title: Seven challenges in modeling pathogen dynamics within-host and across scales.
abstract: The population dynamics of infectious disease is a mature field in terms of theory and to some extent, application. However for microparasites, the theory and application of models of the dynamics within a single infected host is still an open field. Further, connecting across the scales--from cellular to host level, to population level--has potential to vastly improve our understanding of pathogen dynamics and evolution. Here, we highlight seven challenges in the following areas: transmission bottlenecks, heterogeneity within host, dynamic fitness landscapes within hosts, making use of next-generation sequencing data, capturing superinfection and when and how to model more than two scales.
authors.affiliation: Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, United Kingdom. Electronic address: jrg20@cam.ac.uk.
authors.forename: Julia R
authors.initials: JR
authors.lastname: Gog
authors.affiliation: Warwick Infectious Disease Epidemiology Research Centre (WIDER) and Warwick Mathematics Institute, University of Warwick, Coventry CV4 7AL, United Kingdom.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Pellis
authors.affiliation: Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom.
authors.forename: James L N
authors.initials: JL
authors.lastname: Wood
authors.affiliation: Department of Zoology, Oxford Martin School, 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 Infectious Disease Epidemiology, School of Public Health, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom.
authors.forename: Nimalan
authors.initials: N
authors.lastname: Arinaminpathy
authors.affiliation: Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.
authors.forename: James O
authors.initials: JO
authors.lastname: Lloyd-Smith
mesh_terms: D005075:Biological Evolution; D003141:Communicable Diseases / Q000453:epidemiology* / Q000235:genetics / Q000635:transmission; D014644:Genetic Variation / Q000235:genetics; D054884:Host-Pathogen Interactions / Q000235:genetics / Q000276:immunology; D006801:Humans; D015233:Models, Statistical; D011157:Population Dynamics; D015163:Superinfection / Q000453:epidemiology / Q000235:genetics / Q000276:immunology
keywords: Deep-sequencing; Multiple scales; Superinfection; Transmission bottlenecks; Within-host