DOI: 10.1101/190918Sep 19, 2017Paper

Effects of multiple sources of genetic drift on pathogen variation within hosts

BioRxiv : the Preprint Server for Biology
David A Kennedy, G Dwyer

Abstract

Changes in pathogen genetic variation within hosts alter the severity and spread of infectious diseases, with important implications for clinical disease and public health. Genetic drift may play a strong role in shaping pathogen variation, but analyses of drift in pathogens have oversimplified pathogen population dynamics, either by considering dynamics only at a single scale (within hosts, between hosts), or by making drastic simplifying assumptions (host immune systems can be ignored, transmission bottlenecks are complete). Moreover, previous studies used genetic data to infer the strength of genetic drift, whereas we test whether the genetic drift imposed by pathogen population processes can be used to explain genetic data. We first constructed and parameterized a mathematical model of gypsy moth baculovirus dynamics that allows genetic drift to act within and between hosts. We then quantified the genome-wide diversity of baculovirus populations within each of 143 field-collected gypsy moth larvae using Illumina sequencing. Finally, we determined whether the genetic drift imposed by host-pathogen population dynamics in our model explains the levels of pathogen diversity in our data. We found that when the model allows drift...Continue Reading

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