Joint Inference of Migration and Reassortment Patterns for Viruses with Segmented Genomes.

ABSTRACT: The structured coalescent allows inferring migration patterns between viral subpopulations from genetic sequence data. However, these analyses typically assume that no genetic recombination process impacted the sequence evolution of pathogens. For segmented viruses, such as influenza, that can undergo reassortment this assumption is broken. Reassortment reshuffles the segments of different parent lineages upon a coinfection event, which means that the shared history of viruses has to be represented by a network instead of a tree. Therefore, full genome analyses of such viruses are complex or even impossible. Although this problem has been addressed for unstructured populations, it is still impossible to account for population structure, such as induced by different host populations, wherea

SUBMITTER: Stolz U 

PROVIDER: S-EPMC8789051 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature