Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

  1. Bette Korber
  2. Will M. Fischer
  3. Sandrasegaram Gnanakaran
  4. Hyejin Yoon
  5. James Theiler
  6. Werner Abfalterer
  7. Nick Hengartner
  8. Elena E. Giorgi
  9. Tanmoy Bhattacharya
  10. Brian Foley
  11. Kathryn M. Hastie
  12. Matthew D. Parker
  13. David G. Partridge
  14. Cariad M. Evans
  15. Timothy M. Freeman
  16. Thushan I. de Silva
  17. Adrienne Angyal
  18. Rebecca L. Brown
  19. Laura Carrilero
  20. Luke R. Green
  21. Danielle C. Groves
  22. Katie J. Johnson
  23. Alexander J. Keeley
  24. Benjamin B. Lindsey
  25. Paul J. Parsons
  26. Mohammad Raza
  27. Sarah Rowland-Jones
  28. Nikki Smith
  29. Rachel M. Tucker
  30. Dennis Wang
  31. Matthew D. Wyles
  32. Charlene McDanal
  33. Lautaro G. Perez
  34. Haili Tang
  35. Alex Moon-Walker
  36. Sean P. Whelan
  37. Celia C. LaBranche
  38. Erica O. Saphire
  39. David C. Montefiori

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Abstract

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  1. ScreenIT

    SciScore for 10.1101/2020.04.29.069054: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    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.

  2. Version published to 10.1016/j.cell.2020.06.043
  3. ScreenIT

    SciScore for 10.1101/2020.04.29.069054: (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

    Antibodies
    SentencesResources
    Site V367 is at the opposite end from where RBD binds to ACE2 receptor; it is on the same face as the epitope of CR3022 , a neutralizing antibody that was isolated from a convalescent SARS-CoV patient when at least two of the RBD regions of the Spike trimer are “up” , ( Fig .
    ACE2
    suggested: None
    Software and Algorithms
    SentencesResources
    The tree shown here was created using PAUP ( Swofford , 2003); the trees generated for the website pipeline updates are based on parsimony ( Goloboff , 2014) . 2 .
    PAUP
    suggested: (PAUP, SCR_014931)
    Plots were generated with Python Matplotlib ( Hunter , 2007) .
    Python
    suggested: (IPython, SCR_001658)
          <div style="margin-bottom:8px">
        <div><b>Matplotlib</b></div>
        <div>suggested: (MatPlotLib, <a href="https://scicrunch.org/resources/Any/search?q=SCR_008624">SCR_008624</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">STAR METHODS RESOURCE AVAILABILITY Lead Contact Further information and requests for resources should be directed to and will be fulfilled by the Lead Contact , Bette Korber ( btk@lanl . gov) .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>STAR</b></div>
        <div>suggested: (STAR, <a href="https://scicrunch.org/resources/Any/search?q=SCR_015899">SCR_015899</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">KEY RESOURCES TABLE The R Foundation for Statistical Computing , http://www.R-project.org R packages ( https://cran.r-project.org/ except as noted ) The R Foundation for Statistical Computing , http://www.R-project.org R packages ( https://cran.r-project.org/ except as noted ) phangorn ( version 2.5.5 ) ggplot2 ( version 3.3.0 ) beeswarm</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>https://cran.r-project.org/</b></div>
        <div>suggested: (CRAN, <a href="https://scicrunch.org/resources/Any/search?q=SCR_003005">SCR_003005</a>)</div>
      </div>
    
      <div style="margin-bottom:8px">
        <div><b>ggplot2</b></div>
        <div>suggested: (ggplot2, <a href="https://scicrunch.org/resources/Any/search?q=SCR_014601">SCR_014601</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">l VMD: Visual Molecular Dynamics: https://www.ks.uiuc.edu/Research/vmd/ Highlighter: A tool to highlight matches, mismatches, and specific mutations in aligned protein or nucleotide sequences. https://www.hiv.lanl.gov/content/sequence/HIGHLIGHT/highlighter_top.html Rainbow Tree: https://www.hiv.lanl.gov/content/sequence/RAINBOWTREE/rainbowtree.html Aliview, a sequence alignment viewer and editor: https://ormbunkar.se/aliview/ Add COVID tools Sequence resconstruction: ARTIC network protocol (accessed the 19th of April, https://artic.network/ncov-2019.) Base call resolution: Nanopolish (https://github.com/jts/nanopolish) Matplotlib: A 2D Graphics Environment (Hunter, 2007) PAUP https://paup.phylosolutions.com</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>https://www.ks.uiuc.edu/Research/vmd/</b></div>
        <div>suggested: (Visual Molecular Dynamics, <a href="https://scicrunch.org/resources/Any/search?q=SCR_001820">SCR_001820</a>)</div>
      </div>
    
      <div style="margin-bottom:8px">
        <div><b>Aliview</b></div>
        <div>suggested: (AliView, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002780">SCR_002780</a>)</div>
      </div>
    
      <div style="margin-bottom:8px">
        <div><b>https://github.com/jts/nanopolish</b></div>
        <div>suggested: (Nanopolish, <a href="https://scicrunch.org/resources/Any/search?q=SCR_016157">SCR_016157</a>)</div>
      </div>
    </td></tr></table>

    Results from OddPub: We did not find a statement about open data. We also did not find a statement about open code. Researchers are encouraged to share open data when possible (see Nature blog).

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2020.04.29.069054 on bioRxiv