Genetic diversity of the E protein of dengue type 3 virus

Abstract

Background: Dengue is the most important arbovirus disease in tropical and subtropical countries. The viral envelope (E) protein is responsible for cell receptor binding and is the main target of neutralizing antibodies. The aim of this study was to analyze the diversity of the E protein gene of DENV-3. E protein gene sequences of 20 new viruses isolated in Ribeirao Preto, Brazil, and 427 sequences retrieved from GenBank were aligned for diversity and phylogenetic analysis.

Results: Comparison of the E protein gene sequences revealed the presence of 47 variable sites distributed in the protein; most of those amino acids changes are located on the viral surface. The phylogenetic analysis showed the distribution of DENV-3 in four genotypes. Genotypes I, II and III revealed internal groups that we have called lineages and sub-lineages. All amino acids that characterize a group (genotype, lineage, or sub-lineage) are located in the 47 variable sites of the E protein.

Conclusion: Our results provide information about the most frequent amino acid changes and diversity of the E protein of DENV-3.

Figure 1

DENV-3 phylogenetic tree based on the E gene sequences. The three was constructed using the method of Neighbor-joining with 1000 bootstrap replications. The genotypes are labeled according to the scheme of Lanciotti (1994) and the amino acid changes distinguishing each genotype are shown on the tree. Protein E gene sequences of DENV-1, DENV-2 and DENV-4 were used as outgroup. Branch lengths are proportional to percentage of divergence. Tamura Nei (TrN+I+G) nucleotide substitution model was used with a proportion of invariable sites (I) of 0.3305 and gamma distribution (G) of 0.9911. Bootstrap support values are shown for key nodes only.

Figure 2

Genotype I phylogenetic tree constructed using the method of Neighbor-joining with 1000 bootstrap replications. Sequences of each genotype II, III and IV were used as outgroup. Branch lengths are proportional to percentage divergence. Tamura Nei (TrN+I+G) nucleotide substitution model was used with a proportion of invariable sites (I) of 0.5420 and gamma distribution (G) of 2.6122. The lineage and sub-lineages are marked. Amino acids changes are indicated on the tree. Bootstrap support values are shown for key nodes only.

Figure 3

Genotype II phylogenetic tree constructed using the method of Neighbor-joining with 1000 bootstrap replications. Sequences of each genotype I, III and IV were used as outgroup. Branch lengths are proportional to percentage divergence. Tamura Nei (TrN+I+G) nucleotide substitution model was used with a proportion of invariable sites (I) of 0.5041 and gamma distribution (G) of 1.3902. The lineage and sub-lineages are marked. Amino acids changes are indicated on the tree. Bootstrap support values are shown for key nodes only.

Figure 4

Genotype III phylogenetic tree constructed using the method of Neighbor-joining with 1000 bootstrap replications. Some viruses of each genotype I, II and IV were used as outgroup. Branch lengths are proportional to percentage divergence. Tamura Nei (TrN+G) nucleotide substitution model was used with gamma distribution (G) of 0.2796. The Lineage and Sub-lineages are marked. Amino acids changes are indicated on the tree. Bootstrap support values are shown for key nodes only.