Universal H1N1 influenza vaccine development: Identification of consensus class II hemagglutinin and neuraminidase epitopes derived from strains circulating between 1980 and 2011

Human Vaccines and Immunotherapeutics

Volumn 9, Issue 7, 2013, Pages 1598-1607

  Moise, Leonard ^a,b   Terry, Frances ^a   Ardito, Matthew ^a   Tassone, Ryan ^a   Latimer, Howard ^a   Boyle, Christine ^a   Martin, William D ^a   De Groot, Anne S ^a,b  

^a EpiVax Inc   (United States)

^b UNIVERSITY OF RHODE ISLAND   (United States)

Author keywords

Computational immunology; Epitope; H1N1; Immunoinformatics; Influenza; Pandemic influenza; Seasonal influenza; T cell; Universal influenza vaccine; Vaccine

Indexed keywords

EPITOPE; GAMMA INTERFERON; HLA A ANTIGEN; INFLUENZA VACCINE; INFLUENZA VIRUS HEMAGGLUTININ; VIRUS SIALIDASE;

ALLELE; AMINO ACID SEQUENCE; CONFERENCE PAPER; CONTROLLED STUDY; CYTOKINE PRODUCTION; HUMAN; HUMAN CELL; IMMUNOGENETICS; IMMUNOGENICITY; MEDICAL INFORMATICS; PANDEMIC; PERIPHERAL BLOOD MONONUCLEAR CELL; PROTEIN BINDING; T LYMPHOCYTE; VACCINE PRODUCTION; VIRUS STRAIN;

COMPUTATIONAL IMMUNOLOGY; EPITOPE; H1N1; IMMUNOINFORMATICS; INFLUENZA; PANDEMIC INFLUENZA; SEASONAL INFLUENZA; T CELL; UNIVERSAL INFLUENZA VACCINE; VACCINE;

CD4-POSITIVE T-LYMPHOCYTES; CROSS REACTIONS; DRUG DISCOVERY; EPITOPES, T-LYMPHOCYTE; HEMAGGLUTININS; HISTOCOMPATIBILITY ANTIGENS CLASS I; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA VACCINES; INFLUENZA, HUMAN; INTERFERON-GAMMA; LEUKOCYTES, MONONUCLEAR; NEURAMINIDASE; VACCINATION;

EID: 84880855765     PISSN: 21645515     EISSN: 2164554X     Source Type: Journal    
DOI: 10.4161/hv.25598     Document Type: Conference Paper

References (45)

