In classical epidemic models, a neglected aspect is the heterogeneity of disease transmission and progression linked to the viral load of each infected individual. Here, we investigate the interplay between the evolution of individuals' viral load and the epidemic dynamics from a theoretical point of view. We propose a stochastic particle model describing the infection transmission and the individual physiological course of the disease. Agents have a double microscopic state: a discrete label, that denotes the epidemiological compartment to which they belong and switches in consequence of a Markovian process, and a microscopic trait, measuring their viral load, that changes in consequence of binary interactions or interactions with a background. Specifically, we consider Susceptible–Infected–Removed–like dynamics where infectious individuals may be isolated and the isolation rate may depend on the viral load–sensitivity and frequency of tests. We derive kinetic evolution equations for the distribution functions of the viral load of the individuals in each compartment, whence, via upscaling procedures, we obtain macroscopic equations for the densities and viral load momentum. We perform then a qualitative analysis of the ensuing macroscopic model. Finally, we present numerical tests in the case of both constant and viral load–dependent isolation control.