What do T cells see in SARS-CoV2?
Immunoinformatics analysis to identify T cell epitopes from SARS-CoV2 ORF1ab polyprotein
Keywords:
immunoinformatics, ORF1ab, SARS-CoV2, T cell epitopes, epitope-based vaccine
Abstract
The current epidemic caused by a novel coronavirus SARS-CoV2 as well as two previously documented pandemic caused by SARS-CoV and MERS-CoV imposes that a spillover of an animal coronavirus to humans is a continuous threat. The zoonotic nature of the infection contributes to the unpredictability of the pandemic. In such situations, the availability of the ‘off the shelf’ vaccines that target the conserved region of the coronavirus might help in preventing the spread of the diseases. Therefore, efforts to generate such vaccines should be considered as a priority. The whole genome of SARS-CoV2 is readily available in the public database one month after the first case was identified. The platform technology known as the “genome to vaccine” approach would provide useful start to identify parts of the virus proteome which can be the candidate for vaccine components. This study used an immunoinformatic approach to identify T cell epitopes from SARS-CoV2 ORF1ab polyprotein in an attempt to design a genome-derived epitope-based universal coronavirus vaccine.
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References
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Calis JJA, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Kesmir C, Peters B. (2013) Properties of MHC class I presented peptides that enhance immunogenicity. PloS Comp. Biol. 8(1):361.
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Jasper Fuk-Woo Chan, Kin-Hang Kok, Zheng Zhu, Hin Chu, Kelvin Kai-Wang To, Shuofeng Yuan & Kwok-Yung Yuen (2020) Genomic characterization of the 2019 novel human pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan, Emerging Microbes & Infections, 9:1, 221-236.
Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, Nielsen M. (2018) Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology. 2018 Jul;154(3):394-406.
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Kumar, S. (2020) Drug and Vaccine Design against Novel Coronavirus (2019-nCoV) Spike Protein through Computational Approach. Preprints 2020, 2020020071 (doi: 10.20944/preprints202002.0071.v1).
Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M. (2005) An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol. 35(8):2295-303.
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Moise, L., Cousens, L., Fueyo, J., & De Groot, A. S. (2011). Harnessing the power of genomics and immunoinformatics to produce improved vaccines. Expert opinion on drug discovery, 6(1), 9–15.
Nathan P. Croft, Stewart A. Smith, Jana Pickering, John Sidney, Bjoern Peters, Pouya Faridi, Matthew J. Witney, Prince Sebastian, Inge E. A. Flesch, Sally L. Heading, Alessandro Sette, Nicole L. La Gruta, Anthony W. Purcell, David C.
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Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang, Hui-Dong Chen, Jing Chen, Yun Luo, Hua Guo, Ren-Di Jiang, Mei-Qin Liu, Ying Chen, Xu-Rui Shen, Xi Wang, Xiao-Shuang Zheng, Kai Zhao, Quan-Jiao Chen, Fei Deng, Lin-Lin Liu, Bing Yan, Fa-Xian Zhan, Yan-Yi Wang, Gengfu Xiao, Zheng-Li Shi. (2020) Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin, bioRxiv 2020, 01.22.914952; doi: https://doi.org/10.1101/2020.01.22.914952.
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Sharmin, R., Islam, A.B.M.M.K. (2014) A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design. BMC Bioinformatics 15: 161.
St-Jean, J. R., Jacomy, H., Desforges, M., Vabret, A., Freymuth, F., & Talbot, P. J. (2004). Human respiratory coronavirus OC43: genetic stability and neuroinvasion. Journal of virology, 78(16), 8824–8834.
Stranzl T, Larsen MV, Lundegaard C, Nielsen M (2010) NetCTLpan: panspecific MHC class I pathway epitope predictions. Immunogenetics 62:357-368.
Syed Faraz Ahmed, Ahmed A. Quadeer, Matthew R. McKay (2020) Preliminary identification of potential vaccine targets for 2019-nCoV based on SARS-CoV immunological studies, bioRxiv 2020.02.03.933226; doi: https://doi.org/10.1101/2020.02.03.933226.
Sylvester-Hvid C, Nielsen M, Lamberth K, Røder G, Justesen S, Lundegaard C, Worning P, Thomadsen H, Lund O, Brunak S, Buus S. (2004) SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation. Tissue Antigens. 63(5):395-400.
