Population-level waning of protection following immunising exposures is an important determinant of susceptibility to COVID-19 outbreaks. This work outlines an individual-based model (IBM) for the transmission and clinical impact of SARS-CoV-2 that explicitly represents the immunological response to vaccination and infection of each individual. The IBM evaluates waning of immunity to inform risk of infection and related clinical outcomes across a large freely mixing population over time by age and prior exposure status. Modelling immunological responses allows us to investigate the likely impact of immune escape variants based on the landscape in which they emerge. The model described in this paper was motivated by the need to anticipate health and societal impacts of COVID-19 in Australia following emergence of the Omicron variant, in the context of high national vaccine uptake but low infection exposure. It provides a flexible framework for modelling policy-relevant scenarios to inform preparedness and response actions as immunity in a population changes through time.