1. Centers for Disease Control and Prevention. 2012-2013 Influenza Season Week 8 ending February 23, 2013. Centers for Disease Control and Prevention. Retrieved from: http://www.cdc.gov/flu/weekly/.
2. Osterholm MT, Kelley NS, Sommer A, Belongia EA. Efficacy and effectiveness of influenza vaccines: a systematic review and meta-analysis. [Erratum in: Lancet Infect Dis 2012; 12:655; PMID:22032844; http://dx.doi.org/ 10.1016/S1473-3099] [11] [70295-X]. Lancet Infect Dis 2012; 12:36-44; PMID:22032844; http://dx.doi.org/10.1016/S1473-3099(11)70295-X
3. Centers for Disease Control and Prevention (CDC). Serum cross-reactive antibody response to a novel influenza A (H1N1) virus after vaccination with seasonal influenza vaccine. MMWR Morb Mortal Wkly Rep 2009; 58:521-4; PMID:19478718
4. De Groot AS, Ardito M, McClaine EM, Moise L, Martin WD. Immunoinformatic comparison of T-cell epitopes contained in novel swine-origin influenza A (H1N1) virus with epitopes in 2008-2009 conventional influenza vaccine. Vaccine 2009; 27:5740-7; PMID:19660593; http://dx.doi.org/10.1016/j.vaccine.2009.07.040
5. Schanen BC, De Groot AS, Moise L, Ardito M, McClaine E, Martin W, et al. Coupling sensitive in vitro and in silico techniques to assess cross-reactive CD4(+) T cells against the swine-origin H1N1 influenza virus. Vaccine 2011; 29:3299-309; PMID:21349362; http://dx.doi.org/10.1016/j.vaccine.2011.02.019
6. Koita OA, Dabitao D, Mahamadou I, Tall M, Dao S, Tounkara A, et al. Confirmation of immunogenic consensus sequence HIV-1 T-cell epitopes in Bamako, Mali and Providence, Rhode Island. Hum Vaccin 2006; 2:119-28; PMID:17012903
7. De Groot AS, Bishop EA, Khan B, Lally M, Marcon L, Franco J, et al. Engineering immunogenic consensus T helper epitopes for a cross-clade HIV vaccine. Methods 2004; 34:476-87; PMID:15542374; http://dx.doi.org/10.1016/j. ymeth.2004.06.003
8. Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, et al. The immune epitope database 2.0. Nucleic Acids Res 2010; 38(Database issue):D854-62; PMID:19906713; http://dx.doi.org/10.1093/nar/gkp1004
9. Moise L, Gutierrez AH, Bailey-Kellogg C, Terry F, Leng Q, Abdel Hady KM, et al. The two-faced T cell epitope: Examining the host-microbe interface with JanusMatrix. Hum Vaccin Immunother 2013; 9: In press; PMID:23584251; http://dx.doi.org/10.4161/hv.24615.
10. De Groot AS, Ardito M, Moise L, Gustafson EA, Spero D, Tejada G, et al. Immunogenic consensus sequence T helper epitopes for a pan-Burkholderia biodefense vaccine. Immunome Res 2011; 7:7; PMID:22130150
11. Moise L, McMurry JA, Pappo J, Lee DS, Moss SF, Martin WD, et al. Identification of genome-derived vaccine candidates conserved between human and mouse-adapted strains of H. pylori. Hum Vaccin 2008; 4:219-23; PMID:18376134; http://dx.doi.org/10.4161/hv.4.3.5394
12. De Groot AS, Martin W. Reducing risk, improving outcomes: bioengineering less immunogenic protein therapeutics. Clin Immunol 2009; 131:189-201; PMID:19269256; http://dx.doi.org/10.1016/j.clim.2009.01.009
13. Hancock K, Veguilla V, Lu X, Zhong W, Butler EN, Sun H, et al. Cross-reactive antibody responses to the 2009 pandemic H1N1 influenza virus. N Engl J Med 2009; 361:1945-52; PMID:19745214; http://dx.doi.org/10.1056/ NEJMoa0906453
14. Jain S, Kamimoto L, Bramley AM, Schmitz AM, Benoit SR, Louie J, et al.; 2009 Pandemic Influenza A (H1N1) Virus Hospitalizations Investigation Team. Hospitalized patients with 2009 H1N1 influenza in the United States, April-June 2009. N Engl J Med 2009; 361:1935-44; PMID:19815859; http://dx.doi.org/10.1056/ NEJMoa0906695
15. Greenbaum JA, Kotturi MF, Kim Y, Oseroff C, Vaughan K, Salimi N, et al. Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population. Proc Natl Acad Sci U S A 2009; 106:20365-70; PMID:19918065; http://dx.doi.org/10.1073/pnas.0911580106
