Westaway EG, Brinton MA, Gaidamovich SYA, Horzinek MC, Igarashi A, Kääriäinen L, et al. Flaviviridae. Intervirology. 1985;24(4):183–92.
Guzman MG, Halstead SB, Artsob H, Buchy P, Farrar J, Gubler DJ, et al. Dengue: a continuing global threat. Nat Rev Microbiol. 2010;8(12 Suppl):S7–16.
CAS
PubMed
PubMed Central
Google Scholar
WHO. Dengue and severe dengue [Internet]. World Health Organization. 2019 [cited 2019 April 24]. Available from: http://www.who.int/en/news-room/fact-sheets/detail/dengue-and-severe-dengue.
Mackenzie JS, Gubler DJ, Petersen LR. Emerging flaviviruses: the spread and resurgence of japanese encephalitis, west nile and dengue viruses. Nat Med. 2004;10(12 Suppl):S98–109.
CAS
PubMed
Google Scholar
Faustino AF, Martins IC, Carvalho FA, Castanho MARB, Maurer-Stroh S, Santos NC. Understanding dengue virus capsid protein interaction with key biological targets. Sci Rep. 2015;5:10592.
PubMed
PubMed Central
Google Scholar
Chambers T, Hahn C, Galler R, Rice C. Flavivirus genome organization, expression, and replication. Annu Rev Microbiol. 1990;44:649–88.
CAS
PubMed
Google Scholar
Steinhauer DA, Domingo E, Holland JJ. Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase. Gene. 1992;122(2):281–8.
CAS
PubMed
Google Scholar
Grande-pérez A, Garcia-arriaza J. Viruses as quasispecies: Biological implications article in current topics in microbiology and immunology · February 2006. 2006; 299: 51–82.
Weaver SC, Vasilakis N. Molecular evolution of dengue viruses: contributions of phylogenetics to understanding the history and epidemiology of the preeminent arboviral disease. Infect Genet Evol. 2009;9(4):523–40.
CAS
PubMed
PubMed Central
Google Scholar
Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nat. 2013;496(7446):504–7.
CAS
Google Scholar
Mustafa MS, Rasotgi V, Jain S, Gupta V. Discovery of fifth serotype of dengue virus (denv-5): a new public health dilemma in dengue control. Med J Armed Forces India. 2015;71:67–70.
CAS
PubMed
Google Scholar
Holmes EC, Twiddy SS. The origin, emergence and evolutionary genetics of dengue virus. Infect Genet Evol. 2003;3(1):19–28.
PubMed
Google Scholar
Green S, Rothman A. Immunopathological mechanisms in dengue and dengue hemorrhagic fever. Curr Opin Infect Dis. 2006;19(5):429–36.
PubMed
Google Scholar
Khan AM, Heiny AT, Lee KX, Srinivasan KN, Tan TW, August JT, et al. Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus. BMC Bioinform. 2006;7(Suppl 5):S4.
Google Scholar
Domingo E, Sheldon J, Perales C. Viral quasispecies evolution. Microbiol Mol Biol Rev. 2012;76(2):159–216.
CAS
PubMed
PubMed Central
Google Scholar
Behura SK, Severson DW. Nucleotide substitutions in dengue virus serotypes from Asian and American countries: insights into intracodon recombination and purifying selection. BMC Microbiol. 2013;13:37.
PubMed
PubMed Central
Google Scholar
Kurosu T. Quasispecies of dengue virus. Trop Med Health. 2011;39(4 Suppl):29–36.
PubMed
PubMed Central
Google Scholar
Soo KM, Khalid B, Ching SM, Chee HY. Meta-analysis of dengue severity during infection by different dengue virus serotypes in primary and secondary infections. PLoS One. 2016;11(5):e154760.
Google Scholar
Duan ZL, Liu HF, Huang X, Wang SN, Yang JL, Chen XY, et al. Identification of conserved and HLA-A*2402-restricted epitopes in dengue virus serotype 2. Virus Res. 2015;196:5–12.
CAS
PubMed
Google Scholar
Sant AJ, McMichael A. Revealing the role of CD4+ T cells in viral immunity. J Exp Med. 2012;209(8):1391–5.
