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Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

https://doi.org/10.1016/j.cell.2015.06.007

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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broadinstitute/viral-ngs: 3.0.0

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Viral intra-host evolutionary dynamics revealed via serial passage of Japanese encephalitis virus in vitro

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Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales

inferred← citeshttps://doi.org/10.1093/ve/vew016openalex-snapshot

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases

inferred← citeshttps://doi.org/10.1093/ve/vew022openalex-snapshot

Challenges in the analysis of viral metagenomes

inferred← citeshttps://doi.org/10.1093/ve/vey005openalex-snapshot

Private collection: high correlation of sample collection and patient admission date in clinical microbiological testing complicates sharing of phylodynamic metadata

inferred← citeshttps://doi.org/10.1093/ve/vey027openalex-snapshot

Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains

inferred← citeshttps://doi.org/10.1093/ve/vey034openalex-snapshot

Ebola virus, but not Marburg virus, replicates efficiently and without required adaptation in snake cells

inferred← citeshttps://doi.org/10.1097/ede.0000000000001367openalex-snapshot

Leveraging Pathogen Sequence and Contact Tracing Data to Enhance Vaccine Trials in Emerging Epidemics

inferred← citeshttps://doi.org/10.1098/rsif.2017.0583openalex-snapshot

Identifying spatio-temporal dynamics of Ebola in Sierra Leone using virus genomes

inferred← citeshttps://doi.org/10.1098/rstb.2016.0297openalex-snapshot

The Ebola outbreak, 2013–2016: old lessons for new epidemics

inferred← citeshttps://doi.org/10.1101/075168openalex-snapshot

Identification of important amino acid replacements in the 2013-2016 Ebola virus outbreak

inferred← citeshttps://doi.org/10.1101/105171openalex-snapshot

Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas

inferred← citeshttps://doi.org/10.1101/109348openalex-snapshot

Genome sequencing reveals Zika virus diversity and spread in the Americas

inferred← citeshttps://doi.org/10.1101/2020.03.27.012013openalex-snapshot

SARS-CoV-2 and ORF3a: Non-Synonymous Mutations and Polyproline Regions

inferred← citeshttps://doi.org/10.1101/2020.07.02.184481openalex-snapshot

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

inferred← citeshttps://doi.org/10.1101/2020.08.07.242263openalex-snapshot

Worldwide tracing of mutations and the evolutionary dynamics of SARS-CoV-2

inferred← citeshttps://doi.org/10.1101/2021.04.21.440871openalex-snapshot

3’ untranslated regions of Marburg and Ebola virus mRNAs possess negative regulators of translation that are modulated by ADAR1 editing

inferred← citeshttps://doi.org/10.1101/2021.07.01.450528openalex-snapshot

High confidence identification of intra-host single nucleotide variants for person-to-person influenza transmission tracking in congregate settings

inferred← citeshttps://doi.org/10.1101/2021.10.27.21265424openalex-snapshot

Intrahost-diversity of influenza A virus in upper and lower respiratory tract derived samples from a college community

inferred← citeshttps://doi.org/10.1101/2023.10.14.23297039openalex-snapshot

Inferring Viral Transmission Pathways from Within-Host Variation

inferred← citeshttps://doi.org/10.1101/2024.03.13.584779openalex-snapshot

Comparative Evaluation of Bioinformatic Pipelines for Full-Length Viral Genome Assembly

inferred← citeshttps://doi.org/10.1101/2025.01.09.632079openalex-snapshot

Comprehensive Infectome Analysis Reveals Diverse Infectious Agents with Zoonotic Potential in Wildlife

inferred← citeshttps://doi.org/10.1101/2025.10.17.683141openalex-snapshot

Evidence of latency reshapes our understanding of Ebola virus reservoir dynamics

inferred← citeshttps://doi.org/10.1101/341248openalex-snapshot

PI(4,5)P 2 Binding Sites in the Ebola Virus Matrix Protein Modulate Assembly and Budding

inferred← citeshttps://doi.org/10.1101/630269openalex-snapshot

Glycosylation-dependent enhanced cell-binding and infectivity through DC-SIGN in the West African Ebola virus Makona

