The ability of single genes vs full genomes to resolve time and space in outbreak analysis.

ABSTRACT: BACKGROUND:Inexpensive pathogen genome sequencing has had a transformative effect on the field of phylodynamics, where ever increasing volumes of data have promised real-time insight into outbreaks of infectious disease. As well as the sheer volume of pathogen isolates being sequenced, the sequencing of whole pathogen genomes, rather than select loci, has allowed phylogenetic analyses to be carried out at finer time scales, often approaching serial intervals for infections caused by rapidly evolving RNA viruses. Despite its utility, whole genome sequencing of pathogens has not been adopted universally and targeted sequencing of loci is common in some pathogen-specific fields. RESULTS:In this study we highlighted the utility of sequencing whole genomes of pathogens by re-analysing a well-ch

SUBMITTER: Dudas G 

PROVIDER: S-EPMC6933756 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature