Krammer, F. et al. Influenza. Nat. Rev. Dis. Primers 4, 3 (2018).
Nussing, S. et al. Innate and adaptive T cells in influenza disease. Front. Med. 12, 34–47 (2018).
Paules, C. & Subbarao, K. Influenza. Lancet 390, 697–708 (2017).
Koutsakos, M., Nguyen, T. H., Barclay, W. S. & Kedzierska, K. Knowns and unknowns of influenza B viruses. Future Microbiol. 11, 119–135 (2016).
Matsuzaki, Y. et al. Clinical features of influenza C virus infection in children. J. Infect. Dis. 193, 1229–1235 (2006).
Chen, Y. Q. et al. Influenza infection in humans induces broadly cross-reactive and protective neuraminidase-reactive antibodies. Cell 173, 417–429 e410 (2018).
Corti, D. et al. Tackling influenza with broadly neutralizing antibodies. Curr. Opin. Virol. 24, 60–69 (2017).
Dreyfus, C. et al. Highly conserved protective epitopes on influenza B viruses. Science 337, 1343–1348 (2012).
Hayward, A. C. et al. Natural T cell-mediated protection against seasonal and pandemic influenza. Results of the Flu Watch Cohort Study. Am. J. Respir. Crit. Care. Med. 191, 1422–1431 (2015).
McMichael, A. J., Gotch, F. M., Noble, G. R. & Beare, P. A. Cytotoxic T-cell immunity to influenza. New Engl. J. Med. 309, 13–17 (1983).
van de Sandt, C. E. et al. Influenza B virus-specific CD8+T-lymphocytes strongly cross-react with viruses of the opposing influenza B lineage. J. Gen. Virol. 96, 2061–2073 (2015).
Gras, S. et al. Cross-reactive CD8+T-cell immunity between the pandemic H1N1-2009 and H1N1-1918 influenza A viruses. Proc. Natl Acad. Sci. USA 107, 12599–12604 (2010).
Greenbaum, J. A. et al. Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population. Proc. Natl Acad. Sci. USA 106, 20365–20370 (2009).
Quinones-Parra, S. M. et al. A role of influenza virus exposure history in determining pandemic susceptibility and CD8+ T cell responses. J. Virol. 90, 6936–6947 (2016).
Sridhar, S. et al. Cellular immune correlates of protection against symptomatic pandemic influenza. Nat. Med. 19, 1305–1312 (2013).
Quinones-Parra, S. et al. Preexisting CD8+ T-cell immunity to the H7N9 influenza A virus varies across ethnicities. Proc. Natl Acad. Sci. USA 111, 1049–1054 (2014).
Wang, Z. et al. Recovery from severe H7N9 disease is associated with diverse response mechanisms dominated by CD8(+) T cells. Nat. Commun. 6, 6833 (2015).
Wang, Z. et al. Clonally diverse CD38(+)HLA-DR(+)CD8(+) T cells persist during fatal H7N9 disease. Nat. Commun. 9, 824 (2018).
Koutsakos, M. et al. Circulating TFH cells, serological memory, and tissue compartmentalization shape human influenza-specific B cell immunity. Sci. Transl. Med. 10, eaan8405 (2018).
Ramarathinam, S. H. et al. Identification of native and posttranslationally modified HLA-B*57:01-restricted HIV envelope derived epitopes using immunoproteomics. Proteomics 18, e1700253 (2018).
Williamson, N. A. & Purcell, A. W. Use of proteomics to define targets of T-cell immunity. Expert. Rev. Proteomics 2, 367–380 (2005).
Alexander, J. et al. Identification of broad binding class I HLA supertype epitopes to provide universal coverage of influenza A virus. Hum. Immunol. 71, 468–474 (2010).
Rosendahl Huber, S. K. et al. Chemical modification of influenza CD8+ T-cell epitopes enhances their immunogenicity regardless of immunodominance. PLoS ONE 11, e0156462 (2016).
Terajima, M., Babon, J. A., Co, M. D. & Ennis, F. A. Cross-reactive human B cell and T cell epitopes between influenza A and B viruses. Virol. J. 10, 244 (2013).
Zemmour, J., Little, A. M., Schendel, D. J. & Parham, P. The HLA-A,B “negative” mutant cell line C1R expresses a novel HLA-B35 allele, which also has a point mutation in the translation initiation codon. J. Immunol. 148, 1941–1948 (1992).
Falk, K., Rotzschke, O., Stevanovic, S., Jung, G. & Rammensee, H. G. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 351, 290–296 (1991).
Alanio, C., Lemaitre, F., Law, H. K., Hasan, M. & Albert, M. L. Enumeration of human antigen-specific naive CD8+T cells reveals conserved precursor frequencies. Blood 115, 3718–3725 (2010).
Moon, J. J. et al. Naive CD4(+) T cell frequency varies for different epitopes and predicts repertoire diversity and response magnitude. Immunity 27, 203–213 (2007).
Nguyen, T. H. O. et al. Perturbed CD8(+) T cell immunity across universal influenza epitopes in the elderly. J. Leukoc. Biol. 103, 321–339 (2018).
Chandele, A. et al. Characterization of human CD8 T Cell responses in Dengue virus-infected patients from India. J. Virol. 90, 11259–11278 (2016).
Jozwik, A. et al. RSV-specific airway resident memory CD8+T cells and differential disease severity after experimental human infection. Nat. Commun. 6, 10224 (2015).
Miller, J. D. et al. Human effector and memory CD8+T cell responses to smallpox and yellow fever vaccines. Immunity 28, 710–722 (2008).
Hillaire, M. L. et al. Characterization of the human CD8(+) T cell response following infection with 2009 pandemic influenza H1N1 virus. J. Virol. 85, 12057–12061 (2011).
de Bree, G. J. et al. Selective accumulation of differentiated CD8+T cells specific for respiratory viruses in the human lung. J. Exp. Med. 202, 1433–1442 (2005).
Piet, B. et al. CD8(+) T cells with an intraepithelial phenotype upregulate cytotoxic function upon influenza infection in human lung. J. Clin. Invest. 121, 2254–2263 (2011).
Sathaliyawala, T. et al. Distribution and compartmentalization of human circulating and tissue-resident memory T cell subsets. Immunity 38, 187–197 (2013).
Allen, R. J., Koutsakos, M., Hurt, A. C. & Kedzierska, K. Uncomplicated cystitis in an adult male following influenza B virus infection. Am. J. Case Rep. 18, 190–193 (2017).
Valkenburg, S. A. et al. Molecular basis for universal HLA-A*0201-restricted CD8+T-cell immunity against influenza viruses. Proc. Natl Acad. Sci. USA 113, 4440–4445 (2016).
Pascolo, S. et al. HLA-A2.1-restricted education and cytolytic activity of CD8(+) T lymphocytes from beta2 microglobulin (beta2m) HLA-A2.1 monochain transgenic H-2Db beta2m double knockout mice. J. Exp. Med. 185, 2043–2051 (1997).
Nguyen, T. H. et al. Understanding CD8(+) T-cell responses toward the native and alternate HLA-A*02:01-restricted WT1 epitope. Clin. Transl. Immunology 6, e134 (2017).
Epstein, S. L., Lo, C. Y., Misplon, J. A. & Bennink, J. R. Mechanism of protective immunity against influenza virus infection in mice without antibodies. J. Immunol. 160, 322–327 (1998).
Babon, J. A., Cruz, J., Ennis, F. A., Yin, L. & Terajima, M. A human CD4+ T cell epitope in the influenza hemagglutinin is cross-reactive to influenza A virus subtypes and to influenza B virus. J. Virol. 86, 9233–9243 (2012).
Pedersen, S. R. et al. Immunogenicity of HLA class I and II double restricted influenza A-derived peptides. PLoS ONE 11, e0145629 (2016).
Tan, A. C. et al. The design and proof of concept for a CD8(+) T cell-based vaccine inducing cross-subtype protection against influenza A virus. Immunol. Cell Biol. 91, 96–104 (2013).
Wang, L. et al. Functional genomics reveals linkers critical for influenza virus polymerase. J. Virol. 90, 2938–2947 (2015).
Fulton, B. O., Sun, W., Heaton, N. S. & Palese, P. The influenza B virus hemagglutinin head domain is less tolerant to transposon mutagenesis than that of the influenza A virus. J. Virol. 92, e00754-18 (2018).
Allen, E. K. et al. SNP-mediated disruption of CTCF binding at the IFITM3 promoter is associated with risk of severe influenza in humans. Nat. Med. 23, 975–983 (2017).
Oshansky, C. M. et al. Mucosal immune responses predict clinical outcomes during influenza infection independently of age and viral load. Am. J. Respir. Crit. Care. Med. 189, 449–462 (2014).
Bird, N. L. et al. Oseltamivir prophylaxis reduces inflammation and facilitates establishment of cross-strain protective T cell memory to influenza viruses. PLoS ONE 10, e0129768 (2015).
Valkenburg, S. A. et al. Protective efficacy of cross-reactive CD8+ T cells recognising mutant viral epitopes depends on peptide-MHC-I structural interactions and T cell activation threshold. PLoS Pathog. 6, e1001039 (2010).
Bao, Y. et al. The influenza virus resource at the National Center for Biotechnology Information. J. Virol. 82, 596–601 (2008).
Nguyen, T. H. et al. Maintenance of the EBV-specific CD8(+) TCRalphabeta repertoire in immunosuppressed lung transplant recipients. Immunol. Cell Biol. 95, 77–86 (2017).
Dudek, N. L. et al. Constitutive and inflammatory immunopeptidome of pancreatic beta-cells. Diabetes 61, 3018–3025 (2012).
Andreatta, M. & Nielsen, M. Gapped sequence alignment using artificial neural networks: application to the MHC class I system. Bioinformatics 32, 511–517 (2016).
Lundegaard, C. et al. NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res. 36, W509–W512 (2008).
Nielsen, M. et al. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci. 12, 1007–1017 (2003).
Colaert, N., Helsens, K., Martens, L., Vandekerckhove, J. & Gevaert, K. Improved visualization of protein consensus sequences by iceLogo. Nat. Methods 6, 786–787 (2009).
Eltahla, A. A. et al. Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells. Immunol. Cell Biol. 94, 604–611 (2016).
Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171–181 (2014).