A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutation.
Diane J. Schmidt,Brett E. Pickett,Daría Elena Camacho,Guillermo Comach,Kris Xhaja,Niall J. Lennon,Kamran Rizzolo,N. de Bosch,Aniuska Becerra,Maurício Lacerda Nogueira,Adriano Mondini,E. V. da Silva,P.F. Vasconcelos,Jorge L. Muñoz-Jordán,Gilberto A. Santiago,R. Ocazionez,Lee Gehrke,Elliot J. Lefkowitz,Bruce W. Birren,Matthew R. Henn,Irene Bosch +20 more
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TLDR
In this paper, the authors sequenced 187 new dengue virus serotype 3 (DENV-3) genotype III whole genomes isolated from Asia and the Americas and analyzed them together with previously-sequenced isolates to gain a more detailed understanding of the evolutionary adaptations existing in this prevalent American serotype.About:
This article is published in Infection, Genetics and Evolution.The article was published on 2011-12-01 and is currently open access. It has received 20 citations till now. The article focuses on the topics: Dengue virus & Phylogenetic tree.read more
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Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends
José Ramos-Castañeda,Flavia Barreto dos Santos,Ruth Aralí Martínez-Vega,Josélio Maria Galvão de Araújo,Graham Joint,Elsa Sarti +5 more
TL;DR: Several gaps in molecular epidemiological information across Latin America and the Caribbean were identified that provide avenues for future research; in particular, sequence determination of the dengue virus genome is important for more precise phylogenetic classification and correlation with clinical outcome and disease severity.
Journal ArticleDOI
Unsupervised genome-wide recognition of local relationship patterns
Neda Zamani,Pamela Russell,Henrik Lantz,Marc P. Hoeppner,Jennifer R. S. Meadows,Nagarjun Vijay,Evan Mauceli,Federica Di Palma,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Patric Jern,Manfred Grabherr,Manfred Grabherr +12 more
TL;DR: Saguaro detects distinct cacti describing local phylogenetic relationships without requiring any a priori hypotheses, and successfully demonstrated the software’s utility with two contrasting data sets, one containing many members with short sequences, and the other with few members but complex genomes.
Journal ArticleDOI
Circulation of different lineages of Dengue virus 2, genotype American/Asian in Brazil: dynamics and molecular and phylogenetic characterization.
Betânia Paiva Drumond,Adriano Mondini,Diane J. Schmidt,Roberta Vieira de Morais Bronzoni,Irene Bosch,Maurício Lacerda Nogueira +5 more
TL;DR: There is a delay between the introduction and detection of DENV-2 lineages in Brazil, reinforcing the importance and need for surveillance programs to detect and trace the evolution of these viruses.
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Dengue Virus Type 3 Adaptive Changes during Epidemics in Sao Jose de Rio Preto, Brazil, 2006–2007
Christian Julian Villabona-Arenas,Adriano Mondini,Irene Bosch,Diane Schimitt,Carlos Eduardo Calzavara-Silva,Paolo Marinho de Andrade Zanotto,Maurício Lacerda Nogueira +6 more
TL;DR: This study sequenced the complete polyprotein-coding region of thirty-three DENV-3 isolates to characterize variants circulating under high endemicity in the city of São José de Rio Preto, Brazil, during the onset of the 2006-07 epidemic and highlights the existence of significant and informative DENV variability at the spatio-temporal scale of an urban outbreak.
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Population dynamics of DENV-1 genotype V in Brazil is characterized by co-circulation and strain/lineage replacement.
Betânia Paiva Drumond,Adriano Mondini,Diane J. Schmidt,Irene Bosch,Maurício Lacerda Nogueira +4 more
TL;DR: It is demonstrated that the dynamics of DENV-1 in Brazil is characterized by introduction, movement, local evolution, and lineage replacement, which strengthens the relevance of genotype surveillance in order to identify, trace, and control virus populations circulating in Brazil and Latin America.
References
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Elements of information theory
Thomas M. Cover,Joy A. Thomas +1 more
TL;DR: The author examines the role of entropy, inequality, and randomness in the design of codes and the construction of codes in the rapidly changing environment.
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UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F. Pettersen,Thomas D. Goddard,Conrad C. Huang,Gregory S. Couch,Daniel M. Greenblatt,Elaine C. Meng,Thomas E. Ferrin +6 more
TL;DR: Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
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MrBayes 3: Bayesian phylogenetic inference under mixed models
TL;DR: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
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MRBAYES: Bayesian inference of phylogenetic trees
TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
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BEAST: Bayesian evolutionary analysis by sampling trees
TL;DR: BEAST is a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree that provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions.