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Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

https://doi.org/10.1101/104794
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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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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
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Origin of the dengue virus outbreak in Martin County, Florida, USA 2013
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Potential for Zika virus introduction and transmission in resource-limited countries in Africa and the Asia-Pacific region: a modelling study
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Superspreading and the effect of individual variation on disease emergence
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Fast gapped-read alignment with Bowtie 2
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jModelTest 2: more models, new heuristics and parallel computing
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Model-based projections of Zika virus infections in childbearing women in the Americas
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Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
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Zika Virus Outbreak on Yap Island, Federated States of Micronesia
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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
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Identification of Dengue Fever Cases in Houston, Texas, with Evidence of Autochthonous Transmission Between 2003 and 2005
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr026openalex-snapshot
Quality control and preprocessing of metagenomic datasets
inferredcites →https://doi.org/10.1093/bioinformatics/bts199openalex-snapshot
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/infdis/jiw302openalex-snapshot
Outbreak of Zika Virus Infection, Chiapas State, Mexico, 2015, and First Confirmed Transmission byAedes aegyptiMosquitoes in the Americas
inferredcites →https://doi.org/10.1093/jme/tjv234openalex-snapshot
Temporal and Spatial Variability of Entomological Risk Indices for West Nile Virus Infection in Northern Colorado: 2006–2013
inferredcites →https://doi.org/10.1093/molbev/msi103openalex-snapshot
Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
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/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/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/sysbio/syq085openalex-snapshot
Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection
inferredcites →https://doi.org/10.1093/trstmh/trv106openalex-snapshot
Evidence of vertical transmission and co-circulation of chikungunya and dengue viruses in field populations ofAedes aegypti(L.) from Guerrero, Mexico: Table 1.
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/rsif.2015.0468openalex-snapshot
Big city, small world: density, contact rates, and transmission of dengue across Pakistan
inferredcites →https://doi.org/10.1111/j.2041-210x.2011.00105.xopenalex-snapshot
Estimating abundance from presence/absence maps
inferredcites →https://doi.org/10.1111/jmwh.12483_3openalex-snapshot
CENTERS FOR DISEASE CONTROL AND PREVENTION ISSUES INTERIM GUIDELINES FOR PREGNANT WOMEN AND INFANTS EXPOSED TO ZIKA VIRUS AND PREVENTION OF SEXUALLY TRANSMITTED ZIKA INFECTION
inferredcites →https://doi.org/10.1126/science.1251449openalex-snapshot
Measuring the path toward malaria elimination
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.aag0219openalex-snapshot
Countering the Zika epidemic in Latin America
inferredcites →https://doi.org/10.1128/jcm.00279-16openalex-snapshot
Zika Virus: Diagnostics for an Emerging Pandemic Threat
inferredcites →https://doi.org/10.1128/jvi.00252-16openalex-snapshot
Zika Virus: New Clinical Syndromes and Its Emergence in the Western Hemisphere
inferredcites →https://doi.org/10.1136/bmj.i212openalex-snapshot
First US case of Zika virus infection is identified in Texas
inferredcites →https://doi.org/10.1177/003335491212700305openalex-snapshot
Return of Epidemic Dengue in the United States: Implications for the Public Health Practitioner
inferredcites →https://doi.org/10.1186/s12976-016-0046-1openalex-snapshot
Estimating the subcritical transmissibility of the Zika outbreak in the State of Florida, USA, 2016
inferredcites →https://doi.org/10.1214/ss/1028905934openalex-snapshot
Simulating normalizing constants: from importance sampling to bridge sampling to path sampling
inferredcites →https://doi.org/10.1371/currents.outbreaks.50dfc7f46798675fc63e7d7da563da76openalex-snapshot
On the Seasonal Occurrence and Abundance of the Zika Virus Vector Mosquito Aedes Aegypti in the Contiguous United States
inferredcites →https://doi.org/10.1371/currents.outbreaks.ac6d0f8c9c35e88825c1a1147697531copenalex-snapshot
Travel Volume to the United States from Countries and U.S. Territories with Local Zika Virus Transmission
inferredcites →https://doi.org/10.1371/journal.pcbi.1003327openalex-snapshot
Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission
inferredcites →https://doi.org/10.1371/journal.pntd.0002769openalex-snapshot
Air Travel Is Associated with Intracontinental Spread of Dengue Virus Serotypes 1–3 in Brazil
inferredcites →https://doi.org/10.1371/journal.pntd.0003278openalex-snapshot
International Dispersal of Dengue through Air Travel: Importation Risk for Europe
inferredcites →https://doi.org/10.1371/journal.pntd.0004543openalex-snapshot
Differential Susceptibilities of Aedes aegypti and Aedes albopictus from the Americas to Zika Virus
inferredcites →https://doi.org/10.1371/journal.pntd.0005101openalex-snapshot
Vector Competence of American Mosquitoes for Three Strains of Zika Virus
inferredcites →https://doi.org/10.1371/journal.pone.0161365openalex-snapshot
Modeling Mosquito-Borne Disease Spread in U.S. Urbanized Areas: The Case of Dengue in Miami
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.15585/mmwr.mm6503e1eropenalex-snapshot
Zika Virus Spreads to New Areas — Region of the Americas, May 2015–January 2016
inferredcites →https://doi.org/10.15585/mmwr.mm6518e1openalex-snapshot
Interim Guidance for Zika Virus Testing of Urine — United States, 2016
inferredcites →https://doi.org/10.15585/mmwr.mm6521e1openalex-snapshot
Interim Guidance for Interpretation of Zika Virus Antibody Test Results
inferredcites →https://doi.org/10.15585/mmwr.mm6538e1openalex-snapshot
Local Mosquito-Borne Transmission of Zika Virus — Miami-Dade and Broward Counties, Florida, June–August 2016
inferredcites →https://doi.org/10.15585/mmwr.rr6504a1openalex-snapshot
U.S. Selected Practice Recommendations for Contraceptive Use, 2016
inferredcites →https://doi.org/10.1590/0074-02760160332openalex-snapshot
First detection of natural infection of Aedes aegypti with Zika virus in Brazil and throughout South America
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/10.3201/eid1408.080287openalex-snapshot
Genetic and Serologic Properties of Zika Virus Associated with an Epidemic, Yap State, Micronesia, 2007
inferredcites →https://doi.org/10.3201/eid1711.110419openalex-snapshot
Mosquito-associated Dengue Virus, Key West, Florida, USA, 2010
inferredcites →https://doi.org/10.4230/oasics.gcb.2012.49openalex-snapshot
Building and Documenting Workflows with Python-Based Snakemake
inferredcites →https://doi.org/10.4269/ajtmh.2008.78.364openalex-snapshot
Epidemic Dengue and Dengue Hemorrhagic Fever at the Texas–Mexico Border: Results of a Household-based Seroepidemiologic Survey, December 2005
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/10.1101/105171openalex-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
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