Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence

Borucki, Monica K.; Collette, Nicole M.; Coffey, Lark L.; Van Rompay, Koen K. A.; Hwang, Mona H.; Thissen, James B.; Allen, Jonathan E.; Zemla, Adam T.; Khudyakov, ed., Yury E.

doi:10.1371/journal.pone.0225699

Title: Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence

Authors:

; Collette, Nicole M.; Coffey, Lark L.; Van Rompay, Koen K. A.; Hwang, Mona H.;

; Allen, Jonathan E.; Zemla, Adam T.; Khudyakov, ed., Yury E.

Publication Date:: Fri Dec 06 00:00:00 EST 2019

Research Org.:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE National Nuclear Security Administration (NNSA)

OSTI Identifier:: 1630450

Alternate Identifier(s):: OSTI ID: 1629041; OSTI ID: 1776664

Report Number(s):: LLNL-JRNL-800059
Journal ID: ISSN 1932-6203; 10.1371/journal.pone.0225699

Grant/Contract Number:: 17-ER-019; AC52-07NA27344

Resource Type:: Published Article

Journal Name:: PLoS ONE

Additional Journal Information:: Journal Name: PLoS ONE Journal Volume: 14 Journal Issue: 12; Journal ID: ISSN 1932-6203

Publisher:: Public Library of Science (PLoS)

Country of Publication:: United States

Language:: English

Subject:: 60 APPLIED LIFE SCIENCES

Citation Formats


                    Borucki, Monica K., Collette, Nicole M., Coffey, Lark L., Van Rompay, Koen K. A., Hwang, Mona H., Thissen, James B., Allen, Jonathan E., Zemla, Adam T., and Khudyakov, ed., Yury E. Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence.  United States: N. p., 2019. 
Web.  doi:10.1371/journal.pone.0225699.

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                    Borucki, Monica K., Collette, Nicole M., Coffey, Lark L., Van Rompay, Koen K. A., Hwang, Mona H., Thissen, James B., Allen, Jonathan E., Zemla, Adam T., & Khudyakov, ed., Yury E. Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence.  United States.  https://doi.org/10.1371/journal.pone.0225699

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                    Borucki, Monica K., Collette, Nicole M., Coffey, Lark L., Van Rompay, Koen K. A., Hwang, Mona H., Thissen, James B., Allen, Jonathan E., Zemla, Adam T., and Khudyakov, ed., Yury E. Fri .  
"Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence".  United States.  https://doi.org/10.1371/journal.pone.0225699.

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@article{osti_1630450,

  title        = {Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence},

  author       = {Borucki, Monica K. and Collette, Nicole M. and Coffey, Lark L. and Van Rompay, Koen K. A. and Hwang, Mona H. and Thissen, James B. and Allen, Jonathan E. and Zemla, Adam T. and Khudyakov, ed., Yury E.},

  abstractNote = {},

  doi          = {10.1371/journal.pone.0225699},

  journal      = {PLoS ONE},

  number       = 12,

  volume       = 14,

  place        = {United States},

  year         = {Fri Dec 06 00:00:00 EST 2019},

  month        = {Fri Dec 06 00:00:00 EST 2019}

}

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Works referenced in this record:

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Title: Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence

Citation Formats

Zika virus (II). Pathogenicity and physical properties journal, September 1952

Blocking Monoclonal Antibodies Specific for Mouse IFN- α / β Receptor Subunit 1 (IFNAR-1) from Mice Immunized by In Vivo Hydrodynamic Transfection journal, November 2006

Phylogeny of the Genus Flavivirus journal, January 1998

Zika Virus (I). Isolations and serological specificity journal, September 1952

Zika virus preferentially replicates in the female reproductive tract after vaginal inoculation of rhesus macaques journal, July 2017

Role of the mutant spectrum in adaptation and replication of West Nile virus journal, March 2007

The risk of sustained sexual transmission of Zika is underestimated journal, September 2017

Ultra-Deep Sequencing of Intra-host Rabies Virus Populations during Cross-species Transmission journal, November 2013

Rna Virus Mutations and Fitness for Survival journal, October 1997

Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes journal, January 2014

A simple method for displaying the hydropathic character of a protein journal, May 1982

Zika Virus Outbreak in Haiti in 2014: Molecular and Clinical Data journal, April 2016

Intraamniotic Zika virus inoculation of pregnant rhesus macaques produces fetal neurologic disease journal, June 2018

Genetic diversity and purifying selection in West Nile virus populations are maintained during host switching journal, May 2008

Viral Quasispecies Evolution journal, June 2012

Phylogeny of Zika Virus in Western Hemisphere, 2015 journal, May 2016

Cell-specific adaptation of two flaviviruses following serial passage in mosquito cell culture journal, January 2007

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples journal, May 2017

Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance journal, July 2007

Hock immunization: A humane alternative to mouse footpad injections journal, December 2007

The Zika virus envelope protein glycan loop regulates virion antigenicity journal, February 2018

Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs journal, January 2013

AS2TS system for protein structure modeling and analysis journal, July 2005

Quantification of intrahost bottlenecks of West Nile virus in Culex pipiens mosquitoes using an artificial mutant swarm journal, April 2012

Zika Virus Tissue and Blood Compartmentalization in Acute Infection of Rhesus Macaques journal, January 2017

The C-terminal 50 Amino Acid Residues of Dengue NS3 Protein Are Important for NS3-NS5 Interaction and Viral Replication journal, December 2014

Selective Blockade of Interferon-α and -β Reveals Their Non-Redundant Functions in a Mouse Model of West Nile Virus Infection journal, May 2015

An evolutionary NS1 mutation enhances Zika virus evasion of host interferon induction journal, January 2018

