Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Dec;11(8):2011-9.
doi: 10.1016/j.meegid.2011.09.010. Epub 2011 Sep 23.

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

D J Schmidt  1 , B E Pickett, D Camacho, G Comach, K Xhaja, N J Lennon, K Rizzolo, N de Bosch, A Becerra, M L Nogueira, A Mondini, E V da Silva, P F Vasconcelos, J L Muñoz-Jordán, G A Santiago, R Ocazionez, L Gehrke, E J Lefkowitz, B W Birren, M R Henn, I Bosch
Affiliations

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

D J Schmidt et al. Infect Genet Evol. 2011 Dec.

Abstract

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1. Whole Genome Bayesian Phylogenetic Tree
A Bayesian phylogenetic tree reconstruction of DENV-3 whole genomes isolated from various times and places. Sequence names are color-coded to represent the time of isolation for each virus. The large topological separations correlate with the geographical location where each virus was isolated (indicated by black brackets and text). The smaller topological separations within any geographical clade appear to be dependent on the temporal point of viral isolation. Branch lengths are proportional to distance (the number of nucleotide substitutions per site), and the distance scale for the number of changes is provided at the bottom of the figure.
Figure 2
Figure 2. Histogram of the Shannon Entropy Calculated for the DENV-3 E Protein
A stacked column graph showing the Shannon entropy scores calculated for each amino acid position in the DENV-3 E protein. Subsets of sequences were divided based on time and/or place of isolation as follows: Asian sequences from Thailand in 2001 (Asia 2001), Venezuelan sequences isolated before 2001 (Ven pre-2001), the first Venezuelan DENV-3 outbreak in 2001 (Ven 2001), 2002-2006 (Ven 2002-2006), the second Venezuelan DENV-3 outbreak in 2007-2008 (Ven 2007-2008), all new Venezuelan and Asian sequences characterized in the present study (This Study), and all DENV-3 sequences combined (All DENV-3). The height of each color within each peak represents the Shannon entropy for that sequence set alone at the specified position in the E protein. The height of each peak represents the amount of amino acid variability for each individual position in all sequence sets for the E mature protein. Any column that is conserved in the multiple sequence alignment will not have an entropy score. No consistent amino acid substitutions were found to exist between sequences from the two outbreaks.
Figure 3
Figure 3. Histogram of the Shannon Entropy in the DENV-3 NS5 Protein by Time of Isolation
A stacked column graph showing the Shannon entropy scores calculated for each amino acid position in the DENV-3 NS5 protein. Subsets of sequences were divided based on time and/or place of isolation and include: the Asian sequences isolated from Thailand in 2001 (Asia), and various sequences isolated from Venezuela during the first DENV-3 outbreak in 2001 (Ven 2001), 2002-2006 (Ven 2002-2006), the second DENV-3 outbreak in 2007-2008 (Ven 2007-2008), and all Venezuelan DENV-3 sequences combined (Venezuela All). The NS5 G374E mutation occurred between the 2001 and 2007-2008 outbreaks and has been associated with viral resistance to the host interferon response. The height of each color within each peak represents the Shannon entropy for that sequence set alone at the specified position in the NS5 protein. The height of each peak represents the amount of amino acid variability for each individual position in all sequence sets for the NS5 mature protein. Any column that is conserved in the multiple sequence alignment will not have an entropy score.
Figure 4
Figure 4
Historical dissemination of DENV-3 in the Americas. The genomic associations portrayed in the phylogenetic analysis were plotted over this satellite image of the American continents. Each line connects an immediate ancestor with its succeeding viral isolate. Red pins indicate the countries that originated DENV-3 isolates. The green dashed lines represent transmission in and prior to 1998. Yellow lines represent transmission in and after 1999. According to the temporal and phylogenetic data, DENV-3 was re-introduced in Nicaragua in 1994. There is no evidence showing transmission of the virus until its re-appearance in 1998, where it was isolated in Nicaragua and Puerto Rico. Phylogenetic relationships show that the Nicaraguan strain is ancestral to the Puerto Rican strain but the latter experienced sustained transmission in the island. The Puerto Rican isolates lie basal to the rest of all other DENV-3 viruses isolated after 1998 in the Americas, suggesting that Puerto Rico was the springboard that launched the re-emergence of DENV-3 in the Americas.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Amarilla AA, de Almeida FT, Jorge DM, Alfonso HL, de Castro-Jorge LA, Nogueira NA, Figueiredo LT, Aquino VH. Genetic diversity of the E protein of dengue type 3 virus. Virology journal. 2009;6:113. - PMC - PubMed
    1. Aquino JD, Tang WF, Ishii R, Ono T, Eshita Y, Aono H, Makino Y. Molecular epidemiology of dengue virus serotypes 2 and 3 in Paraguay during 2001-2006: the association of viral clade introductions with shifting serotype dominance. Virus research. 2008;137:266–270. - PubMed
    1. Aquino VH, Amarilla AA, Alfonso HL, Batista WC, Figueiredo LT. New genotype of dengue type 3 virus circulating in Brazil and Colombia showed a close relationship to old Asian viruses. PloS one. 2009;4:e7299. - PMC - PubMed
    1. Aquino VH, Anatriello E, Goncalves PF, EV DAS, Vasconcelos PF, Vieira DS, Batista WC, Bobadilla ML, Vazquez C, Moran M, Figueiredo LT. Molecular epidemiology of dengue type 3 virus in Brazil and Paraguay, 2002-2004. The American journal of tropical medicine and hygiene. 2006;75:710–715. - PubMed
    1. Araujo JM, Bello G, Schatzmayr HG, Santos FB, Nogueira RM. Dengue virus type 3 in Brazil: a phylogenetic perspective. Memorias do Instituto Oswaldo Cruz. 2009a;104:526–529. - PubMed

Publication types