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

https://doi.org/10.1101/105171
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What this work says

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

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Bayesian analysis of elapsed times in continuous‐time Markov chains
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ggplot2: Elegant Graphics for Data Analysis
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Estimating Maximum Likelihood Phylogenies with PhyML
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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
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Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone
inferredcites →https://doi.org/10.1016/j.cub.2011.05.058openalex-snapshot
Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline
inferredcites →https://doi.org/10.1016/j.ebiom.2016.06.009openalex-snapshot
Assessing Seasonal Risks for the Introduction and Mosquito-borne Spread of Zika Virus in Europe
inferredcites →https://doi.org/10.1016/j.meegid.2016.03.030openalex-snapshot
Zika virus complete genome from Salvador, Bahia, Brazil
inferredcites →https://doi.org/10.1016/s1473-3099(16)30270-5openalex-snapshot
Potential for Zika virus introduction and transmission in resource-limited countries in Africa and the Asia-Pacific region: a modelling study
inferredcites →https://doi.org/10.1038/emi.2016.109openalex-snapshot
From discovery to outbreak: the genetic evolution of the emerging Zika virus
inferredcites →https://doi.org/10.1038/nature16996openalex-snapshot
Real-time, portable genome sequencing for Ebola surveillance
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The evolution of Ebola virus: Insights from the 2013–2016 epidemic
inferredcites →https://doi.org/10.1038/nature22402openalex-snapshot
Zika virus evolution and spread in the Americas
inferredcites →https://doi.org/10.1038/nmeth.2109openalex-snapshot
jModelTest 2: more models, new heuristics and parallel computing
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.126openalex-snapshot
Model-based projections of Zika virus infections in childbearing women in the Americas
inferredcites →https://doi.org/10.1038/nprot.2017.066openalex-snapshot
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
inferredcites →https://doi.org/10.1056/nejmoa1604037openalex-snapshot
Zika Virus Disease in Colombia — Preliminary Report
inferredcites →https://doi.org/10.1056/nejmp1702172openalex-snapshot
Yellow Fever — Once Again on the Radar Screen in the Americas
inferredcites →https://doi.org/10.1073/pnas.1614303114openalex-snapshot
Global risk model for vector-borne transmission of Zika virus reveals the role of El Niño 2015
inferredcites →https://doi.org/10.1089/vbz.2016.1952openalex-snapshot
Emergence of Human Arboviral Diseases in the Americas, 2000–2016
inferredcites →https://doi.org/10.1093/aje/kwt133openalex-snapshot
A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics
inferredcites →https://doi.org/10.1093/bioinformatics/bti079openalex-snapshot
HyPhy: hypothesis testing using phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btv184openalex-snapshot
ExaML version 3: a tool for phylogenomic analyses on supercomputers
inferredcites →https://doi.org/10.1093/genetics/156.2.879openalex-snapshot
Consequences of Recombination on Traditional Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/molbev/msi105openalex-snapshot
Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection
inferredcites →https://doi.org/10.1093/molbev/msj021openalex-snapshot
Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences
inferredcites →https://doi.org/10.1093/molbev/msj030openalex-snapshot
Application of Phylogenetic Networks in Evolutionary Studies
inferredcites →https://doi.org/10.1093/molbev/msp003openalex-snapshot
Learning to Count: Robust Estimates for Labeled Distances between Molecular Sequences
inferredcites →https://doi.org/10.1093/molbev/mss075openalex-snapshot
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
inferredcites →https://doi.org/10.1093/molbev/mss084openalex-snapshot
Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty
inferredcites →https://doi.org/10.1093/molbev/mss243openalex-snapshot
Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics
inferredcites →https://doi.org/10.1093/molbev/mss265openalex-snapshot
Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1093/ve/vev003openalex-snapshot
RDP4: Detection and analysis of recombination patterns in virus genomes
inferredcites →https://doi.org/10.1093/ve/vew007openalex-snapshot
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)
inferredcites →https://doi.org/10.1098/rstb.2008.0176openalex-snapshot
Fast, accurate and simulation-free stochastic mapping
inferredcites →https://doi.org/10.1101/104794openalex-snapshot
Multiple introductions of Zika virus into the United States revealed through genomic epidemiology
inferredcites →https://doi.org/10.1101/109348openalex-snapshot
Genome sequencing reveals Zika virus diversity and spread in the Americas