CAS
PubMed
PubMed Central
Google Scholar
Rivino L, Lim MQ. CD4+ and CD8+ T-cell immunity to dengue – lessons for the study of Zika virus. Immunol. 2017;150(2):146–54.
CAS
Google Scholar
Weiskopf D, Sette A. T-cell immunity to infection with dengue virus in humans. Front Immunol. 2014;5:93.
PubMed
PubMed Central
Google Scholar
Weiskopf D, Angelo MA, de Azeredo EL, Sidney J, Greenbaum JA, Fernando AN, et al. Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells. Proc Natl Acad Sci U S A. 2013;110(22):E2046–53.
CAS
PubMed
PubMed Central
Google Scholar
Wahala WMPB, de Silva AM. The human antibody response to dengue virus infection. Viruses. 2011;3(12):2374–95.
CAS
PubMed
PubMed Central
Google Scholar
Sanchez-Trincado JL, Gomez-Perosanz M, Reche PA. Fundamentals and methods for T- and B-cell epitope prediction. J Immunol Res. 2017;2680160.
Kalergis AM, Nathenson SG. Altered peptide ligand-mediated TCR antagonism can be modulated by a change in a single amino acid residue within the CDR3 of an MHC class I-restricted TCR. J Immunol. 2000;165(1):280–5.
CAS
PubMed
Google Scholar
Evavold BD, Sloan-Lancaster J, Allen PM. Tickling the TCR: selective T-cell functions stimulated by altered peptide ligands. Immunol Today. 1993;14(12):602–9.
CAS
PubMed
Google Scholar
Madrenas J, Germain RN. Variant TCR ligands: new insights into the molecular basis of antigen-dependent signal transduction and T-cell activation. Semin Immunol. 1996;8(2):83–101.
CAS
PubMed
Google Scholar
Sloan-Lancaster J, Allen PM. Altered peptide ligand-induced partial T cell activation: molecular mechanisms and role in T cell biology. Annu Rev Immunol. 1996;14:1–27.
CAS
PubMed
Google Scholar
Nishimura Y, Chen YZ, Uemura Y, Tanaka Y, Tsukamoto H, Kanai T, et al. Degenerate recognition and response of human CD4+ Th cell clones: implications for basic and applied immunology. Mol Immunol. 2004;40(14–15):1089–94.
CAS
PubMed
Google Scholar
Rothman AL. Dengue: defining protective versus pathologic immunity. J Clin Investig. 2004;113(7):946–51.
CAS
PubMed
PubMed Central
Google Scholar
Loke H, Bethell DB, Phuong CXT, Dung M, Schneider J, White NJ, et al. Strong HLA class I–restricted T cell responses in dengue hemorrhagic fever: a double-edged sword? J Infect Dis. 2002;184(11):1369–73.
Google Scholar
Mongkolsapaya J, Dejnirattisai W, Xu XN, Vasanawathana S, Tangthawornchaikul N, Chairunsri A, et al. Original antigenic sin and apoptosis in the pathogenesis of dengue hemorrhagic fever. Nat Med. 2003;9(7):921–7.
CAS
PubMed
Google Scholar
Mongkolsapaya J, Duangchinda T, Dejnirattisai W, Vasanawathana S, Avirutnan P, Jairungsri A, et al. T cell responses in dengue hemorrhagic fever: are cross-reactive T cells suboptimal? J Immunol. 2014;176(6):3821–9.
Google Scholar
Khan AM, Miotto O, Nascimento EJM, Srinivasan KN, Heiny AT, Zhang GL, et al. Conservation and variability of dengue virus proteins: implications for vaccine design. PLoS Negl Trop Dis. 2008;2(8):e272.
PubMed
PubMed Central
Google Scholar
Mangada MM, Rothman AL. Altered cytokine responses of dengue-specific CD4+ T cells to heterologous serotypes. J Immunol. 2014;175(4):2676–83.
Google Scholar
Khan AM. Mapping targets of immune responses in complete dengue viral genomes. National University of Singapore: Master's Thesis; 2005.
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. NCBI BLAST: A better web interface. Nucleic Acids Res. 2008;36(Web Server issue):W5–9.