Cooperative interactions in the West Nile virus mutant swarm journal, January 2012

Nextstrain: real-time tracking of pathogen evolution journal, May 2018

Mutations present in a low-passage Zika virus isolate result in attenuated pathogenesis in mice journal, April 2019

Genetic and Serologic Properties of Zika Virus Associated with an Epidemic, Yap State, Micronesia, 2007 journal, August 2008

West Nile virus population genetics and evolution journal, March 2012

LGA: a method for finding 3D similarities in protein structures journal, July 2003

Potential Sexual Transmission of Zika Virus journal, February 2015

The I-TASSER Suite: protein structure and function prediction journal, December 2014

Emergence and Transmission of Arbovirus Evolutionary Intermediates with Epidemic Potential journal, June 2014

A Full-Length Infectious cDNA Clone of Zika Virus from the 2015 Epidemic in Brazil as a Genetic Platform for Studies of Virus-Host Interactions and Vaccine Development journal, August 2016

Zika virus: high infectious viral load in semen, a new sexually transmitted pathogen? journal, April 2016

Persistence and infectivity of Zika virus in semen after returning from endemic areas: Report of 5 cases journal, November 2017

Zika Virus Targets Human STAT2 to Inhibit Type I Interferon Signaling journal, June 2016

Establishment and cryptic transmission of Zika virus in Brazil and the Americas journal, May 2017

Zika virus evolution and spread in the Americas journal, May 2017

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase journal, June 2011

Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes journal, May 2017

Quasispecies composition and evolution of a typical Zika virus clinical isolate from Suriname journal, May 2017

Zika virus (II). Pathogenicity and physical properties
journal, September 1952

Blocking Monoclonal Antibodies Specific for Mouse IFN- α / β Receptor Subunit 1 (IFNAR-1) from Mice Immunized by In Vivo Hydrodynamic Transfection
journal, November 2006

Phylogeny of the Genus Flavivirus
journal, January 1998

Zika Virus (I). Isolations and serological specificity
journal, September 1952

Zika virus preferentially replicates in the female reproductive tract after vaginal inoculation of rhesus macaques
journal, July 2017

Role of the mutant spectrum in adaptation and replication of West Nile virus
journal, March 2007

The risk of sustained sexual transmission of Zika is underestimated
journal, September 2017

Ultra-Deep Sequencing of Intra-host Rabies Virus Populations during Cross-species Transmission
journal, November 2013

Rna Virus Mutations and Fitness for Survival
journal, October 1997

Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes
journal, January 2014

A simple method for displaying the hydropathic character of a protein
journal, May 1982

Zika Virus Outbreak in Haiti in 2014: Molecular and Clinical Data
journal, April 2016

Intraamniotic Zika virus inoculation of pregnant rhesus macaques produces fetal neurologic disease
journal, June 2018

Genetic diversity and purifying selection in West Nile virus populations are maintained during host switching
journal, May 2008

Viral Quasispecies Evolution
journal, June 2012

Phylogeny of Zika Virus in Western Hemisphere, 2015
journal, May 2016

Cell-specific adaptation of two flaviviruses following serial passage in mosquito cell culture
journal, January 2007

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
journal, May 2017

Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance
journal, July 2007

Hock immunization: A humane alternative to mouse footpad injections
journal, December 2007

The Zika virus envelope protein glycan loop regulates virion antigenicity
journal, February 2018

Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs
journal, January 2013

AS2TS system for protein structure modeling and analysis
journal, July 2005

Quantification of intrahost bottlenecks of West Nile virus in Culex pipiens mosquitoes using an artificial mutant swarm
journal, April 2012

Zika Virus Tissue and Blood Compartmentalization in Acute Infection of Rhesus Macaques
journal, January 2017

The C-terminal 50 Amino Acid Residues of Dengue NS3 Protein Are Important for NS3-NS5 Interaction and Viral Replication
journal, December 2014

Selective Blockade of Interferon-α and -β Reveals Their Non-Redundant Functions in a Mouse Model of West Nile Virus Infection
journal, May 2015

An evolutionary NS1 mutation enhances Zika virus evasion of host interferon induction
journal, January 2018

Cooperative interactions in the West Nile virus mutant swarm
journal, January 2012

Nextstrain: real-time tracking of pathogen evolution
journal, May 2018

Mutations present in a low-passage Zika virus isolate result in attenuated pathogenesis in mice
journal, April 2019

Genetic and Serologic Properties of Zika Virus Associated with an Epidemic, Yap State, Micronesia, 2007
journal, August 2008

West Nile virus population genetics and evolution
journal, March 2012

LGA: a method for finding 3D similarities in protein structures
journal, July 2003

Potential Sexual Transmission of Zika Virus
journal, February 2015

The I-TASSER Suite: protein structure and function prediction
journal, December 2014

Emergence and Transmission of Arbovirus Evolutionary Intermediates with Epidemic Potential
journal, June 2014

A Full-Length Infectious cDNA Clone of Zika Virus from the 2015 Epidemic in Brazil as a Genetic Platform for Studies of Virus-Host Interactions and Vaccine Development
journal, August 2016

Zika virus: high infectious viral load in semen, a new sexually transmitted pathogen?
journal, April 2016

Persistence and infectivity of Zika virus in semen after returning from endemic areas: Report of 5 cases
journal, November 2017

Zika Virus Targets Human STAT2 to Inhibit Type I Interferon Signaling
journal, June 2016

Establishment and cryptic transmission of Zika virus in Brazil and the Americas
journal, May 2017

Zika virus evolution and spread in the Americas
journal, May 2017

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase
journal, June 2011

Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes
journal, May 2017

Quasispecies composition and evolution of a typical Zika virus clinical isolate from Suriname
journal, May 2017