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. 2012 Jun 20:9:124.
doi: 10.1186/1743-422X-9-124.

Phylogenetic relationship of dengue virus type 3 isolated in Brazil and Paraguay and global evolutionary divergence dynamics

Helda Liz Alfonso  1 , Alberto Anastacio Amarilla, Paula Fernanda Gonçalves, Matheus Takatuba Barros, Flavia Tremeschin de Almeida, Telma R Silva, Eliana V da Silva, Marcio T Nunes, Pedro F C Vasconcelos, Deusilene S Vieira, Weber Cheli Batista, Maria Liz Bobadilla, Cynthia Vazquez, Mirian Moran, Luiz Tadeu Moraes Figueiredo, Victor Hugo Aquino
Affiliations

Phylogenetic relationship of dengue virus type 3 isolated in Brazil and Paraguay and global evolutionary divergence dynamics

Helda Liz Alfonso et al. Virol J. .

Abstract

Background: Dengue is the most important mosquito-borne viral disease worldwide. Dengue virus comprises four antigenically related viruses named dengue virus type 1 to 4 (DENV1-4). DENV-3 was re-introduced into the Americas in 1994 causing outbreaks in Nicaragua and Panama. DENV-3 was introduced in Brazil in 2000 and then spread to most of the Brazilian States, reaching the neighboring country, Paraguay in 2002. In this study, we have analyzed the phylogenetic relationship of DENV-3 isolated in Brazil and Paraguay with viruses isolated worldwide. We have also analyzed the evolutionary divergence dynamics of DENV-3 viruses.

Results: The entire open reading frame (ORF) of thirteen DENV-3 isolated in Brazil (n = 9) and Paraguay (n = 4) were sequenced for phylogenetic analysis. DENV-3 grouped into three main genotypes (I, II and III). Several internal clades were found within each genotype that we called lineage and sub-lineage. Viruses included in this study belong to genotype III and grouped together with viruses isolated in the Americas within the lineage III. The Brazilian viruses were further segregated into two different sub-lineage, A and B, and the Paraguayan into the sub-lineage B. All three genotypes showed internal grouping. The nucleotide divergence was in average 6.7% for genotypes, 2.7% for lineages and 1.5% for sub-lineages. Phylogenetic trees constructed with any of the protein gene sequences showed the same segregation of the DENV-3 in three genotypes.

Conclusion: Our results showed that two groups of DENV-3 genotypes III circulated in Brazil during 2002-2009, suggesting different events of introduction of the virus through different regions of the country. In Paraguay, only one group DENV-3 genotype III is circulating that is very closely related to the Brazilian viruses of sub-lineage B. Different degree of grouping can be observed for DENV-3 and each group showed a characteristic evolutionary divergence. Finally, we have observed that any protein gene sequence can be used to identify the virus genotype.

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Figures

Figure 1
Figure 1
Neighbor-joining phylogenetic trees based on the entire ORFs derived from 542 global samples of the DENV-3 inferred with PAUP program. The bootstrap are indicated at important nodes. The best-fit model of nucleotide substitution for phylogenetic reconstruction used was TrN + I + G model with gamma-distributed rate variation (G = 0.9908) and a proportion of invariable sites (I = 0.3678). Branch lengths are proportional to percentage of divergence.
Figure 2
Figure 2
Bayesian phylogenetic trees based on the entire ORFs derived from 347 global samples of the genotype III DENV-3 inferred with MrBayes program. The posterior probabilities are expressed in percent and indicated at important nodes. The best fit-model of nucleotide substitution for Bayesian phylogenetic reconstruction used was under a General Time Reversible model with gamma-distributed rate variation (G = 1.2923) and a proportion of invariable sites (I = 0.4777) (GTR + G + I).
Figure 3
Figure 3
The frequency distribution profile of pairwise distances among sequences of genotype III, based on the entire ORFs derived from 347 global samples of the genotype III DENV-3. A ). The frequency distribution profile distance of nucleotide (NT). B) The frequency distribution profile distance of amino acids (AA). The NT and AA p-distance are represented on the X axis and the frequency are represented on the Y axis.
Figure 4
Figure 4
Bayesian phylogenetic trees based on the entire ORFs derived from 53 global samples of the genotype I DENV-3 inferred with MrBayes program. The posterior probabilities are expressed in percent and indicated at important nodes. The best fit-model of nucleotide substitution for Bayesian phylogenetic reconstruction used was under a General Time Reversible model with gamma-distributed rate variation (G = 1.1436) and a proportion of invariable sites (I = 0.4716) (GTR + G + I).
Figure 5
Figure 5
Distribution of NT (A) and AA (B) p-distances between 53 complete ORF sequences of genotype I. NT: nucleotides; AA: amino acids.
Figure 6
Figure 6
Bayesian phylogenetic trees based on the entire ORFs derived from 137 global samples of the genotype II DENV-3 inferred with MrBayes program. The posterior probabilities are expressed in percent and indicated at important nodes. The best fit-model of nucleotide substitution for Bayesian phylogenetic reconstruction used was under a General Time Reversible model with gamma-distributed rate variation (G = 1.4745) and a proportion of invariable sites (I = 0.4956) (GTR + G + I). Branch lengths are proportional to percentage of divergence.
Figure 7
Figure 7
Distribution of NT (A) and AA (B) p-distances between 137 complete ORF sequences of genotype II. NT: nucleotides; AA: amino acids.
Figure 8
Figure 8
Distribution of NT (A) and AA (B) p-distances between different genotypes based on the entire ORF of 537 DENV-3. NT: nucleotides; AA: amino acids.
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