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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Durrani M, Aslamkhan M, Babar Alam M, Akhtar M, Hanif A. Transmission and epidemic of dengue and its abatement in islamabad capital territory. Pakistan. Journal of Innovative Sciences, (2016); 2(2):21-36.

Naeem S, Pari A, Gulzar N, Yousaf S, Akhtar MS. Mortality rate of patients with dengue hemorrhagic fever. Pakistan Journal of Medical & Health Sciences, (2018); 12(1):337-339.

Ross TM. Dengue virus. Clinics in Laboratory Medicine,(2010); 30(1):149-160.

Long SS, Prober CG, Fischer M. Chapter 2. Principles and practice of pediatric infectious diseases e-book. 2022 of Publication year; Elsevier Health Sciences.

Cheng NM, Sy CL, Chen BC, Huang TS, Lee SSJ, et al. Isolation of dengue virus from the upper respiratory tract of four patients with dengue fever. PLoS Neglected Tropical Diseases, (2017); 11(4): 1-10.

Kalayanarooj S. Clinical manifestations and management of dengue/dhf/dss. Tropical Medicine and Health, (2011); 39(4): 83-87.

Rajapakse S. Dengue shock. Journal of Emergencies, Trauma and Shock, (2011); 4(1):120-127.

Islam MT, Quispe C, Herrera BJ, Sarkar C, Sharma R, et al. Production, transmission, pathogenesis, and control of dengue virus: A literature-based undivided perspective. BioMed Research International,(2021); 10(4): 1-23.

Tamura T, Zhang J, Madan V, Biswas A, Schwoerer MP, et al. Generation and characterization of genetically and antigenically diverse infectious clones of dengue virus serotypes 1-4. Emerging Microbes & Infections, (2022); 11(1): 227-239.

Guzman MG, Halstead SB, Artsob H, Buchy P, Farrar J, et al. Dengue: A continuing global threat. Nature Reviews Microbiology, (2010); 8(12):7-16.

Haider A, Ullah F, Bilal M, Saif Z, Awais H, et al. Clinical correlation of dengue strains on the basis of seroprevalence in a tertiary care hospital. Pakistan BioMedical Journal, (2022); 5 (4): 149-153.

Bhatt P, Sabeena SP, Varma M, Arunkumar G. Current understanding of the pathogenesis of dengue virus infection. Current Microbiology, (2021); 78(1):17-32.

Sasmono RT, Kalalo LP, Trismiasih S, Denis D, Yohan B, et al. Hayati RF, Haryanto S. Multiple introductions of dengue virus strains contribute to dengue outbreaks in east kalimantan, Indonesia, in 2015–2016. Virology Journal, (2019); 16(1):1-15.

Sayers EW, Beck J, Bolton EE, Bourexis D, Brister JR, et al. Database resources of the national center for biotechnology information. Nucleic Acids Research, (2021); 49(1):10-17.

Tamura K, Dudley J, Nei M, Kumar S. Mega4: Molecular evolutionary genetics analysis (mega) software version 4.0. Molecular biology and evolution, (2007); 24(8):1596-1599.

Thompson JD, Higgins DG, Gibson TJ. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research, (1994); 22(22):4673-4680.

Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular biology and evolution, (1987); 4(4):406-425.

Newman L, Duffus ALJ, Lee C. Using the free program mega to build phylogenetic trees from molecular data. The American Biology Teacher, (2016); 78(7):608-612.

Rombel IT, Sykes KF, Rayner S, Johnston SA. Orf-finder: A vector for high-throughput gene identification. Gene, (2002); 282(1-2):33-41.

Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, et al. Expasy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, (2003); 31(13):3784-3788.

Kouza M, Faraggi E, Kolinski A, Kloczkowski A. The GOR method of protein secondary structure prediction and its application as a protein aggregation prediction tool. Prediction of protein secondary structure, (2017); 148(4): 7-24.

Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, et al. Swiss-model: Homology modelling of protein structures and complexes. Nucleic Acids Research, (2018); 46(1):296-303.

Dang TT, Pham MH, Bui HV, Van Le D. Whole genome sequencing and genetic variations in several dengue virus type 1 strains from unusual dengue epidemic of 2017 in Vietnam. Virology journal, (2020); 17(1):1-10.

King CC, Chao DY, Chien LJ, Chang GJJ, Lin TH, et al. Comparative analysis of full genomic sequences among different genotypes of dengue virus type 3. Virology journal, (2018); 5(63):1-13.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, et al. Database resources of the national center for biotechnology information. Nucleic Acids Research, (2005); 33(1):39-45.

Dang TT, Pham MH, Bui HV, Van Le D. First full-length genome sequence of dengue virus serotype 2 circulating in Vietnam in 2017. Infection and Drug Resistance, (2020); 13 (10):4061-4068.

Baronti C, Piorkowski G, Touret F, Charrel R, Lamballerie X, et al. Complete coding sequences of two dengue virus type 2 strains isolated from an outbreak in Burkina Faso in 2016. Genome Announcements, (2017); 5(17):209-217.

Huang JH, Su CL, Yang CF, Liao TL, Hsu TC, et al. Molecular characterization and phylogenetic analysis of dengue viruses imported into Taiwan during 2008–2010. The American Journal of Tropical Medicine and Hygiene, 2012; 87(2):349.

Awais H, Mushtaq Z, Sarwar S, Jamil A. 2018. Sequence analysis of HMG-CoA synthase like gene from Brassica rapa. Cloning & Transgenesis, (2018); 7 (1): 1-7.

Ali M, Pandey RK, Khatoon N, Narula A, Mishra A, et al. Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing Immuno-informatics

approach to battle against dengue infection. Scientific Reports, (2017); 7(1):1-13.

Garrepelly JP, Kiranmayi P, Bandari T, Erva RR. Molecular approach towards screening of biological targets of berberine and its production sources. Current Trends in Biotechnology and Pharmacy, (2021); 15(2):141-152.

Paul A, Vibhuti A, Raj S, Shaw J. Homology modelling of ns4b protein of dengue using SWISS-PDB viewer. Indian Journal of Pharmaceutical Science & Research, (2015); 5 (4):205-211.


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