWA, RRID:SCR_010910)
    BBmap
    suggested: (BBmap, RRID:SCR_016965)
    Genetic diversity analysis: The Colombian genomes and oligonucleotides from of the in-house protocols were aligned with the Muscle tool (Edgar, 2004) using the MEGA X software (Kumar, Stecher, Li, Knyaz, & Tamura, 2018).
    Muscle
    suggested: (MUSCLE, RRID:SCR_011812)
    MEGA X
    suggested: None

    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. Version published to 10.1101/2020.05.22.20107292 on medRxiv