Early Transmission Dynamics, Spread, and Genomic Characterization of SARS-CoV-2 in Panama

  1. Danilo Franco
  2. Claudia Gonzalez
  3. Leyda E. Abrego
  4. Jean-Paul Carrera
  5. Yamilka Diaz
  6. Yaset Caicedo
  7. Ambar Moreno
  8. Oris Chavarria
  9. Jessica Gondola
  10. Marlene Castillo
  11. Elimelec Valdespino
  12. Melissa Gaitán
  13. Jose Martínez-Mandiche
  14. Lizbeth Hayer
  15. Pablo Gonzalez
  16. Carmen Lange
  17. Yadira Molto
  18. Dalis Mojica
  19. Ruben Ramos
  20. Maria Mastelari
  21. Lizbeth Cerezo
  22. Lourdes Moreno
  23. Christl A. Donnelly
  24. Juan Miguel Pascale
  25. Nuno Rodrigues Faria
  26. Sandra Lopez-Verges
  27. Alexander A. Martinez
  28. on behalf of Gorgas COVID19 team and Panama COVID19 Laboratory Network

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  1. ScreenIT

    SciScore for 10.1101/2020.07.31.20160929: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    All samples were sequenced with MiSeq V2 reagent kits for 500 cycles.
    MiSeq
    suggested: (A5-miseq, RRID:SCR_012148)
    Time-trees were estimated using BEAST v1.10.419 and BEAGLE v320 to enhance computational speed.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    BEAGLE
    suggested: (BEAGLE, RRID:SCR_001789)

    Results from OddPub: Thank you for sharing your code and 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.

  2. Version published to 10.3201/eid2702.203767
  3. Version published to 10.1101/2020.07.31.20160929 on medRxiv