inferred← citeshttps://doi.org/10.1101/gr.210641.116openalex-snapshot

Centrifuge: rapid and sensitive classification of metagenomic sequences

inferred← citeshttps://doi.org/10.1101/gr.266676.120openalex-snapshot

Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region

inferred← citeshttps://doi.org/10.1101/gr.268961.120openalex-snapshot

SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission

inferred← citeshttps://doi.org/10.1111/1365-2656.12766openalex-snapshot

Migratory animals feel the cost of getting sick: A meta‐analysis across species

inferred← citeshttps://doi.org/10.1111/gtc.12463openalex-snapshot

Functional mutations in spike glycoprotein of Zaire ebolavirus associated with an increase in infection efficiency

inferred← citeshttps://doi.org/10.1111/mec.13450openalex-snapshot

Time‐dependent estimates of molecular evolutionary rates: evidence and causes

inferred← citeshttps://doi.org/10.1111/ppc.12666openalex-snapshot

“I'm a hero, but…”: An evaluation of depression, anxiety, and stress levels of frontline healthcare professionals during COVID‐19 pandemic in Turkey

inferred← citeshttps://doi.org/10.1126/science.aaf3823openalex-snapshot

Comment on “Mutation rate and genotype variation of Ebola virus from Mali case sequences”

inferred← citeshttps://doi.org/10.1126/science.aaf4561openalex-snapshot

Response to Comment on “Mutation rate and genotype variation of Ebola virus from Mali case sequences”

inferred← citeshttps://doi.org/10.1126/science.aaf5036openalex-snapshot

Zika virus in the Americas: Early epidemiological and genetic findings

inferred← citeshttps://doi.org/10.1126/science.abe3261openalex-snapshot

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

inferred← citeshttps://doi.org/10.1128/9781555819453.ch1openalex-snapshot

West Africa 2013: Re-examining Ebola

inferred← citeshttps://doi.org/10.1128/9781555819743.ch15openalex-snapshot

Transmission, Human Population, and Pathogenicity: the Ebola Case in Point

inferred← citeshttps://doi.org/10.1128/cmr.00003-16openalex-snapshot

Diagnosis of Ebola Virus Disease: Past, Present, and Future

inferred← citeshttps://doi.org/10.1128/jcm.02142-20openalex-snapshot

Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19

inferred← citeshttps://doi.org/10.1128/jvi.00322-16openalex-snapshot

Both Epistasis and Diversifying Selection Drive the Structural Evolution of the Ebola Virus Glycoprotein Mucin-Like Domain

inferred← citeshttps://doi.org/10.1128/jvi.00590-23openalex-snapshot

Molecular characterization of the 2022 Sudan virus disease outbreak in Uganda

inferred← citeshttps://doi.org/10.1128/jvi.00652-21openalex-snapshot

Marburg and Ebola Virus mRNA 3′ Untranslated Regions Contain Negative Regulators of Translation That Are Modulated by ADAR1 Editing

inferred← citeshttps://doi.org/10.1128/jvi.00804-18openalex-snapshot

Metagenomic Sequencing of HIV-1 in the Blood and Female Genital Tract Reveals Little Quasispecies Diversity during Acute Infection

inferred← citeshttps://doi.org/10.1128/jvi.01056-23openalex-snapshot

Accumulated metagenomic studies reveal recent migration, whole genome evolution, and undiscovered diversity of orthomyxoviruses

inferred← citeshttps://doi.org/10.1128/jvi.01905-17openalex-snapshot

Experimental Adaptive Evolution of Simian Immunodeficiency Virus SIVcpz to Pandemic Human Immunodeficiency Virus Type 1 by Using a Humanized Mouse Model

inferred← citeshttps://doi.org/10.1128/jvi.01913-16openalex-snapshot

Functional Characterization of Adaptive Mutations during the West African Ebola Virus Outbreak

inferred← citeshttps://doi.org/10.1128/jvi.02150-25openalex-snapshot

The magnitude and durability of neutralizing antibody responses to human papillomavirus vaccine do not depend on DNA sensing pathways

inferred← citeshttps://doi.org/10.1128/microbiolspec.ei10-0022-2016openalex-snapshot

West Africa 2013: Re-examining Ebola

inferred← citeshttps://doi.org/10.1128/microbiolspec.mtbp-0003-2016openalex-snapshot

Transmission, Human Population, and Pathogenicity: the Ebola Case in Point

inferred← citeshttps://doi.org/10.1128/mspheredirect.00325-17openalex-snapshot

Deep Sequencing of RNA from Blood and Oral Swab Samples Reveals the Presence of Nucleic Acid from a Number of Pathogens in Patients with Acute Ebola Virus Disease and Is Consistent with Bacterial Translocation across the Gut

inferred← citeshttps://doi.org/10.1128/msystems.00058-16openalex-snapshot

Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents

inferred← citeshttps://doi.org/10.1136/bmj.i2403openalex-snapshot

Deaths, late deaths, and role of infecting dose in Ebola virus disease in Sierra Leone: retrospective cohort study

inferred← citeshttps://doi.org/10.1146/annurev-genom-083115-022446openalex-snapshot

Host Factors in Ebola Infection

inferred← citeshttps://doi.org/10.1146/annurev-virology-101416-041718openalex-snapshot

Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution

inferred← citeshttps://doi.org/10.1146/annurev-virology-110615-035747openalex-snapshot

Genomic Analysis of Viral Outbreaks

inferred← citeshttps://doi.org/10.1146/annurev-virology-110615-040056openalex-snapshot

Epidemiology and Management of the 2013–16 West African Ebola Outbreak

inferred← citeshttps://doi.org/10.1155/2015/678587openalex-snapshot

Local Mutational Pressures in Genomes of Zaire Ebolavirus and Marburg Virus

inferred← citeshttps://doi.org/10.1155/2018/1846207openalex-snapshot

Investigation of Outbreak-Specific Nonsynonymous Mutations on Ebolavirus GP in the Context of Known Immune Reactivity

inferred← citeshttps://doi.org/10.1172/jci.insight.88333openalex-snapshot

Mapping the clinical outcomes and genetic evolution of Ebola virus in Sierra Leone

inferred← citeshttps://doi.org/10.1186/s12859-015-0840-5openalex-snapshot

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

inferred← citeshttps://doi.org/10.1186/s12862-019-1567-0openalex-snapshot

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

inferred← citeshttps://doi.org/10.1186/s12879-015-1302-4openalex-snapshot

The face of Ebola: changing frequency of haemorrhage in the West African compared with Eastern-Central African outbreaks

inferred← citeshttps://doi.org/10.1186/s12879-021-06337-8openalex-snapshot

Knowledge, perceptions and effects of Ebola virus disease outbreak on the pig value chain in the agro-pastoralist district of Luwero, Central Uganda

inferred← citeshttps://doi.org/10.1186/s12889-024-20305-2openalex-snapshot

Community perspectives of Ebola Viral Disease in high-risk transmission border regions of Tanzania: a qualitative inquiry

inferred← citeshttps://doi.org/10.1186/s12967-017-1224-6openalex-snapshot

Mathematical models for devising the optimal Ebola virus disease eradication

inferred← citeshttps://doi.org/10.1186/s12985-023-01995-3openalex-snapshot

Oligonucleotide usage in coronavirus genomes mimics that in exon regions in host genomes

inferred← citeshttps://doi.org/10.1186/s13073-020-00751-4openalex-snapshot

Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples

inferred← citeshttps://doi.org/10.1186/s13073-021-00847-5openalex-snapshot

Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients

inferred← citeshttps://doi.org/10.1186/s13100-015-0047-3openalex-snapshot

Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups

inferred← citeshttps://doi.org/10.1186/s40249-016-0154-5openalex-snapshot

Good laboratory practices guarantee biosafety in the Sierra Leone-China friendship biosafety laboratory

inferred← citeshttps://doi.org/10.1186/s41256-017-0034-yopenalex-snapshot

Phylodynamic applications in 21st century global infectious disease research

inferred← citeshttps://doi.org/10.1371/journal.pbio.3000611openalex-snapshot

Combining genomics and epidemiology to track mumps virus transmission in the United States

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006955openalex-snapshot

Model diagnostics and refinement for phylodynamic models

showing the first 200 of 294

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