Epitope-based vaccine target screening against highly pathogenic MERS-CoV: An In Silico approach applied to emerging infectious diseases

PLoS ONE

Volumn 10, Issue 12, 2015, Pages

  Shi, Jiandong ^a   Zhang, Jing ^a,b   Li, Sijin ^a   Sun, Jing ^a   Teng, Yumei ^a   Wu, Meini ^a   Li, Jianfan ^a   Li, Yanhan ^a   Hu, Ningzhu ^a   Wang, Haixuan ^a   Hu, Yunzhang ^a  

^a INSTITUTE OF MEDICAL BIOLOGY   (China)

^b New Era Hospital for Gynecology and Obstetrics   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ENVELOPE PROTEIN; EPITOPE; HLA ANTIGEN; M PROTEIN; NEUTRALIZING ANTIBODY; NUCLEOCAPSID PROTEIN; VIRUS SPIKE PROTEIN; VIRUS VACCINE; CORONAVIRUS SPIKE GLYCOPROTEIN;

ALLELE; ARTICLE; B LYMPHOCYTE; CELL POPULATION; CELL STIMULATION; CELLULAR IMMUNITY; COMPUTER MODEL; CYTOTOXIC T LYMPHOCYTE; GENETIC ASSOCIATION; GENETIC CONSERVATION; GEOGRAPHIC DISTRIBUTION; HUMORAL IMMUNITY; IMMUNOGENETICS; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; NONHUMAN; OPEN READING FRAME; POPULATION GENETICS; PROTEIN ANALYSIS; SEQUENCE ANALYSIS; T LYMPHOCYTE; VACCINATION; VIRAL GENETICS; CORONAVIRUS INFECTION; HELPER CELL; HUMAN; IMMUNOLOGY; VIROLOGY;

ANTIBODIES, NEUTRALIZING; CORONAVIRUS INFECTIONS; EPITOPES, B-LYMPHOCYTE; EPITOPES, T-LYMPHOCYTE; HUMANS; IMMUNITY, CELLULAR; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; NUCLEOCAPSID PROTEINS; SPIKE GLYCOPROTEIN, CORONAVIRUS; T-LYMPHOCYTES, HELPER-INDUCER; VIRAL VACCINES;

EID: 84955566775     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0144475     Document Type: Article

References (64)

