Mikrobiol. Z. 2021; 83(1):78-86.
Identification of Cytotoxic T-Cell and B-Cell Epitopes in the Nucleocapsid Phosphoprotein
of SARS-COV-2 Using Immunoinformatics
University of Mosul
Almajmuaa Str., Mosul, 41002, Nineveh, Iraq
Last December, a novel coronavirus emerged in Wuhan city, China. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes a high intense acute respiratory syndrome with elevation mortality. Nucleocapsid phosphoprotein (NP) is one of the most structural proteins of the virus. NP possesses active immunogenicity for T-cell response. Because NP considered as a potential vaccine target, our study goal was to identify the cytotoxic T-cell (CTL) and B-cell epitopes inside NP peptides. Methods. We used a series of popular immunoinformatics and algorithm tools such as FASTA-NCBI, CLUSTAL-OMGA, T-COFFEE, SWISS-MODEL, CTLPred and its branches. Results. Homology modeling and alignment of SARS-CoV-2 NP showed high conserved residues compared with related sequences. Different types of the major histocompatibility complex (MHC) alleles were identified, specifically human leukocyte antigens (HLA-A) affinity for NP. We also demonstrate six B-cell epitopes with a high score above the threshold. Conclusions. We recorded high binder HLA-A*02:01 alleles matched between the novel coronavirus SARS-CoV-2 NP and the Bat coronavirus SARS-Bat-CoV NP. Identification of CTL response and B-cell predictions will be helpful in reverse immunogenetic approaches, hence in the strategy process of the plausible design of the vaccine.
Keywords: Nucleocapsid phosphoprotein, SARS-CoV, Immunoinformatics, MHC epitope, Cytotoxic T-cells, Affinity.
Full text (PDF, in English)
- Thomson G. COVID‐19: social distancing, ACE 2 receptors, protease inhibitors and beyond. Int J Clin Prac. 2020; March. https://doi.org/10.1111/ijcp.13503
- Cheepsattayakorn A, Cheepsattayakorn R. Proximal Origin and Phylogenetic Analysis of COVID-19 (2019-nCoV or SARS-CoV-2). EC Mic. 2020:9–12.
- Chen Y, Liu Q, Guo D. Emerging coronaviruses: genome structure, replication and pathogenesis. J Med Virol. 2020; 92:418–423. https://doi.org/10.1002/jmv.25681
- Dawood A. Mutated COVID-19, May Foretells Mankind in a Great Risk in The Future. N Mic N Inf. 2020. https://doi.org/10.1016/j.nmni.2020.100673
- Wu A, Peng Y, Huang B, Ding X, Wang X, Niu P, Meng J, Zhu Z, Zhang Z, Wang L, Sheng A, Quan L, Xia Z, Tan W, Cheng G, Jiang T. Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China. Ce Ho & Mic. 2020. https://doi.org/10.1016/j.chom.2020.02.001
- Guo YR, Cao QD, Hong ZS, Tan YY, Chen SD, Jin HJ, Tan KS, Wang DY, Yan Y. The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak –anupdate on the status. Mil Med Res. 2020; 7:11. https://doi.org/10.1186/s40779-020-00240-0
- Li S, Wu H, Yan H, Ma H, Wang S, Zhang L, Tang M, Temperton X, Weiss N, Brenchley R, et al. T cell responses to whole SARS coronavirus in humans. J Immunol. 2008; 181:5490–5500. https://doi.org/10.4049/jimmunol.181.8.5490
- Kim JM, Chung YS, Jo HJ, Lee NJ, Kim MS, Woo SH, Park S, Kim JW, Kim HM, Han MG. Identification of Coronavirus Isolated from a Patient in Korea with COVID-19. Os Pub He Res Per. 2020; 11(1):3–7. https://doi.org/10.24171/j.phrp.2020.11.1.02
- McBride R, Zyl M, Fielding BC. The coronavirus nucleocapsid is a multifunctional protein. Viruses. 2014; 6:2991–3018. https://doi.org/10.3390/v6082991
- Wurm T, Chen H, Hodgson T, Britton P, Brooks G, Hiscox JA. Localization to the nucleolus is a common feature of coronavirus nucleoproteins, and the protein may disrupt host cell division. J Virol. 2001; 75:9345–9356. https://doi.org/10.1128/JVI.75.19.9345-9356.2001
- You J, Dove BK, Enjuanes L, DeDiego ML, Alvarez E, Howell G, Heinen P, Zambon M, Hiscox JA. Subcellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein. J Gen Virol. 2005; 86(12):3303–3310. https://doi.org/10.1099/vir.0.81076-0
- Baruah V, Bose S. Immunoinformatics‐aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019‐nCoV. J Med Virol. 2020; 92:495–500. https://doi.org/10.1002/jmv.25698
- Lana R, Coellaho FC, Gomes MF, Cruz OG, Bastos LS, Villela, Codeco CT. The novel coronavirus (SARS-CoV-2) emergency and the role of timely and effective national health surveillance. Rep in Pub He. 2020.
- Dawood A, Alnori H. Tunicamycin Anticancer Drug May Reliable to Treat Coronavirus Disease-19. OAMJMS. 2020; 8(1):129–133. https://doi.org/10.3889/oamjms.2020.4954
- Dawood A. Glycosylation, Ligand Binding Sites and Antigenic Variations Between Membrane Glycoprotein of COVID-19 and Related Coronaviruses. Vacunas. 2020. https://doi.org/10.1016/j.vacun.2020.09.005
- Baglivo M, Baronio M, Natalini G, Beccari T, Fuulcheri PC, Petralia P, Michelini S, Fiorentini G, Miggiano GA, Morresi A, Tonini G, Bertelli M. Natural small molecules as inhibitors of coronavirus lipid dependent attachment to host cells: a possible strategy for reducing SARS-COV-2 infectivity? Acta Biomed. 2020; 91(1):161–164.
- Yin C. Genotyping coronavirus SARS-CoV-2: methods and implications. Arxiv. 2003; 10965v1.
- Leung D, Tam F, Ma CH, Chan PK, Cheung JL, Niu H, Tam JS, Lim PL. Antibody Response of Patients with Severe Acute Respiratory Syndrome (SARS) Targets Viral Nucleocapsid. T J Inf Dis. 2004; 190:379–86. https://doi.org/10.1086/422040
- Peters B, Bulik S, Tampa R, Endert PM, Holzhutter HG. Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol. 2003; 171:1741–1749. https://doi.org/10.4049/jimmunol.171.4.1741
- Chen J. Pathogenicity and transmissibility of 2019-nCoV — a quick overview and comparison with other emerging viruses. Microb & Inf. 2020; 22:69–71. https://doi.org/10.1016/j.micinf.2020.01.004
- Zhang L, Zhang F, Yu W, He T, Yu J, Yi CE, Ba L, Li W, Farzan M, Chen Z, Yuen KY, Ho D. Antibody responses against SARS coronavirus are correlated with the disease outcome of Infected Individuals. J Med Virol. 2006; 78:1–8. https://doi.org/10.1002/jmv.20499
- Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M. 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. 2005; 35:2295–2303. https://doi.org/10.1002/eji.200425811
- Nielsen M, Lundegaard C, Lund O, Kasmir C. The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogen. 2005; 57:33–41. https://doi.org/10.1007/s00251-005-0781-7