SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity

  1. Chantal B.F. Vogels
  2. Anne E. Watkins
  3. Christina A. Harden
  4. Doug E. Brackney
  5. Jared Shafer
  6. Jianhui Wang
  7. César Caraballo
  8. Chaney C. Kalinich
  9. Isabel M. Ott
  10. Joseph R. Fauver
  11. Eriko Kudo
  12. Peiwen Lu
  13. Arvind Venkataraman
  14. Maria Tokuyama
  15. Adam J. Moore
  16. M. Catherine Muenker
  17. Arnau Casanovas-Massana
  18. John Fournier
  19. Santos Bermejo
  20. Melissa Campbell
  21. Rupak Datta
  22. Allison Nelson
  23. Kelly Anastasio
  24. Michael H. Askenase
  25. Maria Batsu
  26. Sean Bickerton
  27. Kristina Brower
  28. Molly L. Bucklin
  29. Staci Cahill
  30. Yiyun Cao
  31. Edward Courchaine
  32. Giuseppe DeIuliis
  33. Rebecca Earnest
  34. Bertie Geng
  35. Benjamin Goldman-Israelow
  36. Ryan Handoko
  37. William Khoury-Hanold
  38. Daniel Kim
  39. Lynda Knaggs
  40. Maxine Kuang
  41. Sarah Lapidus
  42. Joseph Lim
  43. Melissa Linehan
  44. Alice Lu-Culligan
  45. Anjelica Martin
  46. Irene Matos
  47. David McDonald
  48. Maksym Minasyan
  49. Maura Nakahata
  50. Nida Naushad
  51. Jessica Nouws
  52. Abeer Obaid
  53. Camila Odio
  54. Ji Eun Oh
  55. Saad Omer
  56. Annsea Park
  57. Hong-Jai Park
  58. Xiaohua Peng
  59. Mary Petrone
  60. Sarah Prophet
  61. Tyler Rice
  62. Kadi-Ann Rose
  63. Lorenzo Sewanan
  64. Lokesh Sharma
  65. Albert C. Shaw
  66. Denise Shepard
  67. Mikhail Smolgovsky
  68. Nicole Sonnert
  69. Yvette Strong
  70. Codruta Todeasa
  71. Jordan Valdez
  72. Sofia Velazquez
  73. Pavithra Vijayakumar
  74. Elizabeth B. White
  75. Yexin Yang
  76. Charles S. Dela Cruz
  77. Albert I. Ko
  78. Akiko Iwasaki
  79. Harlan M. Krumholz
  80. J.D. Matheus
  81. Pei Hui
  82. Chen Liu
  83. Shelli F. Farhadian
  84. Robby Sikka
  85. Anne L. Wyllie
  86. Nathan D. Grubaugh

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Abstract

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  1. ScreenIT

    SciScore for 10.1101/2020.08.03.20167791: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethics: The collection of clinical samples from COVID-19 inpatients and healthcare workers at the Yale-New Haven Hospital was approved by the Institutional Review Board of the Yale Human Research Protection Program (Protocol ID. 2000027690).
    Consent: Informed consent was obtained from all patients and healthcare workers prior to sample collection.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The collection of deidentified specimens from healthy or asymptomatic individuals from the NBA was approved by the Institutional Review Board of the Yale Human Research Protection Program (Protocol ID. 2000028394).
    Yale Human Research Protection Program
    suggested: None
    Saliva specimens were tested in triplicate and were treated with ThermoFisher Scientific proteinase K and tested with the ThermoFisher TaqPath RT-qPCR kit on the Bio-Rad CFX96.
    ThermoFisher TaqPath
    suggested: None
    Combined AN/OP swabs were collected by Quest and followed their EUA specimen collection guidelines (Quest Diagnostics, 2020; U.S. Food & Drug Administration, 2020e).
    Quest
    suggested: (QUEST, RRID:SCR_005210)
    Statistical analysis: GraphPad Prism 8.3.0 was used to make the figures and perform all statistical analyses.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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: We detected the following sentences addressing limitations in the study:
    Limitations of use: Our intended use of SalivaDirect is for the clear and liquid saliva that naturally pools in the mouth. The protocol as currently written is not intended for use of hospitalized COVID-19 patients who are unable to produce “true” saliva. While our previous analysis indicates that saliva is more sensitive for SARS-CoV-2 detection than nasopharyngeal swabs in COVID-19 inpatients (Wyllie et al., 2020), saliva from patients can contain blood or mucus, which can interfere with PCR or make it difficult to pipet. We can overcome many of these issues by having specific collection procedures for saliva collection and using proteinase K to make samples easier to pipet, but some samples can still be invalid if they are not collected properly. While we show that invalid samples are rare from our NBA cohort, our study was biased towards adult men. Saliva collection techniques for adolescents and children, in particular, still need to be refined. Despite the simplified protocol, SalivaDirect is not a rapid point-of-care test and still requires a complex laboratory. Our method requires electricity and specialized RT-qPCR instruments which can be a limiting factor when such equipment is not available, especially in low- and middle-income countries. Target populations and future improvements: To date, there is only one SARS-CoV-2 laboratory diagnostic test authorized by the FDA for asymptomatic testing (U.S. Food & Drug Administration, 2020d), and additional authorized tests...

    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.medj.2020.12.010
  3. Version published to 10.1101/2020.08.03.20167791 on medRxiv