A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutation

University of Massachusetts Medical School. Worcester, MA, USA. University of Alabama at Birmingham. Birmingham, Al, USA. Biomed, Universidad de Carabobo. Maracay, Venezuela. Biomed, Universidad de Carabobo. Maracay, Venezuela. University of Massachusetts Medical School. Worcester, MA, USA. The Broad Institute of MIT and Harvard. Cambridge, MA, USA. University of Massachusetts Medical School. Worcester, MA, USA. Universidad Central de Venezuela. Caracas, Venezuela / Banco Municipal de Sangre del Distrito Capital. Caracas, Venezuela. University of Massachusetts Medical School. Worcester, MA, USA. Faculdade de Medicina de S?o Jos? do Rio Preto. Departamento de Doen?as Infecciosas e Parasit?rias. Laborat?rio de Pesquisas em Virologia. S?o Jos? do Rio Preto, SP, Brasil. Faculdade de Medicina de S?o Jos? do Rio Preto. Departamento de Doen?as Infecciosas e Parasit?rias. Laborat?rio de Pesquisas em Virologia. S?o Jos? do Rio Preto, SP, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Instituto Nacional de Ci?ncia e Tecnologia para Febres Hemorr?gicas. Ananindeua, PA, Brasil / Universidade Federal de Minas Gerais. Instituto de Ci?ncias Biol?gicas. Departamento de Bioqu?mica e Imunologia. Instituto Nacional de Ci?ncia e Tecnologia em Dengue. Belo Horizonte, MG, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Instituto Nacional de Ci?ncia e Tecnologia para Febres Hemorr?gicas. Ananindeua, PA, Brasil / Universidade Federal de Minas Gerais. Instituto de Ci?ncias Biol?gicas. Departamento de Bioqu?mica e Imunologia. Instituto Nacional de Ci?ncia e Tecnologia em Dengue. Belo Horizonte, MG, Brasil. Centers for Disease Control and Prevention. SanJuan, Puerto Rico, USA. Centers for Disease Control and Prevention. SanJuan, Puerto Rico, USA. Universidad Industrial de Santander. Santander, Colombia. Massachusetts Institute of Technology. Division of Heath Science and Technology. Cambridge, MA, USA. University of Alabama at Birmingham. Birmingham, Al, USA. The Broad Institute of MIT and Harvard. Cambridge, MA, USA. The Broad Institute of MIT and Harvard. Cambridge, MA, USA. University of Massachusetts Medical School. Worcester, MA, USA. Dengue virus currently causes 50?100 million infections annually. Comprehensive knowledge about the evolution of Dengue in response to selection pressure is currently unavailable, but would greatly enhance vaccine design efforts. In the current study, we sequenced 187 new dengue virus serotype 3 (DENV-3) genotype III whole genomes isolated from Asia and the Americas. We analyzed them together with previously-sequenced isolates to gain a more detailed understanding of the evolutionary adaptations existing in this prevalent American serotype. In order to analyze the phylogenetic dynamics of DENV-3 during outbreak periods; we incorporated datasets of 48 and 11 sequences spanning two major outbreaks in Venezuela during 2001 and 2007?2008, respectively. Our phylogenetic analysis of newly sequenced viruses shows that subsets of genomes cluster primarily by geographic location, and secondarily by time of virus isolation. DENV-3 genotype III sequences from Asia are significantly divergent from those from the Americas due to their geographical separation and subsequent speciation. We measured amino acid variation for the E protein by calculating the Shannon entropy at each position between Asian and American genomes. We found a cluster of seven amino acid substitutions having high variability within E protein domain III, which has previously been implicated in serotype-specific neutralization escape mutants. No novel mutations were found in the E protein of sequences isolated during either Venezuelan outbreak. Shannon entropy analysis of the NS5 polymerase mature protein revealed that a G374E mutation, in a region that contributes to interferon resistance in other flaviviruses by interfering with JAK-STAT signaling was present in both the Asian and American sequences from the 2007?2008 Venezuelan outbreak, but was absent in the sequences from the 2001 Venezuelan outbreak. In addition to E, several NS5 amino acid changes were unique to the 2007?2008 epidemic in Venezuela and may give additional insight into the adaptive response of DENV-3 at the population level.