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

PLoS Currents
Kevin J EmmettRaul Rabadan

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 information theory to measure a lower bound on transmission bottleneck size. We identify several SSV that shed light on phylogenetic relationships not captured by consensus-based analyses. We find that transmission bottleneck size is larger than one founder population, yet significantly smaller than the intrahost effective population. Our results demonstrate the important role of shared subclonal variants in genomic surveillance.

Citations

Oct 27, 2016·Nature Microbiology·Ming NiDi Liu
Jan 5, 2016·Nature Genetics·Leo L M PoonElodie Ghedin
Apr 17, 2020·Journal of Virology·Mahan GhafariChristopher J R Illingworth
Aug 9, 2016·Annual Review of Virology·Shirlee WohlPardis C Sabeti
Mar 12, 2017·American Journal of Clinical Dermatology·Marina PerperKeyvan Nouri
May 19, 2020·The Journal of Dermatological Treatment·Sarah OtbAbeer Attia Tawfik
Sep 2, 2021·Frontiers in Cellular and Infection Microbiology·Yuanhao LiangShixing Tang

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Datasets Mentioned

BETA
PRJNA257197

Software Mentioned

DendroPy
Bowtie 2
PHYLIP

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