1. Bermingham A, Chand MA, Brown CS, Aarons E, Tong C, Langrish C, et al. Severe respiratory illness caused by a novel coronavirus, in a patient transferred to the United Kingdom from the Middle East, September 2012. Euro Surveill. 2012; 17(40): 20290. PMID: 23078800
2. Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012; 367(19): 1814-20. doi: 10.1056/NEJMoa1211721 PMID: 23075143
3. Coleman CM, Frieman MB. Coronaviruses: Important emerging human pathogens. J Virol. 2014; 88 (10): 5209-12. doi: 10.1128/JVI.03488-13 PMID: 24600003
4. Ithete NL, Stoffberg S, Corman VM, Cottontail VM, Richards LR, Schoeman MC, et al. Close relative of human Middle East respiratory syndrome coronavirus in bat, South Africa. Emerg Infect Dis. 2013; 19 (10): 1697-9. doi: 10.3201/eid1910.130946 PMID: 24050621
5. Briese T, Mishra N, Jain K, Zalmout IS, Jabado OJ, Karesh WB, et al. Middle East respiratory syndrome coronavirus quasispecies that include homologues of human isolates revealed through whole-genome analysis and virus cultured from dromedary camels in Saudi Arabia. MBio. 2014; 5(3): E01146-14. doi: 10.1128/mBio.01146-14 PMID: 24781747
6. Mackay IM, Arden KE. Middle East respiratory syndrome: An emerging coronavirus infection tracked by the crowd. Virus Res. 2015; 202: 60-88. doi: 10.1016/j.virusres.2015.01.021 PMID: 25656066
7. Zumla A, Hui DS, Perlman S. Middle East respiratory syndrome. Lancet. 2015; 386(9997): 995-1007. doi: 10.1016/S0140-6736(15)60454-8 PMID: 26049252
8. World Health Organization. Middle East respiratory syndrome coronavirus (MERSCoV)-Republic of Korea. 26 June 2015. Available: Http://www.who.int/csr/don/26-june-2015-mers-korea/en/. Accessed 2015 Jul 16.
9. Song F, Fux R, Provacia LB, Volz A, Eickmann M, Becker S, et al. Middle East respiratory syndrome coronavirus spike protein delivered by modified vaccinia virus Ankara efficiently induces virus-neutralizing antibodies. J Virol. 2013; 87(21): 11950-4. doi: 10.1128/JVI.01672-13 PMID: 23986586
10. Wang L, Shi W, Joyce MG, Modjarrad K, Zhang Y, Leung K, et al. Evaluation of candidate vaccine approaches for MERS-CoV. Nat Commun. 2015; 6: 7712. doi: 10.1038/ncomms8712 PMID: 26218507
11. Guo X, Deng Y, Chen H, Lan J, Wang W, Zou X, et al. Systemic and mucosal immunity in mice elicited by a single immunization with human adenovirus type 5 or 41 vector-based vaccines carrying the spike protein of Middle East respiratory syndrome coronavirus. Immunology. 2015; 145(4): 476-84. doi: 10.1111/imm.12462 PMID: 25762305
12. Du L, Zhao G, Kou Z, Ma C, Sun S, Poon VK, et al. Identification of a receptor-binding domain in the S protein of the novel human coronavirus Middle East respiratory syndrome coronavirus as an essential target for vaccine development. J Virol. 2013; 87(17): 9939-42. doi: 10.1128/JVI.01048-13 PMID: 23824801
13. Kim E, Okada K, Kenniston T, Raj VS, AlHajri MM, Farag EA, et al. Immunogenicity of an adenoviralbased Middle East Respiratory Syndrome coronavirus vaccine in BALB/c mice. Vaccine. 2014; 32 (45): 5975-82. doi: 10.1016/j.vaccine.2014.08.058 PMID: 25192975
14. Tang J, Zhang N, Tao X, Zhao G, Guo Y, Tseng CT, et al. Optimization of antigen dose for a receptorbinding domain-based subunit vaccine against MERS coronavirus. Hum Vaccin Immunother. 2015; 11 (5): 1244-50. doi: 10.1080/21645515.2015.1021527 PMID: 25874632
15. Volz A, Kupke A, Song F, Jany S, Fux R, Shams-Eldin H, et al. Protective Efficacy of Recombinant Modified Vaccinia Virus Ankara Delivering Middle East Respiratory Syndrome Coronavirus Spike Glycoprotein. J Virol. 2015; 89(16): 8651-6. doi: 10.1128/JVI.00614-15 PMID: 26018172
16. Mou H, Raj VS, van Kuppeveld FJ, Rottier PJ, Haagmans BL, Bosch BJ. The receptor binding domain of the new Middle East respiratory syndrome coronavirus maps to a 231-residue region in the spike protein that efficiently elicits neutralizing antibodies. J Virol. 2013; 87(16): 9379-83. doi: 10.1128/JVI. 01277-13 PMID: 23785207
17. Du L, Zhao G, Kou Z, Ma C, Sun S, Poon VK, et al. Identification of a receptor-binding domain in the S protein of the novel human coronavirus Middle East respiratory syndrome coronavirus as an essential target for vaccine development. J Virol. 2013; 87(17): 9939-42. doi: 10.1128/JVI.01048-13 PMID: 23824801
18. Du L, Kou Z, Ma C, Tao X, Wang L, Zhao G, et al. A truncated receptor-binding domain of MERS-CoV spike protein potently inhibits MERS-CoV infection and induces strong neutralizing antibody responses: Implication for developing therapeutics and vaccines. PLoS One. 2013; 8(12): E81587. doi: 10.1371/Journal.pone.0081587 PMID: 24324708
