Seven challenges in modeling pathogen dynamics within-host and across scales

Julia R. Gog, Lorenzo Pellis, James L. N. Wood, Angela R. McLean, Nimalan Arinaminpathy, James O. Lloyd-Smith

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish
Pages (from-to)45-48
Number of pages4
Publication statusPublished - Mar 2015


  • Within-host
  • Multiple scales
  • Superinfection
  • Transmission bottlenecks
  • Deep-sequencing


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