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Research Paper

COVID-19 coronavirus vaccine T cell epitope prediction analysis based on distributions of HLA class I loci (HLA-A, -B, -C) across global populations

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Pages 1097-1108 | Received 28 Apr 2020, Accepted 09 Sep 2020, Published online: 11 Nov 2020

References

  • Hui DS, Madani EIA, Ntoumi TA, Kock F, Dar RO, et al. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health - The latest 2019 novel coronavirus outbreak in Wuhan, China. Int J Infect Dis. 2020;91:264–66.
  • Lu H, Stratton CW, Tang YW. Outbreak of pneumonia of unknown etiology in Wuhan, China: the mystery and the miracle. J Med Virol. 2020;92(4):401–02. doi:10.1002/jmv.25678.
  • Wang D, Hu B, Hu C, Zhu F, Liu X, Zhang J, Wang B, Xiang H, Cheng Z, Xiong Y, et al. Clinical Characteristics of 138 hospitalized patients with 2019 novel coronavirus–infected pneumonia in Wuhan, China. JAMA. 2020;323(11):1061. doi:10.1001/jama.2020.1585.
  • Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382(8):727–33. doi:10.1056/NEJMoa2001017.
  • Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020;395(10224):565–74. doi:10.1016/S0140-6736(20)30251-8.
  • Chan JF, Kok KH, Zhu Z, Chu H, To KK, Yuan S, Yuen K-Y. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect. 2020;9(1):221–36. doi:10.1080/22221751.2020.1719902.
  • Jiang S, Du L, Shi Z. An emerging coronavirus causing pneumonia outbreak in Wuhan, China: calling for developing therapeutic and prophylactic strategies. Emerg Microbes Infect. 2020;9(1):275–77. doi:10.1080/22221751.2020.1723441.
  • Leung DT, Tam FC, Ma CH, Chan PK, Cheung JL, Niu H, et al. Antibody response of patients with severe acute respiratory syndrome (SARS) targets the viral nucleocapsid. J Infect Dis. 2004;190:379–86.
  • Shi Y, Wan Z, Li L, Li P, Li C, Ma Q, et al. Antibody responses against SARS-coronavirus and its nucleocaspid in SARS patients. J Clin Virol. 2004;31(1):66–68. doi:10.1016/j.jcv.2004.05.006.
  • He Y, Zhou Y, Wu H, Luo B, Chen J, Li W, et al. Identification of immunodominant sites on the spike protein of severe acute respiratory syndrome (SARS) coronavirus: implication for developing SARS diagnostics and vaccines. J Immunol. 2004;173:4050–57.
  • Zhou M, Xu D, Li X, Li H, Shan M, Tang J, Wang M, Wang F-S, Zhu X, Tao H, et al. Screening and identification of severe acute respiratory syndrome-associated coronavirus-specific CTL epitopes. J Immunol. 2006;177(4):2138–45. doi:10.4049/jimmunol.177.4.2138.
  • Coleman CM, Sisk JM, Halasz G, Zhong J, Beck SE, Matthews KL, et al. CD8+ T cells and macrophages regulate pathogenesis in a mouse model of middle east respiratory syndrome. J Virol. 2017;91.
  • Tang F, Quan Y, Xin ZT, Wrammert J, Ma MJ, Lv H, Wang T-B, Yang H, Richardus JH, Liu W, et al. Lack of peripheral memory B cell responses in recovered patients with severe acute respiratory syndrome: a six-year follow-up study. J Immunol. 2011;186(12):7264–68. doi:10.4049/jimmunol.0903490.
  • Peng H, Yang LT, Wang LY, Li J, Huang J, Lu ZQ, Koup RA, Bailer RT, Wu C-Y. Long-lived memory T lymphocyte responses against SARS coronavirus nucleocapsid protein in SARS-recovered patients. Virology. 2006;351(2):466–75. doi:10.1016/j.virol.2006.03.036.
  • Fan -Y-Y, Huang Z-T, Li L, Wu M-H, Yu T, Koup RA, Bailer RT, Wu C-Y. Characterization of SARS-CoV-specific memory T cells from recovered individuals 4 years after infection. Arch Virol. 2009;154(7):1093–99. doi:10.1007/s00705-009-0409-6.