19. Zhang N, Jiang S, Du L. Current advancements and potential strategies in the development of MERSCoV vaccines. Expert Rev Vaccines. 2014; 13(6): 761-74. doi: 10.1586/14760584.2014.912134 PMID: 24766432
20. Almazán F, DeDiego ML, Sola I, Zuñiga S, Nieto-Torres JL, Marquez-Jurado S, et al. Engineering a replication-competent, propagation-defective Middle East respiratory syndrome coronavirus as a vaccine candidate. MBio. 2013; 4(5): E00650-13. doi: 10.1128/mBio.00650-13 PMID: 24023385
21. Purcell AW, McCluskey J, Rossjohn J. More than one reason to rethink the use of peptides in vaccine design. Nat Rev Drug Discov. 2007; 6(5): 404-14. PMID: 17473845
22. Firbas C, Jilma B, Tauber E, Buerger V, Jelovcan S, Lingnau K, et al. Immunogenicity and safety of a novel therapeutic hepatitis C virus (HCV) peptide vaccine: A randomized, placebo controlled trial for dose optimization in 128 healthy subjects. Vaccine. 2006; 24(20): 4343-53. PMID: 16581161
23. Staneková Z, Varecková E. Conserved epitopes of influenza A virus inducing protective immunity and their prospects for universal vaccine development. Virol J. 2010; 7: 351. doi: 10.1186/1743-422X-7-351 PMID: 21118546
24. He L, Cheng Y, Kong L, Azadnia P, Giang E, Kim J, et al. Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding. Sci Rep. 2015; 5: 12501. doi: 10.1038/srep12501 PMID: 26238798
25. Sominskaya I, Skrastina D, Dislers A, Vasiljev D, Mihailova M, Ose V, et al. Construction and immunological evaluation of multivalent hepatitis B virus (HBV) core virus-like particles carrying HBV and HCV epitopes. Clin Vaccine Immunol. 2010; 17(6): 1027-33. doi: 10.1128/CVI.00468-09 PMID: 20410327
26. Terry FE, Moise L, Martin RF, Torres M, Pilotte N, Williams SA, et al. Time for T? Immunoinformatics addresses vaccine design for neglected tropical and emerging infectious diseases. Expert Rev Vaccines. 2015; 14(1): 21-35. doi: 10.1586/14760584.2015.955478 PMID: 25193104
27. Doytchinova IA, Flower DR. VaxiJen: A server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics. 2007; 8: 4. PMID: 17207271
28. Wilkins MR, Gasteiger E, Bairoch A, Sanchez JC, Williams KL, Appel RD, et al. Protein identification and analysis tools in the ExPASy server. Methods Mol Biol. 1999; 112: 531-52. PMID: 10027275
29. Combet C, Blanchet C, Geourjon C, Deléage G. NPS@: Network protein sequence analysis. Trends Biochem Sci. 2000; 25(3): 147-50. PMID: 10694887
30. Källberg M, Margaryan G, Wang S, Ma J, Xu J. RaptorX server: A resource for template-based protein structure modeling. Methods Mol Biol. 2014; 1137: 17-27. doi: 10.1007/978-1-4939-0366-5-2 PMID: 24573471
31. Kolaskar AS, Tongaonkar PC. A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett. 1990; 276(1-2): 172-4. PMID: 1702393
32. Vihinen M, Torkkila E, Riikonen P. Accuracy of protein flexibility predictions. Proteins. 1994; 19 (2): 141-9. PMID: 8090708
33. Emini EA, Hughes JV, Perlow DS, Boger J. Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol. 1985; 55(3): 836-9. PMID: 2991600
34. Wilson JA, Hart MK. Protection from Ebola virus mediated by cytotoxic T lymphocytes specific for the viral nucleoprotein. J Virol. 2001; 75(6): 2660-4. PMID: 11222689
35. Karosiene E, Rasmussen M, Blicher T, Lund O, Buus S, Nielsen M. NetMHCIIpan-3.0, a common panspecific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ. ImmunoGenetics. 2013; 65(10): 711-24. doi: 10.1007/s00251-013-0720-y PMID: 23900783
36. Zhang L, Udaka K, Mamitsuka H, Zhu S. Toward more accurate pan-specific MHC-peptide binding prediction: A review of current methods and tools. Brief Bioinform. 2012; 13(3): 350-64. doi: 10.1093/bib/bbr060 PMID: 21949215
37. Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, et al. NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS One. 2007; 2(8): E796. PMID: 17726526
38. Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, et al. NetMHCpan, a method for MHC class I binding prediction beyond humans. ImmunoGenetics. 2009; 61(1): 1-13. doi: 10.1007/s00251-008-0341-z PMID: 19002680
39. Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, et al. Immune epitope database analysis resource. Nucleic Acids Res. 2012; 40(Web Server issue): W525-30. doi: 10.1093/nar/gks438 PMID: 22610854
40. Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, et al. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci. 2003; 12 (5): 1007-17.: PMID: 12717023
41. Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M. 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. 2008; 36(Web Server issue): W509-12. doi: 10.1093/nar/gkn202 PMID: 18463140
42. Peters B, Sette A. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics. 2005; 6: 132. PMID: 15927070
43. Sidney J, Assarsson E, Moore C, Ngo S, Pinilla C, Sette A, et al. Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res. 2008; 4: 2. doi: 10.1186/1745-7580-4-2 PMID: 18221540