Tan PT, Heiny AT, Miotto O, Salmon J, Marques ET, Lemonnier F, August JT (2010) Conservation and diversity of influenza A H1N1 HLA-restricted T cell epitope candidates for epitope-based vaccines. PLoS One 5:e8754.
Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheeler DK, Sette A, Peters B. (2018) The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 47(D1): D339-D343.
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WHO MERS Global Summary and Assessment of Risk https://www.who.int/csr/disease/coronavirus_infections/risk-assessment-august-2018.pdf?ua=1
Xu, X., & Dang, Z. (2020). Promising Inhibitor for 2019-nCoV in Drug Development. https://doi.org/10.31219/osf.io/3hcm6.
Yuliwulandari R, Kashiwase K, Nakajima H, Uddin J, Susmiarsih TP, Sofro AS, Tokunaga K (2009) Polymorphisms of HLA genes in Western Javanese (Indonesia): close affinities to Southeast Asian populations. Tissue Antigens 73:46-53.
Zhao J, Zhao J, Mangalam AK, Channappanavar R, Fett C, Meyerholz DK, Agnihothram S, Baric RS, David CS, Perlman S. (2016) Airway Memory CD4(+) T Cells Mediate Protective Immunity against Emerging Respiratory Coronaviruses. Immunity 44(6):1379-91.
Zhavoronkov, Alex; Aladinskiy, Vladimir; Zhebrak, Alexander; Zagribelnyy, Bogdan; Terentiev, Victor; Bezrukov, Dmitry S.; et al. (2020): Potential 2019-nCoV 3C-like Protease Inhibitors Designed Using Generative Deep Learning Approaches. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.11829102.v1.
Ziebuhr J. (2005) The coronavirus replicase. Curr Top Microbiol Immunol. 287:57-94.
Backert, L., & Kohlbacher, O. (2015). Immunoinformatics and epitope prediction in the age of genomic medicine. Genome medicine 7: 119.
Bettini, M., & Vignali, D. A. (2009). Regulatory T cells and inhibitory cytokines in autoimmunity. Current opinion in immunology 21(6): 612–618.
Biddison WE, Martin R (2001) Peptide binding motifs for MHC class I and II molecules. Curr Protoc Immunol, Appendix 1: Appendix 1I.
Bishajit Sarkar, Md. Asad Ullah, Fatema Tuz Johora, Masuma Afrin Taniya, Yusha Araf (2020) The Essential Facts of Wuhan Novel Coronavirus Outbreak in China and Epitope-based Vaccine Designing against 2019-nCoV, bioRxiv 2020.02.05.935072; doi: https://doi.org/10.1101/2020.02.05.935072.
Bo Diao, Chenhui Wang, Yingjun Tan, Xiewan Chen, Ying Liu, Lifeng Ning, Li Chen, Min Li, Yueping Liu, Gang Wang, Zilin Yuan, Zeqing Feng, Yuzhang Wu, Yongwen Chen, (2020) Reduction and Functional Exhaustion of T Cells in Patients with Coronavirus Disease 2019 (COVID-19), medRxiv, doi: https://doi.org/10.1101/2020.02.18.20024364.
Bui H. H, Sidney J, Dinh K, Southwood S, Newman M. J, Sette A. (2006). Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics 17:153.
Bui H. H,Sidney J, Li W, Fusseder N, Sette A., (2007) Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics 8(1):361.
Calis JJA, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Kesmir C, Peters B. (2013) Properties of MHC class I presented peptides that enhance immunogenicity. PloS Comp. Biol. 8(1):361.
Ethan Fast, Binbin Chen (2020) Potential T-cell and B-cell Epitopes of 2019-nCoV, bioRxiv 2020.02.19.955484; doi: https://doi.org/10.1101/2020.02.19.955484.
Fan YY, Huang ZT, Li L, Wu MH, Yu T, Koup RA, Bailer RT, Wu CY. (2009) Characterization of SARS-CoV-specific memory T cells from recovered individuals 4 years after infection. Arch Virol: 154(7):1093-9.
Gonzalez-Galarza FF, Takeshita LY, Santos EJ, Kempson F, Maia MH, Silva AL, Silva AL, Ghattaoraya GS, Alfirevic A, Jones AR and Middleton D (2015) Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations. Nucleic Acid Research 28, D784-8.
Grifoni, Alba and Sidney, John and Zhang, Yun and Scheuermann, Richard H. and Peters, Bjoern and Sette, Alessandro, Candidate Targets for Immune Responses to 2019-Novel Coronavirus (nCoV): Sequence Homology- and Bioinformatic-Based Predictions. CELL-HOST-MICROBE-D-20-00119. SSRN: https://ssrn.com/abstract=3541361 or http://dx.doi.org/10.2139/ssrn.3541361.
Gustiananda M, Cox D, McMurtrey C, Jackson KW, Mojsilovic D, Bardet W, Schafer F, Cate S, Yaciuk J, Kaabinejadian S and Hildebrand WH (2013). Motifs of the naturally processed peptides presented by HLA-A*24:07. Front. Immunol. Conference Abstract: 15th International Congress of Immunology (ICI). doi: 10.3389/conf.fimmu.2013.02.01033.
Hsueh-Ling Janice Oh, Samuel Ken-En Gan, Antonio Bertoletti & Yee-Joo Tan (2012) Understanding the T cell immune response in SARS coronavirus infection, Emerging Microbes & Infections 1:1, 1-6.
Huang C, Wang Y, Li X, et al. (2020) Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 395(10223):497-506.
Janice Oh HL, Ken-En Gan S, Bertoletti A, Tan YJ. (2012) Understanding the T cell immune response in SARS coronavirus infection. Emerg Microbes Infect. 1(9):e23.
Jasper Fuk-Woo Chan, Kin-Hang Kok, Zheng Zhu, Hin Chu, Kelvin Kai-Wang To, Shuofeng Yuan & Kwok-Yung Yuen (2020) Genomic characterization of the 2019 novel human pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan, Emerging Microbes & Infections, 9:1, 221-236.
Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, Nielsen M. (2018) Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology. 2018 Jul;154(3):394-406.
Kaifu Gao, Duc Duy Nguyen, Rui Wang, Guo-Wei Wei (2020) Machine intelligence design of 2019-nCoV drugs, bioRxiv 2020.01.30.927889; doi: https://doi.org/10.1101/2020.01.30.927889.
Koh D, Sng J. (2010) Lessons from the past: perspectives on severe acute respiratory syndrome. Asia-Pacific journal of public health. 22(3 Suppl):132s-136s.
Kumar, S. (2020) Drug and Vaccine Design against Novel Coronavirus (2019-nCoV) Spike Protein through Computational Approach. Preprints 2020, 2020020071 (doi: 10.20944/preprints202002.0071.v1).
Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M. (2005) An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol. 35(8):2295-303.
Li, C. K., Wu, H., Yan, H., Ma, S., Wang, L., Zhang, M., Tang, X., Temperton, N. J., Weiss, R. A., Brenchley, J. M., Douek, D. C., Mongkolsapaya, J., Tran, B. H., Lin, C. L., Screaton, G. R., Hou, J. L., McMichael, A. J., & Xu, X. N. (2008). T cell responses to whole SARS coronavirus in humans. Journal of Immunology 181(8): 5490–5500.
Liu J, Sun Y, Qi J, Chu F, Wu H, Gao F, Li T, Yan J, Gao GF. (2010) The membrane protein of severe acute respiratory syndrome coronavirus acts as a dominant immunogen revealed by a clustering region of novel functionally and structurally defined cytotoxic T-lymphocyte epitopes. J Infect Dis. 15;202(8):1171-80.
Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, et al., (2020) Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.Lancet, 6736, 1–10.
Moise, L., Cousens, L., Fueyo, J., & De Groot, A. S. (2011). Harnessing the power of genomics and immunoinformatics to produce improved vaccines. Expert opinion on drug discovery, 6(1), 9–15.
Nathan P. Croft, Stewart A. Smith, Jana Pickering, John Sidney, Bjoern Peters, Pouya Faridi, Matthew J. Witney, Prince Sebastian, Inge E. A. Flesch, Sally L. Heading, Alessandro Sette, Nicole L. La Gruta, Anthony W. Purcell, David C.
Tscharke (2019) Most viral peptides displayed by class I MHC on infected cells are immunogenic, Proceedings of the National Academy of Sciences 116 (8) 3112-3117.
Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang, Hui-Dong Chen, Jing Chen, Yun Luo, Hua Guo, Ren-Di Jiang, Mei-Qin Liu, Ying Chen, Xu-Rui Shen, Xi Wang, Xiao-Shuang Zheng, Kai Zhao, Quan-Jiao Chen, Fei Deng, Lin-Lin Liu, Bing Yan, Fa-Xian Zhan, Yan-Yi Wang, Gengfu Xiao, Zheng-Li Shi. (2020) Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin, bioRxiv 2020, 01.22.914952; doi: https://doi.org/10.1101/2020.01.22.914952.
Schietinger, A., & Greenberg, P. D. (2014). Tolerance and exhaustion: defining mechanisms of T cell dysfunction. Trends in immunology, 35(2), 51–60.
Sharmin, R., Islam, A.B.M.M.K. (2014) A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design. BMC Bioinformatics 15: 161.
St-Jean, J. R., Jacomy, H., Desforges, M., Vabret, A., Freymuth, F., & Talbot, P. J. (2004). Human respiratory coronavirus OC43: genetic stability and neuroinvasion. Journal of virology, 78(16), 8824–8834.
Stranzl T, Larsen MV, Lundegaard C, Nielsen M (2010) NetCTLpan: panspecific MHC class I pathway epitope predictions. Immunogenetics 62:357-368.
Syed Faraz Ahmed, Ahmed A. Quadeer, Matthew R. McKay (2020) Preliminary identification of potential vaccine targets for 2019-nCoV based on SARS-CoV immunological studies, bioRxiv 2020.02.03.933226; doi: https://doi.org/10.1101/2020.02.03.933226.
Sylvester-Hvid C, Nielsen M, Lamberth K, Røder G, Justesen S, Lundegaard C, Worning P, Thomadsen H, Lund O, Brunak S, Buus S. (2004) SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation. Tissue Antigens. 63(5):395-400.
Tan PT, Heiny AT, Miotto O, Salmon J, Marques ET, Lemonnier F, August JT (2010) Conservation and diversity of influenza A H1N1 HLA-restricted T cell epitope candidates for epitope-based vaccines. PLoS One 5:e8754.
Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheeler DK, Sette A, Peters B. (2018) The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 47(D1): D339-D343.
WHO COVID-19 situation reports. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports.
WHO MERS Global Summary and Assessment of Risk https://www.who.int/csr/disease/coronavirus_infections/risk-assessment-august-2018.pdf?ua=1
Xu, X., & Dang, Z. (2020). Promising Inhibitor for 2019-nCoV in Drug Development. https://doi.org/10.31219/osf.io/3hcm6.
Yuliwulandari R, Kashiwase K, Nakajima H, Uddin J, Susmiarsih TP, Sofro AS, Tokunaga K (2009) Polymorphisms of HLA genes in Western Javanese (Indonesia): close affinities to Southeast Asian populations. Tissue Antigens 73:46-53.
Zhao J, Zhao J, Mangalam AK, Channappanavar R, Fett C, Meyerholz DK, Agnihothram S, Baric RS, David CS, Perlman S. (2016) Airway Memory CD4(+) T Cells Mediate Protective Immunity against Emerging Respiratory Coronaviruses. Immunity 44(6):1379-91.
Zhavoronkov, Alex; Aladinskiy, Vladimir; Zhebrak, Alexander; Zagribelnyy, Bogdan; Terentiev, Victor; Bezrukov, Dmitry S.; et al. (2020): Potential 2019-nCoV 3C-like Protease Inhibitors Designed Using Generative Deep Learning Approaches. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.11829102.v1.
Ziebuhr J. (2005) The coronavirus replicase. Curr Top Microbiol Immunol. 287:57-94.
Published
2020-03-31
How to Cite
Gustiananda, M. (2020). What do T cells see in SARS-CoV2?. Indonesian Journal of Life Sciences, 2(1), 29-43. https://doi.org/https://doi.org/10.54250/ijls.v2i1.36
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