Patterns of genetic variation in populations of infectious agents

Background: The analysis of genetic variation in populations of infectious agents may help us understand their epidemiology and evolution. Here we study a model for assessing the levels and patterns of genetic diversity in populations of infectious agents. The population is structured into many small subpopulations, which correspond to their hosts, that are connected according to a specific type of contact network. We considered different types of networks, including fully connected networks and scale free networks, which have been considered as a model that captures some properties of real contact networks. Infectious agents transmit between hosts, through migration, where they grow and mutate until elimination by the host immune system. Results: We show how our model is closely related to the classical SIS model in epidemiology and find that: depending on the relation between the rate at which infectious agents are eliminated by the immune system and the within host effective population size, genetic diversity increases with R0 or peaks at intermediate R0 levels; patterns of genetic diversity in this model are in general similar to those expected under the standard neutral model, but in a scale free network and for low values of R0 a distortion in the neutral mutation frequency spectrum can be observed; highly connected hosts (hubs in the network) show patterns of diversity different from poorly connected individuals, namely higher levels of genetic variation, lower levels of genetic differentiation and larger values of Tajima's D. Conclusion: We have found that levels of genetic variability in the population of infectious agents can be predicted by simple analytical approximations, and exhibit two distinct scenarios which are met according to the relation between the rate of drift and the rate at which infectious agents are eliminated. In one scenario the diversity is an increasing function of the level of transmission and in a second scenario it is peaked around intermediate levels of transmission. This is independent of the type of host contact structure. Furthermore for low values of R0, very heterogeneous host contact structures lead to lower levels of diversity. Background Patterns of genetic diversity in populations of infectious agents contain important information about their epidemiology and evolution. They depend on the population dynamics of the infectious agents, which involves their replication within hosts and transmission between hosts, their mutation and recombination rate. Infectious agents vary enormously in their ability to mutate and to transmit, Published: 13 July 2007 BMC Evolutionary Biology 2007, 7:116 doi:10.1186/1471-2148-7-116 Received: 25 September 2006 Accepted: 13 July 2007 This article is available from: http://www.biomedcentral. com/1471-2148/7/116 © 2007 Gordo and Campos; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.