44. Calis JJ, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, et al. Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol. 2013; 9(10): E1003266. doi: 10.1371/Journal.pcbi.1003266 PMID: 24204222http://www.ncbi.nlm.nih.gov/pubmed/24204222
45. Bui HH, Sidney J, Li W, Fusseder N, Sette A. Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics. 2007; 8: 361. PMID: 17897458
46. Muh HC, Tong JC, Tammi MT. AllerHunter: A SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins. PLoS One. 2009; 4(6): E5861. doi: 10.1371/Journal.pone.0005861 PMID: 19516900
47. Bui HH, Sidney J, Dinh K, Southwood S, Newman MJ, Sette A. Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics. 2006; 7: 153. PMID: 16545123
48. Le TM, Wong HH, Tay FP, Fang S, Keng CT, Tan YJ, et al. Expression, post-translational modification and biochemical characterization of proteins encoded by subgenomic mRNA8 of the severe acute respiratory syndrome coronavirus. FEBS J. 2007; 274(16): 4211-22. PMID: 17645546
49. Wang N, Shi X, Jiang L, Zhang S, Wang D, Tong P, et al. Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4. Cell Res. 2013; 23(8): 986-93. doi: 10.1038/cr. 2013.92 PMID: 23835475
50. Zheng N, Xia R, Yang C, Yin B, Li Y, Duan C, et al. Boosted expression of the SARS-CoV nucleocapsid protein in tobacco and its immunogenicity in mice. Vaccine. 2009; 27(36): 5001-7. doi: 10.1016/j. vaccine.2009.05.073 PMID: 19523911
51. Ma C, Yao K, Zhou F, Zhu M. Comparative immunization in BALB/c mice with recombinant replicationdefective adenovirus vector and DNA plasmid expressing a SARS-CoV nucleocapsid protein gene. Cell Mol Immunol. 2006; 3(6): 459-65. PMID: 17257500
52. Hu H, Tao L, Wang Y, Chen L, Yang J, Wang H. Enhancing immune responses against SARS-CoV nucleocapsid DNA vaccine by co-inoculating interleukin-2 expressing vector in mice. Biotechnol Lett. 2009; 31(11): 1685-93. doi: 10.1007/s10529-009-0061-y PMID: 19579009
53. Dutta NK, Mazumdar K, Lee BH, Baek MW, Kim DJ, Na YR, et al. Search for potential target site of nucleocapsid gene for the design of an epitope-based SARS DNA vaccine. Immunol Lett. 2008; 118 (1): 65-71. doi: 10.1016/j.imlet.2008.03.003 PMID: 18440652
54. Liu SJ, Leng CH, Lien SP, Chi HY, Huang CY, Lin CL, et al. Immunological characterizations of the nucleocapsid protein based SARS vaccine candidates. Vaccine. 2006; 24(16): 3100-8. PMID: 16494977
55. Zhao J, Huang Q, Wang W, Zhang Y, Lv P, Gao XM. Identification and characterization of dominant helper T-cell epitopes in the nucleocapsid protein of severe acute respiratory syndrome coronavirus. J Virol. 2007; 81(11): 6079-88. PMID: 17392374
56. Zhou M, Xu D, Li X, Li H, Shan M, Tang J, et al. Screening and identification of severe acute respiratory syndrome-associated coronavirus-specific CTL epitopes. J Immunol. 2006; 177(4): 2138-45. PMID: 16887973
57. Han Z, Zhao F, Shao Y, Liu X, Kong X, Song Y, et al. Fine level epitope mapping and conservation analysis of two novel linear B-cell epitopes of the avian infectious bronchitis coronavirus nucleocapsid protein. Virus Res. 2013; 171(1): 54-64. doi: 10.1016/j.virusres.2012.10.028 PMID: 23123213
58. Gupta V, Tabiin TM, Sun K, Chandrasekaran A, Anwar A, Yang K, et al. SARS coronavirus nucleocapsid immunodominant T-cell epitope cluster is common to both exogenous recombinant and endogenous DNA-encoded immunogens. Virology. 2006; 347(1): 127-39. PMID: 16387339
59. Liu DQ, Ge JW, Qiao XY, Jiang YP, Liu SM, Li YJ. High-level mucosal and systemic immune responses induced by oral administration with Lactobacillus-expressed porcine epidemic diarrhea virus (PEDV) S1 region combined with Lactobacillus-expressed N protein. Appl Microbiol Biotechnol. 2012; 93 (6): 2437-46. doi: 10.1007/s00253-011-3734-0 PMID: 22134641
60. Wilson JA, Hart MK. Protection from Ebola virus mediated by cytotoxic T lymphocytes specific for the viral nucleoprotein. J Virol. 2001; 75(6): 2660-4. PMID: 11222689
61. Gao X, Zhou H, Wu C, Xiao Y, Ren L, Paranhos-Baccalà G, et al. Antibody against nucleocapsid protein predicts susceptibility to human coronavirus infection. J Infect. 2015; 71(5): 599-602. doi: 10.1016/j.jinf.2015.07.002 PMID: 26165609
62. Esser MT, Marchese RD, Kierstead LS, Tussey LG, Wang F, Chirmule N, et al. Memory T cells and vaccines. Vaccine. 2003; 21(5-6): 419-30. PMID: 12531640
63. Maenaka K, Jones EY. MHC superfamily structure and the immune system. Curr Opin Struct Biol. 1999; 9(6): 745-53. PMID: 10607669
64. Stern LJ, Wiley DC. Antigenic peptide binding by class I and class II histocompatibility proteins. Structure. 1994; 2(4): 245-51. PMID: 8087551