Phylodynamics of dengue virus 2 in Nicaragua leading up to the 2019 epidemic reveals a role for lineage turnover

[1]  M. Quam,et al.  Global burden for dengue and the evolving pattern in the past 30 years. , 2021, Journal of travel medicine.

[2]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..

[3]  Zhilin Zeng,et al.  Global, regional, and national dengue burden from 1990 to 2017: A systematic analysis based on the global burden of disease study 2017 , 2021, EClinicalMedicine.

[4]  S. Boyer,et al.  Potential role of vector-mediated natural selection in dengue virus genotype/lineage replacements in two epidemiologically contrasted settings , 2021, Emerging microbes & infections.

[5]  E. Harris,et al.  Evolution and epidemiologic dynamics of dengue virus in Nicaragua during the emergence of chikungunya and Zika viruses. , 2020, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[6]  M. Halloran,et al.  Zika virus infection enhances future risk of severe dengue disease , 2020, Science.

[7]  Stephanie J. Spielman,et al.  HyPhy 2.5 - a customizable platform for evolutionary hypothesis testing using phylogenies. , 2019, Molecular biology and evolution.

[8]  T. Friedrich,et al.  Tracking dengue virus type 1 genetic diversity during lineage replacement in an hyperendemic area in Colombia , 2019, PloS one.

[9]  Steven Weaver,et al.  Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes. , 2018, Molecular biology and evolution.

[10]  Daniel L. Ayres,et al.  Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 , 2018, Virus evolution.

[11]  Trevor Bedford,et al.  Nextstrain: real-time tracking of pathogen evolution , 2017, bioRxiv.

[12]  Frédéric Grognard,et al.  Estimating virus effective population size and selection without neutral markers , 2017, PLoS pathogens.

[13]  K. Kizer Dengue and Dengue Hemorrhagic Fever, 2nd edition , 2016 .

[14]  A. Morrison,et al.  Dengue Viruses and Lifelong Immunity: Reevaluating the Conventional Wisdom. , 2016, The Journal of infectious diseases.

[15]  Vaishali P. Waman,et al.  Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes , 2016, PeerJ.

[16]  E. Harris,et al.  Single-Reaction Multiplex Reverse Transcription PCR for Detection of Zika, Chikungunya, and Dengue Viruses , 2016, Emerging infectious diseases.

[17]  E. Harris,et al.  Clinical evaluation of a single-reaction real-time RT-PCR for pan-dengue and chikungunya virus detection. , 2016, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

[18]  D. Gubler,et al.  Insights into the molecular evolution of Dengue virus type 4 in Puerto Rico over two decades of emergence. , 2016, Virus research.

[19]  P. Shi,et al.  Molecular basis for specific viral RNA recognition and 2′-O-ribose methylation by the dengue virus nonstructural protein 5 (NS5) , 2015, Proceedings of the National Academy of Sciences.

[20]  L. Kramer,et al.  Increased Replicative Fitness of a Dengue Virus 2 Clade in Native Mosquitoes: Potential Contribution to a Clade Replacement Event in Nicaragua , 2014, Journal of Virology.

[21]  Anders Larsson,et al.  AliView: a fast and lightweight alignment viewer and editor for large datasets , 2014, Bioinform..

[22]  J. Lescar,et al.  Dengue Virus Non-Structural Protein 5 , 2014, Viruses.

[23]  Kirsten A. Duda,et al.  Global spread of dengue virus types: mapping the 70 year history , 2014, Trends in microbiology.

[24]  E. Harris,et al.  Single-Reaction, Multiplex, Real-Time RT-PCR for the Detection, Quantitation, and Serotyping of Dengue Viruses , 2013, PLoS neglected tropical diseases.

[25]  N. Lennon,et al.  Dynamics of Dengue Disease Severity Determined by the Interplay Between Viral Genetics and Serotype-Specific Immunity , 2011, Science Translational Medicine.

[26]  T. Scott,et al.  Dengue-1 Virus Clade Replacement in Thailand Associated with Enhanced Mosquito Transmission , 2011, Journal of Virology.

[27]  E. Harris,et al.  Evaluation of the Traditional and Revised WHO Classifications of Dengue Disease Severity , 2011, PLoS neglected tropical diseases.