16. Richards KA, Topham D, Chaves FA, Sant AJ. Cutting edge: CD4 T cells generated from encounter with seasonal influenza viruses and vaccines have broad protein specificity and can directly recognize naturally generated epitopes derived from the live pandemic H1N1 virus. J Immunol 2010; 185:4998-5002; PMID:20889549; http://dx.doi.org/10.4049/jimmunol.1001395
17. Tu W, Mao H, Zheng J, Liu Y, Chiu SS, Qin G, et al. Cytotoxic T lymphocytes established by seasonal human influenza cross-react against 2009 pandemic H1N1 influenza virus. J Virol 2010; 84:6527-35; PMID:20410263; http://dx.doi.org/10.1128/JVI.00519-10
18. Boon AC, de Mutsert G, van Baarle D, Smith DJ, Lapedes AS, Fouchier RA, et al. Recognition of homoand heterosubtypic variants of influenza A viruses by human CD8+ T lymphocytes. J Immunol 2004; 172:2453-60; PMID:14764717
19. Kreijtz JH, Bodewes R, van Amerongen G, Kuiken T, Fouchier RA, Osterhaus AD, et al. Primary influenza A virus infection induces cross-protective immunity against a lethal infection with a heterosubtypic virus strain in mice. Vaccine 2007; 25:612-20; PMID:17005299; http://dx.doi.org/10.1016/j.vaccine.2006.08.036
20. Ge X, Tan V, Bollyky PL, Standifer NE, James EA, Kwok WW. Assessment of seasonal influenza A virus-specific CD4 T-cell responses to 2009 pandemic H1N1 swine-origin influenza A virus. J Virol 2010; 84:3312-9; PMID:20071564; http://dx.doi.org/10.1128/JVI.02226-09
21. Ellebedy AH, Ducatez MF, Duan S, Stigger-Rosser E, Rubrum AM, Govorkova EA, et al. Impact of prior seasonal influenza vaccination and infection on pandemic A (H1N1) influenza virus replication in ferrets. Vaccine 2011; 29:3335-9; PMID:20840835; http://dx.doi.org/10.1016/j.vaccine.2010.08.067
22. Garcia-Garcia L, Valdespino-Gómez JL, Lazcano-Ponce E, Jimenez-Corona A, Higuera-Iglesias A, Cruz-Hervert P, et al. Partial protection of seasonal trivalent inactivated vaccine against novel pandemic influenza A/H1N1 2009: case-control study in Mexico City. BMJ 2009; 339:b3928; PMID:19808768; http://dx.doi.org/10.1136/bmj.b3928
23. Powell TJ, Peng Y, Berthoud TK, Blais ME, Lillie PJ, Hill AV, et al. Examination of influenza specific T cell responses after influenza virus challenge in individuals vaccinated with MVA-NP+M1 vaccine. PLoS One 2013; 8:e62778; PMID:23658773; http://dx.doi.org/10.1371/journal.pone.0062778
24. Kamperschroer C, Dibble JP, Meents DL, Schwartzberg PL, Swain SL. SAP is required for Th cell function and for immunity to influenza. J Immunol 2006; 177:5317-27; PMID:17015717
25. Belz GT, Wodarz D, Diaz G, Nowak MA, Doherty PC. Compromised influenza virus-specific CD8(+)-Tcell memory in CD4(+)-T-cell-deficient mice. J Virol 2002; 76:12388-93; PMID:12414983; http://dx.doi.org/10.1128/JVI.76.23.12388- 12393.2002
26. Cardin RD, Brooks JW, Sarawar SR, Doherty PC. Progressive loss of CD8+ T cell-mediated control of a gamma-herpesvirus in the absence of CD4+ T cells. J Exp Med 1996; 184:863-71; PMID:9064346; http://dx.doi.org/10.1084/jem.184.3.863
27. Brooks JW, Hamilton-Easton AM, Christensen JP, Cardin RD, Hardy CL, Doherty PC. Requirement for CD40 ligand, CD4(+) T cells, and B cells in an infectious mononucleosis-like syndrome. J Virol 1999; 73:9650-4; PMID:10516078
28. Marshall D, Sealy R, Sangster M, Coleclough C. TH cells primed during influenza virus infection provide help for qualitatively distinct antibody responses to subsequent immunization. J Immunol 1999; 163:4673-82; PMID:10528164
29. Lee LY, Ha LA, Simmons C, de Jong MD, Chau NV, Schumacher R, et al. Memory T cells established by seasonal human influenza A infection cross-react with avian influenza A (H5N1) in healthy individuals. J Clin Invest 2008; 118:3478-90; PMID:18802496
