title: Five challenges in modelling interacting strain dynamics.
abstract: Population epidemiological models where hosts can be infected sequentially by different strains have the potential to help us understand many important diseases. Researchers have in recent years started to develop and use such models, but the extra layer of complexity from multiple strains brings with it many technical challenges. It is therefore hard to build models which have realistic assumptions yet are tractable. Here we outline some of the main challenges in this area. First we begin with the fundamental question of how to translate from complex small-scale dynamics within a host to useful population models. Next we consider the nature of so-called "strain space". We describe two key types of host heterogeneities, and explain how models could help generate a better understanding of their effects. Finally, for diseases with many strains, we consider the challenge of modelling how immunity accumulates over multiple exposures.
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom; Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Wikramaratna
authors.affiliation: Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom.
authors.forename: Adam
authors.initials: A
authors.lastname: Kucharski
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
authors.forename: Sunetra
authors.initials: S
authors.lastname: Gupta
authors.affiliation: Department of Mathematics and Physics, Roskilde University, DK-4000 Roskilde, Denmark.
authors.forename: Viggo
authors.initials: V
authors.lastname: Andreasen
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
authors.forename: Angela R
authors.initials: AR
authors.lastname: McLean
authors.affiliation: Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom; Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: jrg20@cam.ac.uk.
authors.forename: Julia R
authors.initials: JR
authors.lastname: Gog
mesh_terms: D056704:Adaptive Immunity; D003141:Communicable Diseases / Q000453:epidemiology* / Q000276:immunology / Q000635:transmission; D056738:Cross Protection / Q000276:immunology; D054884:Host-Pathogen Interactions / Q000276:immunology; D006801:Humans; D015233:Models, Statistical; D011157:Population Dynamics; D013045:Species Specificity
keywords: Adaptive immunity; Cross-immunity; Mathematical modelling; Multiple strains; Pathogen evolution