A novel framework for inferring parameters of transmission from viral sequence data.

ABSTRACT: Transmission between hosts is a critical part of the viral lifecycle. Recent studies of viral transmission have used genome sequence data to evaluate the number of particles transmitted between hosts, and the role of selection as it operates during the transmission process. However, the interpretation of sequence data describing transmission events is a challenging task. We here present a novel and comprehensive framework for using short-read sequence data to understand viral transmission events, designed for influenza virus, but adaptable to other viral species. Our approach solves multiple shortcomings of previous methods for this purpose; for example, we consider transmission as an event involving whole viruses, rather than sets of independent alleles. We demonstrate how selection durin

SUBMITTER: Lumby CK 

PROVIDER: S-EPMC6203404 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature