Nucleotide sequence and deduced amino acid sequence of the nonstructural proteins of dengue type 3 virus, Bangkok genotype

Abstract

The nucleotide sequence of the nonstructural protein gene (1,610 bases) of dengue 3 virus (Bangkok genotype ; CH53489 isolated in 1973) has been determined in both forward and reverse directions. The PCR based cycle sequencing technic by the enzymatic method of Sanger et al using a sequencing primer 5'-end labeled with γ-32p-ATP was the method of our choice for sequence analysis. Two cDNA templates were prepared by RT-PCR technic starting from the nucleotides 6,306 - 6,969 and 6,925 - 7,915 of the dengue 3 genome with the lengths of 663 and 990 base pairs respectively. In our cycle sequencing experiments, it has been observed that the substitution of 7 - deaza- dG for dG in DNA eliminated most of the secondary structures that produce gel artifacts. The final sequence results of these two cDNA templates were established from their sequence data determined on both strands in opposite directions. Alignment between the newly established nucleotide sequences as well as their deduced amino acid sequences of the Bangkok dengue 3 (CH53489) virus and the published sequence data of the dengue 3 prototype (H87) was manipulated by the PC-DOS-GIBIO DNASIS TM 06-00 software. The homology of the nucleotide sequences between the two dengue 3 viruses was 96.65%. The deduced amino acid sequence from nucleotides 6,306-7,915 of the two viruses showed conserved amino acids of the nonstructural protein NS4a and 6 amino acid changes in NS4b and NS5.