Dylan J. Morris | Searcharxiv

arXiv2026

Bayesian inference for disease transmission models informed by viral dynamics

Infectious disease dynamics operate across multiple biological scales, with within-host viral dynamics being a key driver of between-host transmission. However, while models that explicitly link these scales exist, none have been developed with statistical inference as a primary goal. In this paper we propose a multiscale model that jointly captures heterogeneous individual-level viral load trajectories and stochastic household transmission, and develop efficient inference methods to fit it to data. Since full joint inference is computationally difficult, we employ a cut approach that passes information from the within-host to the between-host model but not vice versa. This enables the data on viral loads to inform the transmission parameters such as the infection times and symptom onset thresholds. We evaluate the framework on simulated household outbreak data, assessing parameter recovery, computational efficiency, and the effect of viral load sampling frequency on inference quality. Parameter recovery is unbiased when the sampling frequency of the viral loads is high enough. When sampling is sparse, some bias is introduced, but incorporating external viral load data can mitigate this.

stat.AP↗

arXiv2025

Random time-shift approximation enables hierarchical Bayesian inference of mechanistic within-host viral dynamics models on large datasets

Mechanistic mathematical models of within-host viral dynamics are tools for understanding how a virus' biology and its interaction with the immune system shape the infectivity of a host. The biology of the process is encoded by the structure and parameters of the model that can be inferred statistically by fitting to viral load data. The main drawback of mechanistic models is that this inference is computationally expensive because the model must be repeatedly solved. This limits the size of the datasets that can be considered or the complexity of the models fitted. In this paper we develop a much cheaper inference method for this class of models by implementing a novel approximation of the model dynamics that uses a combination of random and deterministic processes. This approximation also properly accounts for process noise early in the infection when cell and virion numbers are small, which is important for the viral dynamics but often overlooked. Our method runs on a consumer laptop and is fast enough to facilitate a full hierarchical Bayesian treatment of the problem with sharing of information to allow for individual level parameter differences. We apply our method to simulated datasets and a reanalysis of COVID-19 monitoring data in an National Basketball Association cohort of 163 individuals.

stat.AP↗