[28]  Mark A. Miller,et al.  Creating the CIPRES Science Gateway for inference of large phylogenetic trees , 2010, 2010 Gateway Computing Environments Workshop (GCE).

[29]  Rosanna W. Peeling,et al.  Dengue: a continuing global threat , 2010, Nature Reviews Microbiology.

[30]  D. Gubler,et al.  Natural attenuation of dengue virus type-2 after a series of island outbreaks: a retrospective phylogenetic study of events in the South Pacific three decades ago. , 2010, Virology.

[31]  N. Lennon,et al.  Emergence of the Asian 1 Genotype of Dengue Virus Serotype 2 in Viet Nam: In Vivo Fitness Advantage and Lineage Replacement in South-East Asia , 2010, PLoS neglected tropical diseases.

[32]  E. Holmes,et al.  Evolution of dengue virus in Mexico is characterized by frequent lineage replacement , 2010, Archives of Virology.

[33]  E. Harris,et al.  The Nicaraguan Pediatric Dengue Cohort Study: Study Design, Methods, Use of Information Technology, and Extension to Other Infectious Diseases , 2009, American journal of epidemiology.

[34]  J. Rougemont,et al.  A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.

[35]  K. Hanley,et al.  Superior infectivity for mosquito vectors contributes to competitive displacement among strains of dengue virus , 2008, BMC Ecology.

[36]  E. Holmes,et al.  Molecular evolution of dengue 2 virus in Puerto Rico: positive selection in the viral envelope accompanies clade reintroduction. , 2006, The Journal of general virology.

[37]  Edward C. Holmes,et al.  Clade Replacements in Dengue Virus Serotypes 1 and 3 Are Associated with Changing Serotype Prevalence , 2005, Journal of Virology.

[38]  E. Holmes,et al.  Lineage extinction and replacement in dengue type 1 virus populations are due to stochastic events rather than to natural selection. , 2005, Virology.

[39]  O. Pybus,et al.  Bayesian coalescent inference of past population dynamics from molecular sequences. , 2005, Molecular biology and evolution.

[40]  Sergei L. Kosakovsky Pond,et al.  Datamonkey: rapid detection of selective pressure on individual sites of codon alignments , 2005, Bioinform..

[41]  R. Rico-Hesse,et al.  Selection for Virulent Dengue Viruses Occurs in Humans and Mosquitoes , 2005, Journal of Virology.

[42]  Chonticha Klungthong,et al.  The molecular epidemiology of dengue virus serotype 4 in Bangkok, Thailand. , 2004, Virology.

[43]  E. Holmes,et al.  Selection-driven evolution of emergent dengue virus. , 2003, Molecular biology and evolution.

[44]  D. Gubler,et al.  Emergence and Global Spread of a Dengue Serotype 3, Subtype III Virus , 2003, Emerging infectious diseases.

[45]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[46]  E. Harris,et al.  Application of molecular typing techniques in the 1998 dengue epidemic in Nicaragua. , 1999, The American journal of tropical medicine and hygiene.

[47]  R. Rico-Hesse,et al.  Origins of dengue type 2 viruses associated with increased pathogenicity in the Americas. , 1997, Virology.

[48]  D. Gubler,et al.  Dengue/dengue hemorrhagic fever: the emergence of a global health problem. , 1995, Emerging infectious diseases.

[49]  D. Gubler,et al.  Emergence of epidemic dengue/dengue hemorrhagic fever as a public health problem in the Americas. , 1993, Infectious agents and disease.

[50]  Dengue and severe dengue , 2019 .

[51]  S. Halstead,et al.  Dengue infection , 2016, Nature Reviews Disease Primers.

[52]  Juan Carlos Albarracín Matute,et al.  Trends in patterns of dengue transmission over 4 years in a pediatric cohort study in Nicaragua. , 2010, The Journal of infectious diseases.

[53]  Graziano Pesole,et al.  BMC Evolutionary Biology BioMed Central , 2007 .

[54]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[55]  Sergei L. Kosakovsky Pond,et al.  BIOINFORMATICS APPLICATIONS , 2022 .