CAS
PubMed
PubMed Central
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinform. 2009;10:421.
Google Scholar
Consortium TU. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019;47(D1):D506–15.
Google Scholar
Bateman A, Martin MJ, O’Donovan C, Magrane M, Alpi E, Antunes R, et al. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017;45(Database issue):D158–69.
CAS
Google Scholar
Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30(14):3059–66.
CAS
PubMed
PubMed Central
Google Scholar
Hall TA. BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/ NT. Nucleic Acids Symp Ser. 1999;41:95–8.
CAS
Google Scholar
Hall TA. BioEdit: an important software for molecular biology software review. GERF Bull Biosci. 2011;2(1):60–1.
Google Scholar
Shannon CE. A mathematical theory of communication. Bell Syst Tech J 1948; 27: 379–423, 623-56.
Miotto O, Heiny AT, Tan TW, August JT, Brusic V. Identification of human-to-human transmissibility factors in PB2 proteins of influenza a by large-scale mutual information analysis. BMC Bioinform. 2008;9(Suppl 1):S18.
Google Scholar
Miotto O, Heiny AT, Albrecht R, García-Sastre A, Tan TW, August JT, et al. Complete-proteome mapping of human influenza a adaptive mutations: implications for human transmissibility of zoonotic strains. PLoS One. 2010;5(2):e9025.
PubMed
PubMed Central
Google Scholar
Paninski L. Estimation of entropy and mutual information. Neural Comput. 2003;15:1191–253.
Google Scholar
Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, et al. CDD: a conserved domain database for protein classification. Nucleic Acids Res. 2005;33(Database issue):D192–6.
CAS
PubMed
Google Scholar
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42(Database issue):D222–30.
CAS
PubMed
Google Scholar
de Castro E, Sigrist CJA, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, et al. ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res. 2006;34(Web Server issue):W362–5.
PubMed
PubMed Central
Google Scholar
Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, et al. Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunol. 2018;154(3):394–406.
CAS
Google Scholar
Stranzl T, Larsen MV, Lundegaard C, Nielsen M. NetCTLpan: pan-specific MHC class I pathway epitope predictions. Immunogenet. 2010;62(6):357–68.
CAS
Google Scholar
Del Guercio MF, Sidney J, Hermanson G, Perez C, Grey HM, Kubo RT, et al. Binding of a peptide antigen to multiple HLA alleles allows definition of an A2-like supertype. J Immunol. 1995;154(2):685–93.
PubMed
Google Scholar
Kangueane P. HLA supertypes. In: bioinformation discovery. New York: Springer; 2009.
Google Scholar
Zhao W, Sher X. Systematically benchmarking peptide-MHC binding predictors: from synthetic to naturally processed epitopes. PLoS Comput Biol. 2018;14(11):e1006457.
PubMed
PubMed Central
Google Scholar
Andreatta M, Trolle T, Yan Z, Greenbaum JA, Peters B, Nielsen M. An automated benchmarking platform for MHC class II binding prediction methods. Bioinform. 2018;34(9):1522–8.
CAS
Google Scholar
Sette A, Sidney J. Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenet. 1999;50(3–4):201–12.
CAS
Google Scholar
Sidney J, Peters B, Frahm N, Brander C, Sette A. HLA class I supertypes: a revised and updated classification. BMC Immunol. 2008;9:1.
PubMed
PubMed Central
Google Scholar
Southwood S, Sidney J, Kondo A, del Guercio MF, Appella E, Hoffman S, et al. Several common HLA-DR types share largely overlapping peptide binding repertoires. J Immunol. 1998;160(7):3363–73.
CAS
PubMed
Google Scholar
Greenbaum J, Sidney J, Chung J, Brander C, Peters B, Sette A. Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes. Immunogenet. 2011;63(6):325–35.
CAS
Google Scholar
Chicz RM, Urban RG, Lane WS, Gorga JC, Stern LJ, Vignali DAA, et al. Predominant naturally processed peptides bound to HLA-DR1 are derived from MHC-related molecules and are heterogeneous in size. Nat. 1992;358(6389):764–8.
CAS
Google Scholar
Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, et al. The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 2015;43(Database issue):D405–12.
CAS
PubMed
Google Scholar
Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, et al. The ClusPro web server for protein-protein docking. Nat Protoc. 2017;12(2):255–78.
CAS
PubMed
PubMed Central
Google Scholar
Porter KA, Xia B, Beglov D, Bohnuud T, Alam N, Schueler-Furman O, et al. ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT. Bioinformatics. 2017;33(20):3299–301.
CAS
PubMed
PubMed Central
Google Scholar
Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, et al. How good is automated protein docking? Proteins Struct Funct Bioinforma. 2013;81(12):2159–66.
CAS
Google Scholar
Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, et al. The protein data bank. Acta Crystallogr Sect D Biol Crystallogr. 2002;28(1):235–42.
Google Scholar
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018;46(W1):W296–303.
CAS
PubMed
PubMed Central
Google Scholar
Gagnon SJ, Borbulevych OY, Davis-Harrison RL, Turner RV, Damirjian M, Wojnarowicz A, et al. T cell receptor recognition via cooperative conformational plasticity. J Mol Biol. 2006;363(1):228–43.
CAS
PubMed
Google Scholar
Tian H, Sun Z, Faria NR, Yang J, Cazelles B, Huang S, et al. Increasing airline travel may facilitate co-circulation of multiple dengue virus serotypes in Asia. PLoS Negl Trop Dis. 2017;11(8):e0005694.
PubMed
PubMed Central
Google Scholar
Yusuf M, Konc J, Choi SB, Trykowska Konc J, Ahmad Khairudin NB, Janezic D, et al. Structurally conserved binding sites of hemagglutinin as targets for influenza drug and vaccine development. J Chem Inf Model. 2013;53(9):2423–36.
CAS
PubMed
Google Scholar
Heiny AT, Miotto O, Srinivasan KN, Khan AM, Zhang GL, Brusic V, et al. Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets. PLoS One. 2007;2(11):e1190.
CAS
PubMed
PubMed Central
Google Scholar
Koo QY, Khan AM, Jung K-OO, Ramdas S, Miotto O, Tan TW, et al. Conservation and variability of West Nile virus proteins. PLoS One. 2009;4:e5352.
PubMed
PubMed Central
Google Scholar
Hu Y, Tan PTJ, Tan TW, August JT, Khan AM. Dissecting the dynamics of HIV-1 protein sequence diversity. PLoS One. 2013;8(4):e59994.
CAS
PubMed
PubMed Central
Google Scholar
Rajão DS, Pérez DR. Universal vaccines and vaccine platforms to protect against influenza viruses in humans and agriculture. Front Microbiol. 2018;9:123.
PubMed
PubMed Central
Google Scholar
Jung K-O, Khan AM, Tan BYL, Hu Y, Simon GG, Nascimento EJM, et al. West nile virus T-cell ligand sequences shared with other flaviviruses: a multitude of variant sequences as potential altered peptide ligands. J Virol. 2012;86(14):7616–24.
CAS
PubMed
PubMed Central
Google Scholar
Chong LC, Khan AM. Vaccine target discovery. Encycl Bioinforma Comput Biol. 2018;3:241–51.
Google Scholar
Venkatachalam R, Subramaniyan V. Homology and conservation of amino acids in E-protein sequences of dengue serotypes. Asian Pacific J Trop Dis. 2014;4(Suppl 2):S573–7.
CAS
Google Scholar
Tay MYF, Smith K, Ng IHW, Chan KWK, Zhao Y, Ooi EE, et al. The C-terminal 18 amino acid region of dengue virus NS5 regulates its subcellular localization and contains a conserved arginine residue essential for infectious virus production. PLoS Pathog. 2016;12(9):e1005886.
PubMed
PubMed Central
Google Scholar
Dong H, Fink K, Züst R, Lim SP, Qin CF, Shi PY. Flavivirus RNA methylation. J Gen Virol. 2014;95(Pt 4):763–78.
CAS
PubMed
Google Scholar
Kapoor M, Zhang L, Ramachandra M, Kusukawa J, Ebner KE, Padmanabhan R. Association between NS3 and NS5 proteins of dengue virus type 2 in the putative RNA replicase is linked to differential phosphorylation of NS5. J Biol Chem. 1995;270(32):19100–6.