30. Townsend AR, Skehel JJ. The influenza A virus nucleoprotein gene controls the induction of both subtype specific and cross-reactive cytotoxic T cells. J Exp Med 1984; 160:552-63; PMID:6206181; http://dx.doi.org/10.1084/jem.160.2.552
31. Assarsson E, Bui HH, Sidney J, Zhang Q, Glenn J, Oseroff C, et al. Immunomic analysis of the repertoire of T-cell specificities for influenza A virus in humans. J Virol 2008; 82:12241-51; PMID:18842709; http://dx.doi.org/10. 1128/JVI.01563-08
32. McElhaney JE, Xie D, Hager WD, Barry MB, Wang Y, Kleppinger A, et al. T cell responses are better correlates of vaccine protection in the elderly. J Immunol 2006; 176:6333-9; PMID:16670345
33. Levitz L, Koita OA, Sangare K, Ardito MT, Boyle CM, Rozehnal J, et al. Conservation of HIV-1 T cell epitopes across time and clades: validation of immunogenic HLA-A2 epitopes selected for the GAIA HIV vaccine. Vaccine 2012; 30:7547-60; PMID:23102976; http://dx.doi.org/10.1016/j.vaccine.2012.10.042
34. De Groot AS, Levitz L, Ardito MT, Skowron G, Mayer KH, Buus S, et al. Further progress on defining highly conserved immunogenic epitopes for a global HIV vaccine: HLA-A3-restricted GAIA vaccine epitopes. Hum Vaccin Immunother 2012; 8:987-1000; PMID:22777092; http://dx.doi.org/10.4161/hv.20528
35. De Groot AS, Rivera DS, McMurry JA, Buus S, Martin W. Identification of immunogenic HLA-B7 "Achilles' heel" epitopes within highly conserved regions of HIV. Vaccine 2008; 26:3059-71; PMID:18206276; http://dx.doi.org/10. 1016/j.vaccine.2007.12.004
36. De Groot AS, Ardito M, Terry F, Levitz L, Ross TM, Moise L, et al. Low immunogenicity predicted for emerging avian-origin H7N9: Implication for influenza vaccine design. Hum Vaccin Immunother 2013; 9: In press; PMID:23807079; http://dx.doi.org/10.4161/hv.24939.
37. Elfaki ME, Khalil EA, Degroot AS, Musa AM, Gutiérrez Núñez A, Younis BM, et al. Immunogenicity and immune modulatory effects of in silico predicted L. donovani candidate peptide vaccines. Hum Vaccin Immunother 2012; 8:1769-74; PMID:22922767; http://dx.doi.org/10.4161/hv. 21881
38. Poland GA. Vaccines against Lyme disease: What happened and what lessons can we learn? Clin Infect Dis 2011; 52(Suppl 3):s253-8; PMID:21217172; http://dx.doi.org/10.1093/cid/ciq116
39. Squires RB, Noronha J, Hunt V, García-Sastre A, Macken C, Baumgarth N, et al. Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respi Viruses 2012; 6:404-16; PMID:22260278; http://dx.doi.org/10.1111/j.1750-2659.2011.00331. x
40. De Groot AS, Jesdale BM, Szu E, Schafer JR, Chicz RM, Deocampo G. An interactive Web site providing major histocompatibility ligand predictions: application to HIV research. AIDS Res Hum Retroviruses 1997; 13:529-31; PMID:9135870; http://dx.doi.org/10.1089/aid.1997.13.529
41. 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; 160:3363-73; PMID:9531296
42. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, et al.; NIH HMP Working Group. The NIH Human Microbiome Project. Genome Res 2009; 19:2317-23; PMID:19819907; http://dx.doi.org/10.1101/gr.096651.109
43. Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, et al.; Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium. Genomics. Genome project standards in a new era of sequencing. Science 2009; 326:236-7; PMID:19815760; http://dx.doi.org/10.1126/science.1180614
44. Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, et al.; Human Microbiome Jumpstart Reference Strains Consortium. A catalog of reference genomes from the human microbiome. Science 2010; 328:994-9; PMID:20489017; http://dx.doi.org/10.1126/science.1183605
45. Steere AC, Klitz W, Drouin EE, Falk BA, Kwok WW, Nepom GT, et al. Antibiotic-refractory Lyme arthritis is associated with HLA-DR molecules that bind a Borrelia burgdorferi peptide. J Exp Med 2006; 203:961-71; PMID:16585267; http://dx.doi.org/10.1084/jem.20052471