Identifiability investigation of within-host models of acute virus infection

Uncertainty in parameter estimates from fitting within-host models to empirical data limits the model's ability to uncover mechanisms of infection, disease progression, and to guide pharmaceutical interventions. Understanding the effect of model structure and data availability on model predictions is important for informing model development and experimental design. To address sources of uncertainty in parameter estimation, we use four mathematical models of influenza A infection with increased degrees of biological realism. We test the ability of each model to reveal its parameters in the presence of unlimited data by performing structural identifiability analyses. We then refine the results by predicting practical identifiability of parameters under daily influenza A virus titers alone or together with daily adaptive immune cell data. Using these approaches, we present insight into the sources of uncertainty in parameter estimation and provide guidelines for the types of model assumptions, optimal experimental design, and biological information needed for improved predictions.