Functional Immune Deficiency Syndrome via Intestinal Infection in COVID-19

  1. Erica T. Prates
  2. Michael R. Garvin
  3. Mirko Pavicic
  4. Piet Jones
  5. Manesh Shah
  6. Christiane Alvarez
  7. David Kainer
  8. Omar Demerdash
  9. B Kirtley Amos
  10. Armin Geiger
  11. John Pestian
  12. Kang Jin
  13. Alexis Mitelpunkt
  14. Eric Bardes
  15. Bruce Aronow
  16. Daniel Jacobson

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Abstract

Using a Systems Biology approach, we integrated genomic, transcriptomic, proteomic, and molecular structure information to provide a holistic understanding of the COVID-19 pandemic. The expression data analysis of the Renin Angiotensin System indicates mild nasal, oral or throat infections are likely and that the gastrointestinal tissues are a common primary target of SARS-CoV-2. Extreme symptoms in the lower respiratory system likely result from a secondary-infection possibly by a comorbidity-driven upregulation of ACE2 in the lung. The remarkable differences in expression of other RAS elements, the elimination of macrophages and the activation of cytokines in COVID-19 bronchoalveolar samples suggest that a functional immune deficiency is a critical outcome of COVID-19. We posit that using a non-respiratory system as a major pathway of infection is likely determining the unprecedented global spread of this coronavirus.

One Sentence Summary

A Systems Approach Indicates Non-respiratory Pathways of Infection as Key for the COVID-19 Pandemic

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  1. ScreenIT

    SciScore for 10.1101/2020.04.06.028712: (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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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.

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  2. Version published to 10.1101/2020.04.06.028712v2 on bioRxiv
  3. Version published to 10.1101/2020.04.06.028712v1 on bioRxiv