Abstract
The genomic diversity of a parasite population is shaped by its transmission dynamics but superinfection, cotranmission and recombination make this relationship complex and hard to analyse. This paper aims to simplify the problem by introducing the concept of a genomic transmission graph with three basic parameters: the effective number of hosts, the quantum of transmission and the crossing rate of transmission chains. This enables rapid simulation of coalescence times in a recombining parasite population with superinfection and cotransmission, and it also provides a mathematical framework for analysis of within-host variation. Taking malaria as an example, we use this theoretical model to examine how transmission dynamics and migration affect parasite genomic diversity, including the effective recombination rate and haplotypic metrics of recent common ancestry. We show how key transmission parameters can be inferred from deep sequencing data and as a proof of concept we estimate the Plasmodium falciparum transmission bottleneck. Finally we discuss the potential applications of this novel inferential framework in genomic surveillance for malaria control and elimination. Online tools for exploring the genomic transmission graph are available at d-kwiat.github.io/gtg.
Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
