Comparative Computational Modeling of the Bat and Human Immune Response to Viral Infection with the Comparative Biology Immune Agent Based Model
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Abstract
Given the impact of pandemics due to viruses of bat origin, there is increasing interest in comparative investigation into the differences between bat and human immune responses. The practice of comparative biology can be enhanced by computational methods used for dynamic knowledge representation to visualize and interrogate the putative differences between the two systems. We present an agent based model that encompasses and bridges differences between bat and human responses to viral infection: the comparative biology immune agent based model, or CBIABM. The CBIABM examines differences in innate immune mechanisms between bats and humans, specifically regarding inflammasome activity and type 1 interferon dynamics, in terms of tolerance to viral infection. Simulation experiments with the CBIABM demonstrate the efficacy of bat-related features in conferring viral tolerance and also suggest a crucial role for endothelial inflammasome activity as a mechanism for bat systemic viral tolerance and affecting the severity of disease in human viral infections. We hope that this initial study will inspire additional comparative modeling projects to link, compare, and contrast immunological functions shared across different species, and in so doing, provide insight and aid in preparation for future viral pandemics of zoonotic origin.
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SciScore for 10.1101/2021.06.29.450378: (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
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:We accept that there are limitations of the current version of the CBIABM. The CBIABM lacks representation of the adaptive immune response, which does not allow the CBIABM to replicate clinical disease dynamics and associate meditator time-series data. This in turn and limits the ability to use the CBIABM as a test platform for discovering new therapeutic control strategies, which is one of the most potentially impactful roles for …
SciScore for 10.1101/2021.06.29.450378: (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
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:We accept that there are limitations of the current version of the CBIABM. The CBIABM lacks representation of the adaptive immune response, which does not allow the CBIABM to replicate clinical disease dynamics and associate meditator time-series data. This in turn and limits the ability to use the CBIABM as a test platform for discovering new therapeutic control strategies, which is one of the most potentially impactful roles for complex mechanism-based simulation models [50–52]. We will also incorporate more sophisticated representations of “stress,” such as the role of emergence from hibernation and the effect of co-infections on viral spillover. We further recognize that the current set of simulation experiments do not fully explore the different parameter combinations that might lead to the differences between viral tolerance phenotypes, with implications on the relative roles and contributions for cell-specific inflammasome activity and T1IFN anti-viral functions. To address this we will adapt the CBIABM to our developed pipeline for utilizing machine learning and artificial intelligence methods to refine model rule and parameter space while encompassing biological heterogeneity [53]. This approach, in concert with the modular structure of the CBIABM will also allow future developments that include the implementation of virus-specific properties and functions related to invasiveness, replication and countermeasures to anti-viral mechanisms, and the ability to represent ...
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.
Results from scite Reference Check: We found no unreliable references.
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