ArticlePLoS currents2015
High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants.
Article in PLoS currents, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed.
- Evolutionary constraints limit additional mammalian adaptation of bovine-derived H5N1 influenza viruses in ferrets.bioRxiv : the preprint server for biology · 2026Article
- Evolution of clonal hematopoiesis during cancer treatment and its impact on outcomes.The Journal of clinical investigation · 2026Article
- The impact of viral and host factors on the influenza A virus transmission bottleneck.PLoS pathogens · 2026Article
- Clonal Hematopoiesis Dynamics and Evolutionary Fitness During Cancer Treatment Impact Clinical Outcomes.medRxiv : the preprint server for health sciences · 2025Article
- ViralBottleneck: an R package for estimating viral transmission bottlenecks from deep sequencing data using multiple methods.Virus evolution · 2025Article
- The airborne transmission of viruses causes tight transmission bottlenecks.Nature communications · 2024Article
- Transmission Bottleneck Size Estimation from De Novo Viral Genetic Variation.Molecular biology and evolution · 2024Article
- COVID-19 infection and transmission includes complex sequence diversity.PLoS genetics · 2022Article
- Cross-scale dynamics and the evolutionary emergence of infectious diseases.Virus evolution · 2021Article
- Difference of Intrahost Dynamics of the Second Human Pegivirus and Hepatitis C Virus in HPgV-2/HCV-Coinfected Patients.Frontiers in cellular and infection microbiology · 2021Article
- Inferring Transmission Bottleneck Size from Viral Sequence Data Using a Novel Haplotype Reconstruction Method.Journal of virology · 2020Article
- Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Intra-host Ebola viral adaption during human infection.Biosafety and health · 2019Article
- A novel framework for inferring parameters of transmission from viral sequence data.PLoS genetics · 2018Article
- Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data.American journal of epidemiology · 2017Article
- Article
- Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus.Journal of virology · 2017Article
- Genomic Analysis of Viral Outbreaks.Annual review of virology · 2016Review
- Intra-host dynamics of Ebola virus during 2014.Nature microbiology · 2016Article
- Deaths, late deaths, and role of infecting dose in Ebola virus disease in Sierra Leone: retrospective cohort study.BMJ (Clinical research ed.) · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundViral 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.
methodsWe 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. RESULTS AND
conclusionsWe 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.
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