The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

  1. Darren P. Martin
  2. Steven Weaver
  3. Houriiyah Tegally
  4. James Emmanuel San
  5. Stephen D. Shank
  6. Eduan Wilkinson
  7. Alexander G. Lucaci
  8. Jennifer Giandhari
  9. Sureshnee Naidoo
  10. Yeshnee Pillay
  11. Lavanya Singh
  12. Richard J. Lessells
  13. Ravindra K. Gupta
  14. Joel O. Wertheim
  15. Anton Nekturenko
  16. Ben Murrell
  17. Gordon W. Harkins
  18. Philippe Lemey
  19. Oscar A. MacLean
  20. David L. Robertson
  21. Tulio de Oliveira
  22. Sergei L. Kosakovsky Pond

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Abstract

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  1. Version published to 10.1016/j.cell.2021.09.003
  2. Version published to 10.1101/2021.02.23.21252268v3 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.02.23.21252268: (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
    We aligned all sequences from an individual lineage (i.e. V1, V2 or V3) and reference (GISAID unique haplotypes in the corresponding gene/peptide) sequences to the GenBank reference genome protein sequence for the corresponding segment using the codon-aware alignment tool, bealign which is part of the BioExt Python package (https://github.com/veg/BioExt), also used by HIV-TRACE 61 with the HIV-BETWEEN-F scoring matrix (similar viral sequences).
    Python
    suggested: (IPython, RRID:SCR_001658)
    We used HyPhy v2.5.27 (http://www.hyphy.org/) 63 to perform a series of selection analyses.
    HyPhy
    suggested: (HyPhy, RRID:SCR_016162)
    We performed: We combined all the results using a Python script and visualized results using several open source libraries in ObservableHQ (https://observablehq.com/@spond/n501y-clades).
    ObservableHQ
    suggested: (ObservableHQ, RRID:SCR_016173)

    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 10.1101/2021.02.23.21252268v2 on medRxiv
  5. Version published to 10.1101/2021.02.23.21252268v1 on medRxiv