Longitudinal analyses reveal immunological misfiring in severe COVID-19

  1. Carolina Lucas
  2. Patrick Wong
  3. Jon Klein
  4. Tiago B. R. Castro
  5. Julio Silva
  6. Maria Sundaram
  7. Mallory K. Ellingson
  8. Tianyang Mao
  9. Ji Eun Oh
  10. Benjamin Israelow
  11. Takehiro Takahashi
  12. Maria Tokuyama
  13. Peiwen Lu
  14. Arvind Venkataraman
  15. Annsea Park
  16. Subhasis Mohanty
  17. Haowei Wang
  18. Anne L. Wyllie
  19. Chantal B. F. Vogels
  20. Rebecca Earnest
  21. Sarah Lapidus
  22. Isabel M. Ott
  23. Adam J. Moore
  24. M. Catherine Muenker
  25. John B. Fournier
  26. Melissa Campbell
  27. Camila D. Odio
  28. Arnau Casanovas-Massana
  29. Yale IMPACT Team
  30. Abeer Obaid
  31. Alice Lu-Culligan
  32. Allison Nelson
  33. Anderson Brito
  34. Angela Nunez
  35. Anjelica Martin
  36. Annie Watkins
  37. Bertie Geng
  38. Chaney Kalinich
  39. Christina Harden
  40. Codruta Todeasa
  41. Cole Jensen
  42. Daniel Kim
  43. David McDonald
  44. Denise Shepard
  45. Edward Courchaine
  46. Elizabeth B. White
  47. Eric Song
  48. Erin Silva
  49. Eriko Kudo
  50. Giuseppe DeIuliis
  51. Harold Rahming
  52. Hong-Jai Park
  53. Irene Matos
  54. Jessica Nouws
  55. Jordan Valdez
  56. Joseph Fauver
  57. Joseph Lim
  58. Kadi-Ann Rose
  59. Kelly Anastasio
  60. Kristina Brower
  61. Laura Glick
  62. Lokesh Sharma
  63. Lorenzo Sewanan
  64. Lynda Knaggs
  65. Maksym Minasyan
  66. Maria Batsu
  67. Mary Petrone
  68. Maxine Kuang
  69. Maura Nakahata
  70. Melissa Campbell
  71. Melissa Linehan
  72. Michael H. Askenase
  73. Michael Simonov
  74. Mikhail Smolgovsky
  75. Nicole Sonnert
  76. Nida Naushad
  77. Pavithra Vijayakumar
  78. Rick Martinello
  79. Rupak Datta
  80. Ryan Handoko
  81. Santos Bermejo
  82. Sarah Prophet
  83. Sean Bickerton
  84. Sofia Velazquez
  85. Tara Alpert
  86. Tyler Rice
  87. William Khoury-Hanold
  88. Xiaohua Peng
  89. Yexin Yang
  90. Yiyun Cao
  91. Yvette Strong
  92. Roy Herbst
  93. Albert C. Shaw
  94. Ruslan Medzhitov
  95. Wade L. Schulz
  96. Nathan D. Grubaugh
  97. Charles Dela Cruz
  98. Shelli Farhadian
  99. Albert I. Ko
  100. Saad B. Omer
  101. Akiko Iwasaki

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  1. ScreenIT

    SciScore for 10.1101/2020.06.23.20138289: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethics statement: This study was approved by Yale Human Research Protection Program Institutional Review Boards (FWA00002571, Protocol ID.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Flow cytometry: Antibody clones and vendors are as follows: BB515 anti-HLA-DR (G46-6), BV785 anti-CD16 (3G8)
    anti-HLA-DR ( G46-6
    suggested: None
    anti-CD16
    suggested: None
    Software and Algorithms
    SentencesResources
    Ethics statement: This study was approved by Yale Human Research Protection Program Institutional Review Boards (FWA00002571, Protocol ID.
    Yale Human Research Protection Program
    suggested: None
    Data were analysed using FlowJo software version 10.6 software (Tree Star).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistical analysis: The patients and its measurements were clustered using the kmeans algorithm available within the ComplexHeatmap package38.
    ComplexHeatmap
    suggested: (ComplexHeatmap, RRID:SCR_017270)
    To determine the optimum number of clusters, we ran the data matrix within the NBClust package39.
    NBClust
    suggested: None
    Mutual information analyses were performed using the Caret R package and visualized with ggPlot2.
    ggPlot2
    suggested: (ggplot2, RRID:SCR_014601)

    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.
    • Thank you for including a protocol registration statement.

    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 10.1038/s41586-020-2588-y
  3. Version published to 10.1101/2020.06.23.20138289v3 on medRxiv
  4. Version published to 10.1101/2020.06.23.20138289v2 on medRxiv
  5. ScreenIT

    SciScore for 10.1101/2020.06.23.20138289: (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

    Antibodies
    SentencesResources
    A type-2 antibody isotype was also increased; IgE levels were significantly higher in severe patients and continued to increase during the disease course ( Fig . 2e)
    type-2
    suggested: None

    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 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.

  6. Version published to 10.1101/2020.06.23.20138289v1 on medRxiv