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Updated: May 15, 2025

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Building an Adverse Outcome Pathway network for COVID-19.

Penny Nymark1, Laure-Alix Clerbaux2,3, Maria-João Amorim4,5

  • 1Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden.

Frontiers in Systems Biology
|April 10, 2025
PubMed
Summary
This summary is machine-generated.

The CIAO consortium organized COVID-19 pathology data using the Adverse Outcome Pathway (AOP) framework, creating a network that visualizes disease complexity and confirms inflammation

Keywords:
COVID-19adverse outcome pathway (AOP)eventinflammationnetwork

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Area of Science:

  • Toxicology and Pharmacology
  • Computational Biology
  • Infectious Diseases

Background:

  • The COVID-19 pandemic generated extensive data on disease pathogenesis.
  • Organizing this vast knowledge is crucial for understanding COVID-19 pathology.
  • The Adverse Outcome Pathway (AOP) framework offers a structured approach to knowledge organization.

Purpose of the Study:

  • To systematically organize published scientific literature on COVID-19 pathology using the AOP framework.
  • To computationally derive and refine an AOP network for COVID-19.
  • To identify challenges and propose recommendations for building AOP networks for viral diseases.

Main Methods:

  • The CIAO consortium gathered and organized literature on COVID-19 pathology between April 2020 and February 2023.
  • Identified 24 relevant pathways with essential key events (KEs) leading to 19 adverse outcomes.
  • Selected 17 AOPs based on quality criteria to computationally derive an AOP network, followed by manual refinement.

Main Results:

  • The derived AOP network visualized complex interactions of KEs leading to COVID-19 outcomes.
  • Confirmed the central role of the inflammatory response in COVID-19 pathogenesis.
  • Highlighted the importance of tissue specificity, terminology harmonization, and FAIR principles for AOP network development.

Conclusions:

  • AOP network construction requires addressing tissue specificity and harmonizing terminology.
  • The FAIR principles are essential for improving AOP findability, accessibility, interoperability, and reusability.
  • Adaptations to the AOP framework are needed to describe SARS-CoV-2 specific KEs and differentiate physiological from pathological inflammation.