Integrative Modelling of Innate Immune Response Dynamics during Virus Infection

Positive-sense RNA viruses that constitute a large class of human pathogens employ various strategies to evade host immune defences, complicating the development of effective antiviral therapies. Understanding the dynamic interaction between the viral life cycle and immune signaling is critical to designing effective antiviral strategies, yet the quantitative principles governing virus-host interactions remain poorly understood. In this study, we develop a mechanistic mathematical model that integrates the intracellular viral life cycle with key cellular innate immune pathways, including RIG-I–mediated sensing and JAK-STAT signaling. Our model reveals that virus-host interactions exhibit sharp bifurcation behaviour, where minor perturbations in immune strength or viral evasion capacity determine whether infections resolve or persist. Sensitivity analysis further revealed ISG mRNA translation and viral replication kinetics as dominant factors controlling infection outcomes, providing quantitative targets for therapeutic intervention. The model successfully recapitulates IFN desensitization phenomena and predicts optimal timing and dosing strategies for interferon-based prophylactic therapies. Together, our approach reveals fundamental principles that govern the delicate balance between viral persistence and immune control in RNA virus infections and potential avenues for future antiviral strategies.