inferredcites →https://doi.org/10.1126/science.354.6316.1088openalex-snapshot
One year later, Zika scientists prepare for a long war
inferredcites →https://doi.org/10.1126/science.aaf5036openalex-snapshot
Zika virus in the Americas: Early epidemiological and genetic findings
inferredcites →https://doi.org/10.1126/science.aaf8160openalex-snapshot
Assessing the global threat from Zika virus
inferredcites →https://doi.org/10.1126/science.aag0219openalex-snapshot
Countering the Zika epidemic in Latin America
inferredcites →https://doi.org/10.1128/genomea.00917-16openalex-snapshot
Genome Sequence of a Candidate World Health Organization Reference Strain of Zika Virus for Nucleic Acid Testing
inferredcites →https://doi.org/10.1128/jvi.77.20.11296-11298.2003openalex-snapshot
Patterns of Intra- and Interhost Nonsynonymous Variation Reveal Strong Purifying Selection in Dengue Virus
inferredcites →https://doi.org/10.1128/mbio.01239-16openalex-snapshot
How Did Zika Virus Emerge in the Pacific Islands and Latin America?
inferredcites →https://doi.org/10.1186/1471-2334-11-166openalex-snapshot
Time series analysis of dengue incidence in Guadeloupe, French West Indies: Forecasting models using climate variables as predictors
inferredcites →https://doi.org/10.1186/s13690-017-0233-5openalex-snapshot
Zika virus disease, microcephaly and Guillain-Barré syndrome in Colombia: epidemiological situation during 21 months of the Zika virus outbreak, 2015–2017
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pcbi.1000520openalex-snapshot
Bayesian Phylogeography Finds Its Roots
inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
inferredcites →https://doi.org/10.1371/journal.pgen.1005421openalex-snapshot
New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation
inferredcites →https://doi.org/10.1371/journal.pntd.0001322openalex-snapshot
Quantifying the Emergence of Dengue in Hanoi, Vietnam: 1998–2009
inferredcites →https://doi.org/10.1371/journal.pntd.0002636openalex-snapshot
Molecular Evolution of Zika Virus during Its Emergence in the 20th Century
inferredcites →https://doi.org/10.1371/journal.pone.0089783openalex-snapshot
Vectorial Capacity of Aedes aegypti: Effects of Temperature and Implications for Global Dengue Epidemic Potential
inferredcites →https://doi.org/10.1534/genetics.105.048975openalex-snapshot
A Simple and Robust Statistical Test for Detecting the Presence of Recombination
inferredcites →https://doi.org/10.1590/0074-02760150192openalex-snapshot
First report of autochthonous transmission of Zika virus in Brazil
inferredcites →https://doi.org/10.2471/blt.16.171082openalex-snapshot
Zika: the origin and spread of a mosquito-borne virus
inferredcites →https://doi.org/10.2471/blt.16.1740540openalex-snapshot
Times to key events in the course of Zika infection and their implications: a systematic review and pooled analysis
inferredcites →https://doi.org/10.2471/blt.16.174540openalex-snapshot
Times to key events in Zika virus infection and implications for blood donation: a systematic review
inferredcites →https://doi.org/10.2471/blt.16.175950openalex-snapshot
Assay optimization for molecular detection of Zika virus
inferredcites →https://doi.org/10.3201/eid1408.080287openalex-snapshot
Genetic and Serologic Properties of Zika Virus Associated with an Epidemic, Yap State, Micronesia, 2007
inferredcites →https://doi.org/10.3201/eid2110.150847openalex-snapshot
Zika Virus Outbreak, Bahia, Brazil
inferredcites →https://doi.org/10.3201/eid2210.160663openalex-snapshot
Distinct Zika Virus Lineage in Salvador, Bahia, Brazil
inferredcites →https://doi.org/10.7554/elife.08347openalex-snapshot
The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.jinf.2017.07.001openalex-snapshot
Returning ex-patriot Chinese to Guangdong, China, increase the risk for local transmission of Zika virus
inferred← citeshttps://doi.org/10.1017/s0950268818002881openalex-snapshot
Reconstruction and prediction of viral disease epidemics
inferred← citeshttps://doi.org/10.1038/s41564-019-0376-yopenalex-snapshot
Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus
inferred← citeshttps://doi.org/10.1038/s41576-018-0055-5openalex-snapshot
The phylogenomics of evolving virus virulence
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty407openalex-snapshot
Nextstrain: real-time tracking of pathogen evolution
inferred← citeshttps://doi.org/10.1093/molbev/msy059openalex-snapshot
De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria
inferred← citeshttps://doi.org/10.1101/109348openalex-snapshot
Genome sequencing reveals Zika virus diversity and spread in the Americas
inferred← citeshttps://doi.org/10.1111/ppa.13416openalex-snapshot
Nanopore sequencing for the detection and identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material
inferred← citeshttps://doi.org/10.3389/fimmu.2017.01704openalex-snapshot
Placental Histopathology and Clinical Presentation of Severe Congenital Zika Syndrome in a Human Immunodeficiency Virus-Exposed Uninfected Infant
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