Limits of Classical Immune Response Models

We analyze parameter identifiability in a Marchuk-type immune-response model using longitudinal whole-blood transcriptomic signatures from the influenza challenge. Latent states are extracted from curated gene signatures derived from nine symptomatic and eight asymptomatic subjects. The governing delay differential equations are cast in a linear-in-parameters form; derivatives are estimated by smoothing splines, coefficients are fit by ridge regression, and the delay τ is selected by grid search. We find that the parameters governing viral and innate dynamics are consistently identifiable, with low relative error, and are highly determined, whereas adaptive-immunity and tissue-damage parameters are poorly constrained by transcriptomics alone. Introducing a small additive background term and tissue dependence markedly reduces residual variance and stabilizes estimates. Symptomatic patients exhibit a characteristic regulatory delay near 21 h. These results show that aggregated transcriptomic time series can reliably identify some subsystems of classical immune models, but that adaptive immunity and damage dynamics require explicit structural extensions or additional data modalities. The study provides a practical identification pipeline and concrete guidance on model extensions needed for transcriptomic-driven mechanistic inference.