High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants.

ABSTRACT: Viral outbreaks, such as the 2014 ebolavirus, can spread rapidly and have complex evolutionary dynamics, including coinfection and bulk transmission of multiple viral populations. Genomic surveillance can be hindered when the spread of the outbreak exceeds the evolutionary rate, in which case consensus approaches will have limited resolution. Deep sequencing of infected patients can identify genomic variants present in intrahost populations at subclonal frequencies (i.e. <50%). Shared subclonal variants (SSVs) can provide additional phylogenetic resolution and inform about disease transmission patterns. We use metrics from population genetics to analyze data from the 2014 ebolavirus outbreak in Sierra Leone and identify phylogenetic signal arising from SSVs. We use methods derived from inf

SUBMITTER: Emmett KJ 

PROVIDER: S-EPMC4339230 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature