References

Abelin,J.G. et al. (2019) Defining HLA-II ligand processing and binding rules with mass spectrometry enhances cancer epitope prediction. Immunity, 51, 766–779.e17.
Abelin,J.G. et al. (2017) Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction. Immunity, 46, 315–326.
Agrawal,B. (2019) Heterologous immunity: role in natural and vaccine-induced resistance to infections. Frontiers in Immunology, 10, 1–11.
Ahmed,S.F. et al. (2020a) COVIDep: a web-based platform for real-time reporting of vaccine target recommendations for SARS-CoV-2. Nature Protocols, 15, 2141–2142.
Ahmed,S.F. et al. (2020b) Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies. Viruses, 12, 254.
Ahmed,S.F. et al. (2019) Sub-dominant principal components inform new vaccine targets for HIV gag. Bioinformatics, 35, 3884–3889.
Allen,T.M. et al. (2005) Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution. Journal of Virology, 79, 13239–49.
Alwis,R. de et al. (2016) Immunodominant dengue virus-specific CD8+ T cell responses are associated with a memory PD-1+ phenotype. Journal of Virology, 90, 4771–4779.
Andreatta,M. et al. (2015) Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification. Immunogenetics, 67, 641–650.
Andreatta,M. and Nielsen,M. (2016) Gapped sequence alignment using artificial neural networks: application to the MHC class I system. Bioinformatics, 32, 511–517.
Atsmon,J. et al. (2012) Safety and immunogenicity of multimeric-001 - a novel universal influenza vaccine. Journal of Clinical Immunology, 32, 595–603.
Barton,J.P. et al. (2016) Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable. Nature Communications, 7, 11660.
Berthoud,T.K. et al. (2011) Potent CD8+ T-cell immunogenicity in humans of a novel heterosubtypic influenza a vaccine, MVA-NP+M1. Clinical Infectious Diseases, 52, 1–7.
Bhasin,M. and Raghava,G.P.S. (2004) Prediction of CTL epitopes using QM, SVM and ANN techniques. Vaccine, 22, 3195–3204.
Bhatt,S. et al. (2013) The global distribution and burden of dengue. Nature, 496, 504–7.
Bouchaud,J. and Potters,M. (2009) Financial applications of random matrix theory: a short review. IDEAS Working Paper Series from RePEc.
Brady,O.J. et al. (2012) Refining the global spatial limits of dengue virus transmission by evidence-based consensus. PLoS Neglected Tropical Diseases, 6, e1760.
Brumme,Z.L. et al. (2009) HLA-associated immune escape pathways in HIV-1 subtype B gag, pol and nef proteins. PloS ONE, 4, e6687.
Burdick,R.C. et al. (2017) Dynamics and regulation of nuclear import and nuclear movements of HIV-1 complexes. PLoS Pathogens, 13, e1006570.
Cai,Y. et al. (2020) A single dose SARS-CoV-2 simulating particle vaccine induces potent neutralizing activities. bioRxiv, 2020.05.14.093054.
Calis,J.J.A. et al. (2012) Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire. PLoS Computational Biology, 8, e1002412.
Calis,J.J.A. et al. (2013) Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Computational Biology, 9.
Campbell,E.M. and Hope,T.J. (2015) HIV-1 capsid: the multifaceted key player in HIV-1 infection. Nature Reviews Microbiology, 13, 471–483.
Campbell,K.M. et al. (2020) Prioritization of SARS-CoV-2 epitopes using a pan-HLA and global population inference approach. bioRxiv, 2020.03.30.016931.
Centers-of-Disease-Control-and-Prevention (2020) Confirmed 2019-nCoV cases globally.
Chakraborty,A.K. and Barton,J.P. (2017) Rational design of vaccine targets and strategies for HIV: a crossroad of statistical physics, biology, and medicine. Reports on Progress in Physics, 80, 032601.
Channappanavar,R. et al. (2014) T cell-mediated immune response to respiratory coronaviruses. Immunologic Research, 59, 118–128.
Chen,B. et al. (2019) Predicting HLA class II antigen presentation through integrated deep learning. Nature Biotechnology, 37, 1332–1343.
Chour,W. et al. (2020) Shared antigen-specific CD8+ T cell responses against the SARS-COV-2 spike protein in HLA A*02:01 COVID-19 participants. medRxiv, 2020.05.04.20085779.
Chu,H. et al. (2015) CD8+ T-cell responses in flavivirus-naive individuals following immunization with a live-attenuated tetravalent dengue vaccine candidate. Journal of Infectious Diseases, 212, 1618–1628.
Cocco,S. et al. (2013) From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLoS Computational Biology, 9, e1003176.
Corbett,K.S. et al. (2020) SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. Nature, 586, 567–571.
Dahirel,V. et al. (2011) Coordinate linkage of HIV evolution reveals regions of immunological vulnerability. Proceedings of the National Academy of Sciences, 108, 11530–11535.
De Groot,A.S. et al. (2020) Better epitope discovery, precision immune engineering, and accelerated vaccine design using immunoinformatics tools. Frontiers in Immunology, 11, 1–13.
Deming,D. et al. (2006) Vaccine efficacy in senescent mice challenged with recombinant SARS-CoV bearing epidemic and zoonotic spike variants. PLoS Medicine, 3, e525.
Deng,S.Q. et al. (2020) A review on dengue vaccine development. Vaccines, 8, 1–13.
Dhanda,S.K. et al. (2013) Designing of interferon-gamma inducing MHC class-II binders. Biology Direct, 8, 30.
Dhanda,S.K. et al. (2019) IEDB-AR: immune epitope database—analysis resource in 2019. Nucleic Acids Research, 47, W502–W506.
Dhanda,S.K. et al. (2018) ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins. Bioinformatics, 34, 3931–3933.
Diamond,M.S. and Pierson,T.C. (2020) The challenges of vaccine development against a new virus during a pandemic. Cell Host & Microbe, 27, 699–703.
Donoho,D.L. et al. (2018) Optimal shrinkage of eigenvalues in the spiked covariance model. Annals of Statistics, 46, 1742–1778.
Doytchinova,I.A. and Flower,D.R. (2007) VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics, 8, 4.
Dönnes,P. and Elofsson,A. (2002) Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics, 3.
Duangchinda,T. et al. (2010) Immunodominant T-cell responses to dengue virus NS3 are associated with DHF. Proceedings of the National Academy of Sciences, 107, 16922–16927.
Elong Ngono,A. et al. (2016) Protective role of cross-reactive CD8 T cells against dengue virus infection. EBioMedicine, 13, 284–293.
Elong Ngono,A. and Shresta,S. (2019) Cross-reactive T cell immunity to dengue and zika viruses: new insights into vaccine development. Frontiers in immunology, 10, 1316.
Elong Ngono,A. and Shresta,S. (2018) Immune response to dengue and zika. Annual Review of Immunology, 36, 279–308.
Emrich,L.J. and Piedmonte,M.R. (1991) A method for generating high-dimensional multivariate binary variates. The American Statistician, 45, 302–304.
Enayatkhani,M. et al. (2020) Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study. Journal of Biomolecular Structure and Dynamics, 0, 1–16.
Esparza,J. (2013) What has 30 years of HIV vaccine research taught us? Vaccines, 1, 513–26.
Fan,X. et al. (2020) Cryo-EM analysis of the post-fusion structure of the SARS-CoV spike glycoprotein. Nature Communications, 11, 3618.
Fan,Y.-Y. et al. (2009) Characterization of SARS-CoV-specific memory T cells from recovered individuals 4 years after infection. Archives of Virology, 154, 1093–1099.
Feltkamp,M.C.W. et al. (1994) Efficient MHC class I-peptide binding is required but does not ensure MHC class I-restricted immunogenicity. Molecular Immunology, 31, 1391–1401.
Feng,Y. et al. (2020) Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus in China (SARS-CoV-2). bioRxiv, 2020.03.03.962332.
Ferguson,A.L. et al. (2013) Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design. Immunity, 38, 606–617.
Ferretti,A.P. et al. (2020) Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2 that largely reside outside the spike protein. Immunity, 53, 1095—1107.e3.
Fleri,W. et al. (2017) The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design. Frontiers in Immunology, 8, 1–16.
Fonseca,N.J. da et al. (2017) Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains. Biochemical and Biophysical Research Communications, 492, 565–571.
Frahm,N. et al. (2006) Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes. Nature Immunology, 7, 173–178.
Gaardbo,J.C. et al. (2012) Thirty years with HIV infection - nonprogression is still puzzling: lessons to be learned from controllers and long-term nonprogressors. AIDS Research and Treatment, 2012.
Gaiha,G.D. et al. (2019) Structural topology defines protective CD8+ T cell epitopes in the HIV proteome. Science, 364, 480–484.
Gallimore,A. (1998) Protective immunity does not correlate with the hierarchy of virus-specific cytotoxic T cell responses to naturally processed peptides. Journal of Experimental Medicine, 187, 1647–1657.
Gao,A. et al. (2021) Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-COV-2. iScience, 102311.
Gauttier,V. et al. (2020) Tissue-resident memory CD8 T-cell responses elicited by a single injection of a multi-target COVID-19 vaccine. bioRxiv, 2020.08.14.240093.
Gebe,J.A. et al. (2009) Restricted autoantigen recognition associated with deletional and adaptive regulatory mechanisms. The Journal of Immunology, 183, 59–65.
Gonzalez-Galarza,F.F. et al. (2011) Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Research, 39, 913–919.
González-Galarza,F.F. et al. (2015) Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations. Nucleic Acids Research, 43, D784–8.
Gordon,A. et al. (2013) The Nicaraguan pediatric dengue cohort study: incidence of inapparent and symptomatic dengue virus infections, 2004–2010. PLoS Neglected Tropical Diseases, 7, e2462.
Goulder,P.J.R. and Watkins,D.I. (2004) HIV and SIV CTL escape: implications for vaccine design. Nature Reviews Immunology, 4, 630–640.
Gragert,L. et al. (2013) Six-locus high resolution HLA haplotype frequencies derived from mixed-resolution DNA typing for the entire US donor registry. Human Immunology, 74, 1313–20.
Graham,R.L. et al. (2012) A live, impaired-fidelity coronavirus vaccine protects in an aged, immunocompromised mouse model of lethal disease. Nature Medicine, 18, 1820–1826.
Greaney,A.J. et al. (2021) Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Cell Host & Microbe, 29, 44–57.e9.
Grifoni,A. et al. (2020) A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2. Cell Host & Microbe, 27, 1–10.
Grifoni,A. et al. (2019) Characterization of magnitude and antigen specificity of HLA-DP, DQ, and DRB3/4/5 restricted DENV-specific CD4+ T cell responses. Frontiers in Immunology, 10, 1–10.
Grifoni,A. et al. (2017) Global assessment of dengue virus-specific CD4+ T Cell responses in dengue-endemic areas. Frontiers in Immunology, 8, 1–13.
Guan,P. et al. (2003) MHCPred: A server for quantitative prediction of peptide-MHC binding. Nucleic Acids Research, 31, 3621–3624.
Guhr,T. et al. (1998) Random-matrix theories in quantum physics: common concepts. Physics Reports, 299, 189–425.
Guirakhoo,F. et al. (2020) A novel SARS-CoV-2 multitope protein/peptide vaccine candidate is highly immunogenic and prevents lung infection in an adeno associated virus human angiotensin-converting enzyme 2 (AAV hACE2) mouse model. bioRxiv, 2, 2020.11.30.399154.
Guzman,M.G. and Harris,E. (2015) Dengue. The Lancet, 385, 453–465.
Habel,J.R. et al. (2020) Suboptimal SARS-CoV-2−specific CD8+ T cell response associated with the prominent HLA-A*02:01 phenotype. Proceedings of the National Academy of Sciences, 117, 24384–24391.
Halabi,N. et al. (2009) Protein sectors: evolutionary units of three-dimensional structure. Cell, 138, 774–86.
Harvey,W.T. et al. (2021) SARS-CoV-2 variants, spike mutations and immune escape. Nature Reviews Microbiology, 19, 409–424.
He,Y. et al. (2010) Vaxign: The first web-based vaccine design program for reverse vaccinology and applications for vaccine development. Journal of Biomedicine and Biotechnology, 2010, 1–15.
Heiny,A.T. et al. (2007) Evolutionarily conserved protein sequences of influenza A viruses, avian and human, as vaccine targets. PLoS ONE, 2, e1190.
Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences, 89, 10915–10919.
Heymann,D.L. (2020) Data sharing and outbreaks: best practice exemplified. The Lancet, 395, 469–470.
Hoffmann,M. et al. (2020) SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell, 181, 271–280.e8.
Holtappels,R. et al. (2008) Subdominant CD8 T-cell epitopes account for protection against cytomegalovirus independent of immunodomination. Journal of Virology, 82, 5781–96.
Hoof,I. et al. (2009) NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics, 61, 1–13.
Hou,Y.J. et al. (2020) SARS-CoV-2 D614G variant exhibits enhanced replication ex vivo and earlier transmission in vivo. bioRxiv, 1468, 1464–1468.
Huang,C. et al. (2020) Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet, 395, 497–506.
Huber,S.R. et al. (2014) T cell responses to viral infections - opportunities for peptide vaccination. Frontiers in Immunology, 5, 1–12.
Huber,S.R. et al. (2014) T cell responses to viral infections - opportunities for peptide vaccination. Frontiers in Immunology, 5, 1–12.
Hundal,J. et al. (2020) PVACtools: a computational toolkit to identify and visualize cancer neoantigens. Cancer Immunology Research, 8, 409–420.
Huson,D.H. and Scornavacca,C. (2012) Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Systematic Biology, 61, 1061–1067.
Hwang,W.C. et al. (2006) Structural basis of neutralization by a human anti-severe acute respiratory syndrome spike protein antibody, 80R. Journal of Biological Chemistry, 281, 34610–34616.
Hyun-Jung Lee,C. et al. (2020) CD8+ T cell cross-reactivity against SARS-CoV-2 conferred by other coronavirus strains and influenza virus. bioRxiv, 2020.05.20.107292.
Im,E.-J. et al. (2011) Protective efficacy of serially up-ranked subdominant CD8+ T cell epitopes against virus challenges. PLoS Pathogens, 7, e1002041.
Jacques,D.A. et al. (2016) HIV-1 uses dynamic capsid pores to import nucleotides and fuel encapsidated DNA synthesis. Nature, 536, 349–53.
Jakhar,R. et al. (2020) 3CL hydrolase-based multiepitope peptide vaccine against SARS-CoV-2 using immunoinformatics. Journal of Medical Virology, 2114–2123.
Jensen,K.K. et al. (2018) Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology, 154, 394–406.
Joglekar,A.V. and Li,G. (2020) T cell antigen discovery. Nature Methods.
Joshi,A. et al. (2020) Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach. Informatics in Medicine Unlocked, 19, 100338.
Jurtz,V. et al. (2017) NetMHCpan-4.0: improved peptide–MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data. The Journal of Immunology, 199, 3360–3368.
Kalergis,A.M. and Nathenson,S.G. (2000) Altered peptide ligand-mediated TCR antagonism can be modulated by a change in a single amino acid residue within the CDR3 beta of an MHC class I-restricted TCR. Journal of Immunology (Baltimore, Md. : 1950), 165, 280–5.
Karosiene,E. et al. (2013) NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ. Immunogenetics, 65, 711–724.
Katoh,K. and Standley,D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30, 772–780.
Katzelnick,L.C. et al. (2015) Dengue viruses cluster antigenically but not as discrete serotypes. Science, 349, 1338–1343.
Khan,A.M. et al. (2008) Conservation and variability of dengue virus proteins: implications for vaccine design. PLoS Neglected Tropical Diseases, 2.
Klema,V.J. et al. (2016) Dengue virus nonstructural protein 5 (NS5) assembles into a dimer with a unique methyltransferase and polymerase interface. PLoS Pathogens, 12, 1–21.
Korber,B. et al. (2020) Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2. bioRxiv, 2020.04.29.069054.
Kosmrlj,A. et al. (2010) Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature, 465, 350–354.
Košmrlj,A. et al. (2008) How the thymus designs antigen-specific and self-tolerant T cell receptor sequences. Proceedings of the National Academy of Sciences of the United States of America, 105, 16671–16676.
Košmrlj,A. et al. (2009) Thymic selection of T-cell receptors as an extreme value problem. Physical Review Letters, 103.
Kothe,D.L. et al. (2006) Ancestral and consensus envelope immunogens for HIV-1 subtype C. Virology, 352, 438–449.
Kula,T. et al. (2019) T-Scan: a genome-wide method for the systematic discovery of T cell epitopes. Cell, 178, 1016–1028.e13.
Kumai,T. et al. (2017) Peptide vaccines in cancer — old concept revisited. Current Opinion in Immunology, 45, 1–7.
Laloux,L. et al. (1999) Noise dressing of financial correlation matrices. Physical Review Letters, 83, 1467–1470.
Laloux,L. et al. (2000) Random matrix theory and financial correlations. International Journal of Theoretical and Applied Finance, 03, 391–397.
Lam,J.H. et al. (2017) Dengue vaccine–induced CD8+ T cell immunity confers protection in the context of enhancing, interfering maternal antibodies. JCI Insight, 2.
Lan,J. et al. (2020) Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581, 215–220.
Larsen,M.V. et al. (2007) Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics, 8, 424.
Lata,S. et al. (2007) Application of machine learning techniques in predicting MHC binders. In, Flower,D.R. (ed), Immunoinformatics; (clifton, n.j.), Methods in molecular biology. Humana Press, Totowa, NJ, pp. 201–215.
Latinne,A. et al. (2020) Origin and cross-species transmission of bat coronaviruses in China. Nature Communications, 11, 4235.
Le Bert,N. et al. (2020) SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature, 584, 457–462.
Le,T.T. et al. (2020) Evolution of the COVID-19 vaccine development landscape. Nature Reviews Drug Discovery, 19, 667–668.
Letko,M. et al. (2020) Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses. Nature Microbiology, 5, 562–569.
Li,C.K. et al. (2008) T cell responses to whole SARS coronavirus in humans. The Journal of Immunology, 181, 5490–5500.
Li,F. et al. (2005) Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science, 309, 1864–1868.
Li,Y. et al. (2020) Linear epitope landscape of SARS-CoV-2 spike protein constructed from 1,051 COVID-19 patients. SSRN Electronic Journal, 2020.07.13.20152587.
Li,Z. et al. (2017) Flavivirus NS2B/NS3 protease: structure, function, and inhibition. In, Viral proteases and their inhibitors. Elsevier, pp. 163–188.
Lim,S.P. et al. (2015) The dengue virus NS5 protein as a target for drug discovery. Antiviral Research, 119, 57–67.
LIN,Y. et al. (2003) Identification of an epitope of SARS-coronavirus nucleocapsid protein. Cell Research, 13, 141–145.
Lineburg,K.E. et al. (2021) CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses. Immunity.
Liu,L. et al. (2020) Potent neutralizing monoclonal antibodies directed to multiple epitopes on the SARS-CoV-2 spike. bioRxiv, 2020.06.17.153486.
Liu,X. et al. (2004) Profile of antibodies to the nucleocapsid protein of the severe acute respiratory syndrome (SARS)-associated coronavirus in probable SARS patients. Clinical Diagnostic Laboratory Immunology, 11, 227–228.
Liu,X. and Wang,X.-J. (2020) Potential inhibitors for 2019-nCoV coronavirus M protease from clinically approved medicines. bioRxiv.
Liu,Y. et al. (2008) Analysis of correlated mutations in HIV-1 protease using spectral clustering. Bioinformatics, 24, 1243–1250.
Long,Q.-X. et al. (2020) Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections. Nature Medicine, 26, 1200–1204.
Low,J.G.H. et al. (2017) Current status of dengue therapeutics research and development. The Journal of Infectious Diseases, 215, S96—S102.
López,C.S. et al. (2011) Determinants of the HIV-1 core assembly pathway. Virology, 417, 137–146.
Lu,R. et al. (2020) Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet, 395, 565–574.
Lucchese,G. (2020) Epitopes for a 2019-nCoV vaccine. Cellular and Molecular Immunology, 17, 539–540.
Lundegaard,C. et al. (2008) NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11. Nucleic Acids Research, 36, W509–W512.
Luo,D. et al. (2008) Crystal structure of the NS3 protease-helicase from dengue virus. Journal of Virology, 82, 173–183.
Luo,D. et al. (2015) The flavivirus NS2B-NS3 protease-helicase as a target for antiviral drug development. Antiviral Research, 118, 148–158.
Ma,X. et al. (2020) Nanoparticle vaccines based on the receptor binding domain (RBD) and heptad repeat (HR) of SARS-CoV-2 elicit robust protective immune responses. Immunity, 53, 1315–1330.e9.
Ma,Y. et al. (2015) Structural basis and functional analysis of the SARS coronavirus nsp14–nsp10 complex. Proceedings of the National Academy of Sciences, 112, 9436–9441.
Malonis,R.J. et al. (2020) Peptide-based vaccines: current progress and future challenges.
Mann,J.K. et al. (2014) The fitness landscape of HIV-1 gag: advanced modeling approaches and validation of model predictions by in vitro testing. PLoS Computational Biology, 10, e1003776.
Manocheewa,S. et al. (2013) Fitness costs of mutations at the HIV-1 capsid hexamerization interface. PloS ONE, 8, e66065.
Martinez,A.N. et al. (2009) T-cell epitope processing (the epitope flanking regions matter). In, Methods in molecular biology., pp. 407–415.
Maslow,J.N. (2019) Zika vaccine development-current progress and challenges for the future. Tropical Medicine and Infectious Disease, 4.
Menachery,V.D. et al. (2015) A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nature Medicine, 21, 1508–1513.
Messina,J.P. et al. (2014) Global spread of dengue virus types: mapping the 70 year history. Trends in Microbiology, 22, 138–146.
Mirarab,S. et al. (2015) PASTA: ultra-large multiple sequence alignment for nucleotide and amino-acid sequences. Journal of Computational Biology, 22, 377–386.
Moutaftsi,M. et al. (2006) A consensus epitope prediction approach identifies the breadth of murine T\(_{CD8+}\)-cell responses to vaccinia virus. Nature Biotechnology, 24, 817–819.
Moxon,R. et al. (2019) Editorial: reverse vaccinology. Frontiers in Immunology, 10, 1–2.
Murakowski,D.K. et al. (2021) Adenovirus-vectored vaccine containing multidimensionally conserved parts of the HIV proteome is immunogenic in rhesus macaques. Proceedings of the National Academy of Sciences of the United States of America, 118.
Murphy,K. and Weaver,C. (2016) Janeway’s Immunobiology 9th ed. Otagiri,M. and Chuang,V.T.G. (eds) Springer Singapore, Singapore.
Nascimento,E.J.M. et al. (2013) Identification of conserved and HLA promiscuous DENV3 T-cell epitopes. PLoS Neglected Tropical Diseases, 7.
Nelde,A. et al. (2021) SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition. Nature Immunology, 22, 74–85.
Nerli,S. and Sgourakis,N.G. (2020) Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens. bioRxiv, 2020.03.23.004176.
Nevagi,R.J. et al. (2017) Peptide-based vaccines Elsevier Ltd.
Ng,O.-W. et al. (2016) Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection. Vaccine, 34, 2008–2014.
Ngono,A.E. and Shresta,S. (2019) Cross-reactive T cell immunity to dengue and zika viruses: new insights into vaccine development. Frontiers in Immunology, 10, 1–9.
Nguyen,T.H.O. et al. (2021) CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope display high naive precursor frequency and TCR promiscuity. Immunity.
Nielsen,M. et al. (2007) Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics, 8, 238.
Nielsen,M. et al. (2003) Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Science, 12, 1007–1017.
Nielsen,M. et al. (2005) The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics, 57, 33–41.
Noviello,C.M. et al. (2011) Second-site compensatory mutations of HIV-1 capsid mutations. Journal of Virology, 85, 4730–8.
Nunes,E. et al. (2011) Definitions of histocompatibility typing terms. Blood, 118, e180–e183.
O’Brien,C. et al. (2008) Peptide length significantly influences in vitro affinity for MHC class II molecules. Immunome Research, 4, 6.
O’Donnell,T.J. et al. (2020) MHCflurry 2.0: improved pan-allele prediction of MHC class I-presented peptides by incorporating antigen processing. Cell Systems, 11, 42—48.e7.
Ogishi,M. and Yotsuyanagi,H. (2019) Quantitative prediction of the landscape of T cell epitope immunogenicity in sequence space. Frontiers in Immunology, 10, 827.
Olsen,L. et al. (2011) Conservation analysis of dengue virus T-cell epitope-based vaccine candidates using peptide block entropy. Frontiers in Immunology, 2, 1–15.
Oseroff,C. et al. (2005) HLA class I-restricted responses to vaccinia recognize a broad array of proteins mainly involved in virulence and viral gene regulation. Proceedings of the National Academy of Sciences, 102, 13980–13985.
Owen,J.A. et al. (2013) Kuby Immunology 7th ed. Macmillan.
Oyarzún,P. et al. (2013) PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity. BMC Bioinformatics, 14, 52.
Palatnik-de-Sousa,C.B. et al. (2018) Editorial: epitope discovery and synthetic vaccine design. Frontiers in Immunology, 9, 9–11.
Panagioti,E. et al. (2018) Features of effective T cell-inducing vaccines against chronic viral infections. Frontiers in Immunology, 9, 1–11.
Pang,K.C. et al. (2006) Immunoproteasome subunit deficiencies impact differentially on two immunodominant influenza virus-specific CD8+ T cell responses. The Journal of Immunology, 177, 7680–7688.
Pardi,N. et al. (2018) mRNA vaccines-a new era in vaccinology. Nature Reviews Drug Discovery, 17, 261–279.
Patil,V.M. et al. (2019) Dengue virus polymerase Elsevier Inc.
Paul,S. et al. (2016) TepiTool: A pipeline for computational prediction of T cell epitope candidates. Current Protocols in Immunology, 114, 18.19.1—18.19.24.
Peng,H. et al. (2006) Long-lived memory T lymphocyte responses against SARS coronavirus nucleocapsid protein in SARS-recovered patients. Virology, 351, 466–475.
Peng,Y. et al. (2020) Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nature Immunology, 21, 1336–1345.
Pereyra,F. et al. (2014) HIV control is mediated in part by CD8+ T-cell targeting of specific epitopes. Journal of Virology, 88, 12937–48.
Pereyra,F. et al. (2010) The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science (New York, N.Y.), 330, 1551–7.
Peters,B. et al. (2003) Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinformatics, 19, 1765–1772.
Peters,B. et al. (2020) T cell epitope predictions. Annual Review of Immunology, 38, 123–145.
Peters,B. and Sette,A. (2005) Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics, 6.
Piazza,P. et al. (2014) Dengue virus-infected human dendritic cells reveal hierarchies of naturally expressed novel NS3 CD8 T cell epitopes. Clinical and Experimental Immunology, 177, 696–702.
Pickett,B.E. et al. (2012) ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Research, 40, D593–8.
Pincus,D. et al. (2017) An evolution-based strategy for engineering allosteric regulation. Physical Biology, 14, 025002.
Pinto,D. et al. (2020) Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature, 583, 290–295.
Plante,J.A. et al. (2021) Spike mutation D614G alters SARS-CoV-2 fitness. Nature, 592, 116–121.
Pleguezuelos,O. et al. (2015) A synthetic influenza virus vaccine induces a cellular immune response that correlates with reduction in symptomatology and virus shedding in a randomized phase Ib live-virus challenge in humans. Clinical and Vaccine Immunology, 22, 828–835.
Plerou,V. et al. (2002) Random matrix approach to cross correlations in financial data. Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 65.
Poh,C.M. et al. (2020) Potent neutralizing antibodies in the sera of convalescent COVID-19 patients are directed against conserved linear epitopes on the SARS-CoV-2 spike protein. bioRxiv, 1–11.
Poran,A. et al. (2020) Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes. Genome Medicine, 12, 70.
Pornillos,O. et al. (2011) Atomic-level modelling of the HIV capsid. Nature, 469, 424–427.
Pornillos,O. et al. (2009) X-ray structures of the hexameric building block of the HIV capsid. Cell, 137, 1282–92.
Prabakaran,P. et al. (2006) Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody. Journal of Biological Chemistry, 281, 15829–15836.
Prachar,M. et al. (2020) Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools. Scientific Reports, 10, 20465.
prevention,centre for disease and Control,E. (2019) Dengue worldwide overview.
Quadeer,A.A. et al. (2018) Co-evolution networks of HIV/HCV are modular with direct association to structure and function. PLoS Computational Biology, 14, e1006409.
Quadeer,A.A. et al. (2014) Statistical linkage analysis of substitutions in patient-derived sequences of genotype 1a hepatitis C virus nonstructural protein 3 exposes targets for immunogen design. Journal of Virology, 88, 7628–44.
Rahman,N. et al. (2020) Vaccine design from the ensemble of surface glycoprotein epitopes of SARS-CoV-2: an immunoinformatics approach. Vaccines, 8, 1–17.
Ranga,V. et al. (2020) Immunogenic SARS-CoV-2 epitopes: in silico study towards better understanding of COVID-19 disease—paving the way for vaccine development. Vaccines, 8, 408.
Rathore,A.P.S. and St. John,A.L. (2020) Cross-reactive immunity among flaviviruses. Frontiers in Immunology, 11, 1–9.
Raué,H.-P. and Slifka,M.K. (2009) CD8+ T cell immunodominance shifts during the early stages of acute LCMV infection independently from functional avidity maturation. Virology, 390, 197–204.
Reginald,K. et al. (2018) Development of peptide vaccines in dengue. Current Pharmaceutical Design, 24, 1157–1173.
Remakus,S. et al. (2012) Memory CD8+ T cells specific for a single immunodominant or subdominant determinant induced by peptide-dendritic cell immunization protect from an acute lethal viral disease. Journal of Virology, 86, 9748–9759.
Reynisson,B. et al. (2020) NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Research, 48, W449—W454.
Rihn,S.J. et al. (2013) Extreme genetic fragility of the HIV-1 capsid. PLoS Pathogens, 9, e1003461.
Rivino,L. (2016) T cell immunity to dengue virus and implications for vaccine design. Expert Review of Vaccines, 15, 443–453.
Rivoire,O. et al. (2016) Evolution-based functional decomposition of proteins. PLoS Computational Biology, 12, e1004817.
Roider,J. et al. (2014) Comparison of experimental fine-mapping to in silico prediction results of HIV-1 epitopes reveals ongoing need for mapping experiments. Immunology, 143, 193–201.
Rolland,M. et al. (2007) HIV-1 group M conserved elements vaccine. PLoS Pathogens, 3, 1551–1555.
Roth,C. et al. (2019) A modified mRNA vaccine targeting immunodominant NS epitopes protects against dengue virus infection in HLA class I transgenic mice. Frontiers in Immunology, 10, 1–14.
Ruckwardt,T.J. et al. (2010) Responses against a subdominant CD8+ T cell epitope protect against immunopathology caused by a dominant epitope. The Journal of Immunology, 185, 4673–4680.
Safrit,J.T. et al. (2016) Status of vaccine research and development of vaccines for HIV-1. Vaccine, 34, 2921–2925.
Samad,A. et al. (2020) Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach. Journal of Biomolecular Structure and Dynamics, 0, 1–17.
Sanami,S. et al. (2020) Design of a multi-epitope vaccine against SARS-CoV-2 using immunoinformatics approach. International Journal of Biological Macromolecules, 108334.
Sanjuán,R. and Domingo-Calap,P. (2016) Mechanisms of viral mutation. Cellular and molecular life sciences, 73, 4433–4448.
