Coding Genome Sequence and Protein Sequence Analysis of Dengue Strains: In Silico Correlation

Hina Awais, Aasia Zahid, Ayesha Afzaal, Talha Mannan, Huma Habib


Background: DENV-1, DENV-2, DENV-3, and DENV-4 are the four serotypes of dengue viruses (DENV) that are transferred from person to person through the bite of Aedes mosquitoes. Dengue fever has surged 30-fold in occurrence over the last 50 years, making it one of the world's most serious arboviral diseases. The aim of this study is to bioinformatically correlate the coding sequences of four DENV strains to check their genetic & functional diversity on the basis of the similarity of the sequences.

Methods: The coding sequences (CDs) and protein sequences of newly reported dengue strains (DENV 1, DENV 2, DENV 3, and DENV 4) were obtained from the National center for Biotechnology Information (NCBI) nucleotide and protein databases. We compare the genetic and functional compatibility of selected gene sequences from four dengue strains by using various bioinformatics tools and software such as BLAST, MEGA 11.0, ProtParam, GOR4 and SWISS Model.

Results: The total number of amino acids in dengue strains DENV1, 2, 3, and 4 is 3392, 3391, 3390, and 3387, according to physiochemical analysis. The phylogenetic analysis reveals that DENV-1 and DENV-2 have more genetic similarity than DENV-2 and DENV-3, with bootstrap values greater than 90%. While different percentages of alpha helices were predicted in secondary structure, such as 33.23 %, 36.51 %, 31.21%, and 32.27% of DENV1, 2, 3, and 4 show little variation. The non-structural proteins NS1 and NS5 of all four DENV strains show more than 65 percent similarity index in 3D structure analysis.

Conclusion: This study first presented a bioinformatics comparison of all four DENV strains. The 3D and 2D structures of DENV strains (1-4) show some similarity and dissimilarity index, however the four DENV strains differ in their 2D structure's alpha helix (H), random coil, and number of amino acids.

Keywords: Bioinformatics; Dengue strains; Non-structural protein; Coding sequence; viral pathogenesis    

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