title: Pathogen evolution and the immunological niche.
abstract: Host immunity is a major driver of pathogen evolution and thus a major determinant of pathogen diversity. Explanations for pathogen diversity traditionally assume simple interactions between pathogens and the immune system, a view encapsulated by the susceptible-infected-recovered (SIR) model. However, there is growing evidence that the complexity of many host-pathogen interactions is dynamically important. This revised perspective requires broadening the definition of a pathogen's immunological phenotype, or what can be thought of as its immunological niche. After reviewing evidence that interactions between pathogens and host immunity drive much of pathogen evolution, I introduce the concept of a pathogen's immunological phenotype. Models that depart from the SIR paradigm demonstrate the utility of this perspective and show that it is particularly useful in understanding vaccine-induced evolution. This paper highlights questions in immunology, evolution, and ecology that must be answered to advance theories of pathogen diversity.
authors.affiliation: Department of Ecology and Evolution, University of Chicago, Chicago, Illinois.
authors.forename: Sarah
authors.initials: S
authors.lastname: Cobey
mesh_terms: D000818:Animals; D005075:Biological Evolution; D003141:Communicable Diseases / Q000235:genetics / Q000276:immunology; D014644:Genetic Variation; D054884:Host-Pathogen Interactions / Q000276:immunology*; D006801:Humans; D007107:Immune System / Q000166:cytology* / Q000502:physiology; D008954:Models, Biological; D010641:Phenotype; D012641:Selection, Genetic / Q000276:immunology; D055153:Stem Cell Niche / Q000276:immunology*; D014612:Vaccines / Q000494:pharmacology
chemical_list: D014612:Vaccines
keywords: bacteria; evolutionary epidemiology; host-pathogen interactions; infectious diseases; influenza; niche theory; phylodynamics; viruses