CAS
PubMed
Google Scholar
Tian Y, Chen W, Yang Y, Xu X, Zhang J, Wang J, et al. Identification of B cell epitopes of dengue virus 2 NS3 protein by monoclonal antibody. Appl Microbiol Biotechnol. 2013;97(4):1553–60.
CAS
PubMed
Google Scholar
Wu J, Bera AK, Kuhn RJ, Smith JL. Structure of the flavivirus helicase: implications for catalytic activity, protein interactions, and Proteolytic processing. J Virol. 2005;79(16):10268–77.
CAS
PubMed
PubMed Central
Google Scholar
Fleith RC, Lobo FP, Dos Santos PF, Rocha MM, Bordignon J, Strottmann DM, et al. Genome-wide analyses reveal a highly conserved dengue virus envelope peptide which is critical for virus viability and antigenic in humans. Sci Rep. 2016;6:36339.
CAS
PubMed
PubMed Central
Google Scholar
Poggianella M, Campos JLS, Chan KR, Tan HC, Bestagno M, Ooi EE, et al. Dengue e protein domain iii-based dna immunisation induces strong antibody responses to all four viral serotypes. PLoS Negl Trop Dis. 2015;9(7):e0003947.
PubMed
PubMed Central
Google Scholar
Zhang X, Jia R, Shen H, Wang M, Yin Z, Cheng A. Structures and functions of the envelope glycoprotein in flavivirus infections. Viruses. 2017;9(11):338.
PubMed Central
Google Scholar
Lim WC, Khan AM. Mapping HLA-A2, −A3 and -B7 supertype-restricted T-cell epitopes in the ebolavirus proteome. 2018;19(Suppl 1):17–29.
Wilson CC, McKinney D, Anders M, MaWhinney S, Forster J, Crimi C, et al. Development of a DNA vaccine designed to induce cytotoxic T lymphocyte responses to multiple conserved epitopes in HIV-1. J Immunol. 2014;171(10):5611–23.
Google Scholar
Gagnon SJ, Zeng W, Kurane I, Ennis FA. Identification of two epitopes on the dengue 4 virus capsid protein recognized by a serotype-specific and a panel of serotype-cross-reactive human CD4+ cytotoxic T-lymphocyte clones. J Virol. 1996;70(1):141–7.
CAS
PubMed
PubMed Central
Google Scholar
Weiskopf D, Cerpas C, Angelo MA, Bangs DJ, Sidney J, Paul S, et al. Human CD8+ T-cell responses against the 4 dengue virus serotypes are associated with distinct patterns of protein targets. J Infect Dis. 2015;212(11):1743–51.
PubMed
PubMed Central
Google Scholar
Weiskopf D, Angelo MA, Bangs DJ, Sidney J, Paul S, Peters B, et al. The human CD8 + T cell responses induced by a live attenuated tetravalent dengue vaccine are directed against highly conserved epitopes. J Virol. 2014;89(1):120–8.
PubMed
PubMed Central
Google Scholar
de Alwis R, Smith SA, Olivarez NP, Messer WB, Huynh JP, Wahala WMPB, et al. Identification of human neutralizing antibodies that bind to complex epitopes on dengue virions. Proc Natl Acad Sci. 2012;109(19):7439–44.
PubMed
PubMed Central
Google Scholar
Swanstrom JA, Nivarthi UK, Patel B, Delacruz MJ, Yount B, Widman DG, et al. Beyond neutralizing antibody levels: the epitope specificity of antibodies induced by National Institutes of Health monovalent dengue virus vaccines. J Infect Dis. 2019;220(2):219–27.
CAS
PubMed
PubMed Central
Google Scholar
Whitehead SS, Blaney JE, Durbin AP, Murphy BR. Prospects for a dengue virus vaccine. Nat Rev Microbiol. 2007;5(7):518–28.
CAS
PubMed
Google Scholar
Khan AM, Miotto O, Heiny AT, Salmon J, Srinivasan KN, Nascimento EJM, et al. A systematic bioinformatics approach for selection of epitope-based vaccine targets. Cell Immunol. 2006;244(2):141–7.
CAS
PubMed
Google Scholar