| Summary: | The development of multiscale models of infectious disease systems is a scientific endeavour whose progress depends on advances on three main frontiers: (a) the conceptual framework frontier, (b) the mathematical technology or technical frontier, and (c) the scientific applications frontier. The objective of this primer is to introduce foundational concepts in multiscale modelling of infectious disease systems focused on these three main frontiers. On the conceptual framework frontier we propose a three-level hierarchical framework as a foundational idea which enables the discussion of the structure of multiscale models of infectious disease systems in a general way. On the scientific applications frontier we suggest ways in which the different structures of multiscale models can serve as infrastructure to provide new knowledge on the control, elimination and even eradication of infectious disease systems, while on the mathematical technology or technical frontier we present some challenges that modelers face in developing appropriate multiscale models of infectious disease systems. We anticipate that the foundational concepts presented in this primer will be central in articulating an integrated and more refined disease control theory based on multiscale modelling - the all-encompassing quantitative representation of an infectious disease system. Keywords: Multiscale models of infectious diseases, Immuno-epidemiological models, Linking individual/lower/micro and population/upper/macro scales, Comparative effectiveness research
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