  • Li CK, Wu H, Yan H, Ma S, Wang L, Zhang M, Tang X, Temperton NJ, Weiss RA, Brenchley JM, et al. T cell responses to whole SARS coronavirus in humans. J Immunol. 2008;181(8):5490–500. doi:10.4049/jimmunol.181.8.5490.
  • Ng O-W, Chia A, Tan AT, Jadi RS, Leong HN, Bertoletti A, Tan Y-J. Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection. Vaccine. 2016;34(17):2008–14. doi:10.1016/j.vaccine.2016.02.063.
  • Cheung YK, Cheng SC, Sin FW, Chan KT, Xie Y. Investigation of immunogenic T-cell epitopes in SARS virus nucleocapsid protein and their role in the prevention and treatment of SARS infection. Hong Kong Med J. 2008;14:27–30.
  • Liu J, Wu P, Gao F, Qi J, Kawana-Tachikawa A, Xie J, Vavricka CJ, Iwamoto A, Li T, Gao GF, et al. Novel immunodominant peptide presentation strategy: a featured HLA-A*2402-restricted cytotoxic T-lymphocyte epitope stabilized by intrachain hydrogen bonds from severe acute respiratory syndrome coronavirus nucleocapsid protein. J Virol. 2010;84(22):11849–57. doi:10.1128/JVI.01464-10.
  • Tsao YP, Lin JY, Jan JT, Leng CH, Chu CC, Yang YC, et al. HLA-A*0201 T-cell epitopes in severe acute respiratory syndrome (SARS) coronavirus nucleocapsid and spike proteins. Biochem Biophys Res Commun. 2006;344:63–71.
  • Wang B, Chen H, Jiang X, Zhang M, Wan T, Li N, Zhou X, Wu Y, Yang F, Yu Y, et al. Identification of an HLA-A*0201-restricted CD8+ T-cell epitope SSp-1 of SARS-CoV spike protein. Blood. 2004;104(1):200–06. doi:10.1182/blood-2003-11-4072.
  • Wang YD, Sin WY, Xu GB, Yang HH, Wong TY, Pang XW, He X-Y, Zhang H-G, Ng JNL, Cheng CSS, et al. T-cell epitopes in severe acute respiratory syndrome (SARS) coronavirus spike protein elicit a specific T-cell immune response in patients who recover from SARS. J Virol. 2004;78(11):5612–18. doi:10.1128/JVI.78.11.5612-5618.2004.
  • Cheung YK, Cheng SC, Sin FW, Chan KT, Xie Y. Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope. Vaccine. 2007;25(32):6070–77. doi:10.1016/j.vaccine.2007.05.025.
  • Ibrahim HS, Kafi SK. A computational vaccine designing approach for MERS-CoV infections. Methods Mol Biol. 2020;2131:39–145.
  • Bezu L, Kepp O, Cerrato G, Pol J, Fucikova J, Spisek R, Zitvogel L, Kroemer G, Galluzzi L. Trial watch: peptide-based vaccines in anticancer therapy. Oncoimmunology. 2018;7(12):e1511506. doi:10.1080/2162402X.2018.1511506.
  • Germain RN, Margulies DH. The biochemistry and cell biology of antigen processing and presentation. Annu Rev Immunol. 1993;11(1):403–50. doi:10.1146/annurev.iy.11.040193.002155.
  • Heemels MT, Ploegh H. Generation, translocation, and presentation of MHC class I-restricted peptides. Annu Rev Biochem. 1995;64:463–91.
  • Hung CF, Ma B, Monie A, Tsen SW, Wu TC. Therapeutic human papillomavirus vaccines: current clinical trials and future directions. Expert Opin Biol Ther. 2008;8(4):421–39. doi:10.1517/14712598.8.4.421.
  • Dhanda SK, Vaughan K, Schulten V, Grifoni A, Weiskopf D, Sidney J, et al. Development of a novel clustering tool for linear peptide sequences. Immunology. 2018;155(3):331–45. doi:10.1111/imm.12984.
  • Ahmed SF, Quadeer AA, McKay MR. Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies. Viruses. 2020;12(3):254. doi:10.3390/v12030254.
  • Nguyen A, David JK, Maden SK, Wood MA, Weeder BR, Nellore A, et al. Human leukocyte antigen susceptibility map for severe acute respiratory syndrome coronavirus 2. J Virol. 2020;94.