Real-Time Genomic Surveillance for SARS-CoV-2 Variants of Concern, Uruguay

  1. Natalia Rego
  2. Alicia Costábile
  3. Mercedes Paz
  4. Cecilia Salazar
  5. Paula Perbolianachis
  6. Lucía Spangenberg
  7. Ignacio Ferrés
  8. Rodrigo Arce
  9. Alvaro Fajardo
  10. Mailen Arleo
  11. Tania Possi
  12. Natalia Reyes
  13. Ma Noel Bentancor
  14. Andrés Lizasoain
  15. María José Benítez
  16. Viviana Bortagaray
  17. Ana Moller
  18. Gonzalo Bello
  19. Ighor Arantes
  20. Mariana Brandes
  21. Pablo Smircich
  22. Odhille Chappos
  23. Melissa Duquía
  24. Belén González
  25. Luciana Griffero
  26. Mauricio Méndez
  27. Ma Pía Techera
  28. Juan Zanetti
  29. Bernardina Rivera
  30. Matías Maidana
  31. Martina Alonso
  32. Cecilia Alonso
  33. Julio Medina
  34. Henry Albornoz
  35. Rodney Colina
  36. Veronica Noya
  37. Gregorio Iraola
  38. Tamara Fernández-Calero
  39. Gonzalo Moratorio
  40. Pilar Moreno

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Abstract

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  1. Version published to 10.3201/eid2711.211198
  2. ScreenIT

    SciScore for 10.1101/2021.05.20.21256969: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    These primer/probe sets were analyzed with BLAST to rule out similarities with other sequences other than SARS-CoV-2.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Genome Sequencing: Sequencing libraries were prepared according to the Eco PCR tiling of COVID-19 virus protocol (Oxford Nanopore Technologies, United Kingdom), based on the method described by Quick J. [3, 4] with some modifications.
    Quick J
    suggested: None
    Alignment was performed with MAFFT v7.471 [17].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Maximum likelihood (ML) phylogenetic analysis of P.1 samples was conducted using IQ-TREE version 1.6.12 under the GTR+F+R3 nucleotide substitution model selected by the built-in ModelFinder option [18].
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    A time-scaled Bayesian phylogenetic tree was constructed using the Bayesian Markov Chain Monte Carlo (MCMC) approach implemented in BEAST 1.10 [24] with BEAGLE library v3 to improve computational time.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    BEAGLE
    suggested: (BEAGLE, RRID:SCR_001789)
    Convergence (Effective Sample Size > 200) in parameter estimates was assessed using TRACER v1.7 [26].
    TRACER
    suggested: (Tracer, RRID:SCR_019121)
    The maximum clade credibility (MCC) tree was summarized with TreeAnnotator v1.10 [27] and visualized using FigTree v1.4.4 [28].
    TreeAnnotator
    suggested: (BEAST2, RRID:SCR_017307)
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    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.

    Results from scite Reference Check: We found no unreliable references.

    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 10.1101/2021.05.20.21256969v1 on medRxiv