Sarkar,B. et al. (2020) Immunoinformatics-guided designing of epitope-based subunit vaccines against the SARS Coronavirus-2 (SARS-CoV-2). Immunobiology, 225, 151955.
Schommers,P. et al. (2016) Changes in HIV-1 capsid stability induced by common cytotoxic-T-lymphocyte-driven viral sequence mutations. Journal of Virology, 90, 7579–7586.
Schroder,K. et al. (2004) Interferon-\(\gamma\): An overview of signals, mechanisms and functions. Journal of Leukocyte Biology, 75, 163–189.
Schulien,I. et al. (2021) Characterization of pre-existing and induced SARS-CoV-2-specific CD8+ T cells. Nature Medicine, 27, 78–85.
Screaton,G. et al. (2015) New insights into the immunopathology and control of dengue virus infection. Nature Reviews Immunology, 15, 745–759.
Seow,J. et al. (2020) Longitudinal evaluation and decline of antibody responses in SARS-CoV-2 infection. medRxiv, 2020.07.09.20148429.
Sheets,U.N. fact (2019) Dengue and severe dengue.
Shin,M.D. et al. (2020) COVID-19 vaccine development and a potential nanomaterial path forward. Nature Nanotechnology, 15, 646–655.
Shomuradova,A.S. et al. (2020) SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T cell receptors. Immunity, 53, 1245—1257.e5.
Sidney,J. et al. (2020) Epitope prediction and identification - adaptive T cell responses in humans. Seminars in Immunology, 50, 101418.
Singh,H. and Raghava,G.P.S. (2001) ProPred: prediction of HLA-DR binding sites. Bioinformatics, 17, 1236–1237.
Singh,H. and Raghava,G.P.S. (2003) ProPred1: prediction of promiscuous MHC Class-I binding sites. Bioinformatics, 19, 1009–1014.
Slingluff,C.L. (2011) The present and future of peptide vaccines for cancer. The Cancer Journal, 17, 343–350.
Sloan-Lancaster,J. and Allen,P.M. (1996) Altered peptide ligand-induced partial T cell activation: molecular mechanisms and role in T cell biology. Annual Review of Immunology, 14, 1–27.
Slon Campos,J.L. et al. (2018) The immune response against flaviviruses. Nature Immunology, 19, 1189–1198.
Smith,C.C. et al. (2020) Landscape and selection of vaccine epitopes in SARS-CoV-2. bioRxiv.
Smith,T.R.F. et al. (2020) Immunogenicity of a DNA vaccine candidate for COVID-19. Nature Communications, 11, 2601.
Snyder,T.M. et al. (2020) Magnitude and dynamics of the T-cell response to SARS-CoV-2 infection at both individual and population levels. medRxiv, 2020.07.31.20165647.
Sohail,M.S. et al. (2021) In silico T cell epitope identification for SARS-CoV-2: progress and perspectives. Advanced Drug Delivery Reviews, 171, 29–47.
Song,W. et al. (2018) Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2. PLoS Pathogens, 14, e1007236.
Sridhar,S. et al. (2018) Effect of dengue serostatus on dengue vaccine safety and efficacy. New England Journal of Medicine, 379, 327–340.
Stanaway,J.D. et al. (2016) The global burden of dengue: an analysis from the global burden of disease study 2013. The Lancet. Infectious diseases, 16, 712–723.
Stranzl,T. et al. (2010) NetCTLpan: pan-specific MHC class I pathway epitope predictions. Immunogenetics, 62, 357–368.
Sturniolo,T. et al. (1999) Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nature Biotechnology, 17, 555–561.
Swarbrick,C.M.D. et al. (2017) NS3 helicase from dengue virus specifically recognizes viral RNA sequence to ensure optimal replication. Nucleic Acids Research, 45, 12904–12920.
Tang,F. et al. (2011) Lack of peripheral memory B cell responses in recovered patients with severe acute respiratory syndrome: a six-year follow-up study. The Journal of Immunology, 186, 7264–7268.
Tarke,A. et al. (2021) Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees. bioRxiv.
Teramoto,T. et al. (2017) Serotype-specific interactions among functional domains of dengue virus 2 nonstructural proteins (NS) 5 and NS3 are crucial for viral RNA replication. Journal of Biological Chemistry, 292, 9465–9479.
Testa,J.S. et al. (2012) Conserved MHC class I–presented dengue virus epitopes identified by immunoproteomics analysis are targets for cross-serotype reactive T-cell response. The Journal of Infectious Diseases, 205, 647–655.
Thanh Le,T. et al. (2020) The COVID-19 vaccine development landscape. Nature Reviews Drug Discovery, 19, 305–306.
Tian,X. et al. (2020) Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody. bioRxiv, 1751, 2020.01.28.923011.
Tian,Y. et al. (2019) Human T cell response to dengue virus infection. Frontiers in Immunology, 10, 1–9.
Torresi,J. et al. (2017) Vaccines licensed and in clinical trials for the prevention of dengue. Human Vaccines & Immunotherapeutics, 13, 1059–1072.
Trolle,T. et al. (2016) The length distribution of class I–restricted T cell epitopes is determined by both peptide supply and MHC allele–specific binding preference. The Journal of Immunology, 196, 1480–1487.
UNAIDS (2018) UNAIDS fact sheet - Latest statistics on the status of the AIDS epidemic.
Vita,R. et al. (2019) The immune epitope database (IEDB): 2018 update. Nucleic Acids Research, 47, D339–D343.
Vita,R. et al. (2015) The immune epitope database (IEDB) 3.0. Nucleic Acids Research, 43, D405–D412.
Waickman,A.T. et al. (2019) Assessing the diversity and stability of cellular immunity generated in response to the candidate live-attenuated dengue virus vaccine TAK-003. Frontiers in Immunology, 10, 1–13.
Walls,A.C. et al. (2020) Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181, 281–292.e6.
Walls,A.C. et al. (2017) Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion. Proceedings of the National Academy of Sciences, 114, 11157–11162.
Walls,A.C. et al. (2019) Unexpected receptor functional mimicry elucidates activation of coronavirus fusion. Cell, 176, 1026–1039.e15.
Wang,C. et al. (2020) A human monoclonal antibody blocking SARS-CoV-2 infection. Nature Communications, 11, 2251.
Wang,J. et al. (2003) Assessment of immunoreactive synthetic peptides from the structural proteins of severe acute respiratory syndrome coronavirus. Clinical Chemistry, 49, 1989–1996.
Wang,P. et al. (2008) A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Computational Biology, 4.
Wang,Z. et al. (2021) Exposure to SARS-CoV-2 generates T-cell memory in the absence of a detectable viral infection. Nature Communications, 12, 1724.
Wedemeyer,H. et al. (2009) Therapeutic vaccine IC41 as late add-on to standard treatment in patients with chronic hepatitis C. Vaccine, 27, 5142–5151.
Weiskopf,D. et al. (2013) Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells. Proceedings of the National Academy of Sciences of the United States of America, 110, E2046—53.
Weiskopf,D., Cerpas,C., et al. (2015) Human CD8+ T-cell responses against the 4 dengue virus serotypes are associated with distinct patterns of protein targets. Journal of Infectious Diseases, 212, 1743–1751.
Weiskopf,D. et al. (2014) Immunodominance changes as a function of the infecting dengue virus serotype and primary versus secondary infection. Journal of Virology, 88, 11383–11394.
Weiskopf,D. et al. (2020) Phenotype and kinetics of SARS-CoV-2-specific T cells in COVID-19 patients with acute respiratory distress syndrome. Science Immunology, 5, eabd2071.
Weiskopf,D., Angelo,M.A., et al. (2015) The human CD8+ T cell responses induced by a live attenuated tetravalent dengue vaccine are directed against highly conserved epitopes. Journal of Virology, 89, 120–128.
Weiskopf,D. and Sette,A. (2014) T-cell immunity to infection with dengue virus in humans. Frontiers in Immunology, 5, 93.
Welsh,R.M. et al. (2010) Heterologous immunity between viruses. Immunological Reviews, 235, 244–266.
Wen,J. and Shresta,S. (2017) T Cell immunity to zika and dengue viral infections. Journal of Interferon & Cytokine Research, 37, 475–479.
Whitehead,S.S. (2016) Development of TV003/TV005, a single dose, highly immunogenic live attenuated dengue vaccine; what makes this vaccine different from the Sanofi-Pasteur CYD™ vaccine? Expert Review of Vaccines, 15, 509–517.
Wijeratne,D.T. et al. (2018) Quantification of dengue virus specific T cell responses and correlation with viral load and clinical disease severity in acute dengue infection. PLoS Neglected Tropical Diseases, 12, e0006540.
Wilder-Smith,A. et al. (2019) Dengue. The Lancet, 393, 350–363.
World-Health-Organization (2020a) Coronavirus disease (COVID-19) outbreak.
World-Health-Organization (2020b) Middle East respiratory syndrome coronavirus (MERS-CoV).
World-Health-Organization (2020c) Statement on the meeting of the international health regulations (2005) emergency committee regarding the outbreak of novel coronavirus (2019-nCoV).
World-Health-Organization (2020d) Update 49 - SARS case fatality ratio, incubation period.
Wrapp,D. et al. (2020) Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science, 367, 1260–1263.
Yang,Z. et al. (2004) A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice. Nature, 428, 561–564.
Yarmarkovich,M. et al. (2020) Identification of SARS-CoV-2 vaccine epitopes predicted to induce long-term population-scale immunity. Cell Reports Medicine, 100036.
Yauch,L.E. et al. (2009) A protective role for dengue virus-specific CD8+ T cells. The Journal of Immunology, 182, 4865–4873.
Yazdani,Z. et al. (2020) Design an efficient multi-epitope peptide vaccine candidate against SARS-CoV-2: an in silico analysis. Infection and Drug Resistance, 13, 3007–3022.
Zellweger,R.M. et al. (2014) CD8 + T Cells prevent antigen-induced antibody-dependent enhancement of dengue disease in mice. The Journal of Immunology, 193, 4117–4124.
Zellweger,R.M. et al. (2010) Enhanced infection of liver sinusoidal endothelial cells in a mouse model of antibody-induced severe dengue disease. Cell Host and Microbe, 7, 128–139.
Zhang,N. and Bevan,M.J. (2011) CD8+ T cells: foot soldiers of the immune system. Immunity, 35, 161–168.
Zheng,M. et al. (2006) Construction and immunogenicity of a recombinant fowlpox virus containing the capsid and 3C protease coding regions of foot-and-mouth disease virus. Journal of Virological Methods, 136, 230–237.
Zhou,P. et al. (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579, 270–273.
Zhu,Z. et al. (2007) Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies. Proceedings of the National Academy of Sciences, 104, 12123–12128.