Immunoinformatics Prediction of Peptide-Based Vaccine against MERS-Coronaviruses

Esra Babiker; Nadir Abuzeid

doi:10.52981/smlj.v8i1.2561

Esra Babiker Department of Microbiology, Faculty of Medical Laboratory Sciences, National University, Khartoum, Sudan
Nadir Abuzeid Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Khartoum, Sudan https://orcid.org/0000-0003-2074-7892

DOI: https://doi.org/10.52981/smlj.v8i1.2561

الملخص

MERS-Corona-viruses cause massive and pandemic outbreaks of respiratory infection in several regions of continents' and revealed a global epidemic trend. However, no effective antiviral drug or vaccine has been developed to treat coronavirus. Aim of the study to detect epitopes can be as vaccine. A total of 28 outer spike glycoprotein (s) sequences of Corona-viruses were retrieved from the National Center for Biotechnology Information database (NCBI) on them, several tests were conducted using Immune Epitope Analysis Database (IEDB) to detect the highly conserved immunogenic epitopes of B and T cells from which all possible epitopes that can be used as a therapeutic peptide vaccine to be selected. Several conserved cytotoxic T-lymphocyte epitopes, linear and conformational B cell epitopes were predicted for Corona-viruses spike glycoprotein and their antigenicity was calculated. Among Bcell epitopes 106–SQDVKQ-111 is antigenic and in the case of T cell epitopes, 279-FQFATLPVY-287 and 786-FSFGVTQEY-794 and 69-ITYQGLFPY-77 and, 924- AQYVAGYKV-938, 1271ALNESYIDL-1285, and 1300-AGLVALALC-1314 are extremely antigenic promising for vaccination against Corona-viruses They demonstrated population coverage against the whole world 91.81%.The study led to the discovery of various epitopes, conserved among various strains belonging to different countries. The potential antigenic epitopes can be successfully utilized in designing novel vaccines for combating and eradication of MERS Corona-viruses disease.

المراجع

[1] Cao Y, Li Q, Chen J, et al. (2020). Hospital Emergency Management Plan During the COVID-19 Epidemic. Acad Emerg Med 2020 2020/03/04. DOI: 10.1111/acem.13951.
[2] Li M, Lei P, Zeng B, et al. (2020).Coronavirus Disease (COVID-19): Spectrum of CT Findings and Temporal Progression of the Disease. Acad Radiol 2020 2020/03/25. DOI: 10.1016/ j. acra. 2020.03.003.
[3]Cucinotta D and Vanelli M. (2020). WHO Declares COVID-19 a Pandemic. Acta Biomed 2020; 91: 157-160. 2020/03/20. DOI: 10.23750/ abm.v91i1.9397.
[4]Zoia C, Bongetta D, Veiceschi P, et al. (2020). Neurosurgery during the COVID-19 pandemic: update from Lombardy, northern Italy. Acta Neurochir (Wien) 2020 2020/03/31. DOI: 10.1007/s00701-020-04305-w.
[5] Dashraath P, Jing Lin Jeslyn W, Mei Xian Karen L, et al. (2020). Coronavirus Disease 2019 (COVID-19) Pandemic and Pregnancy. Am J Obstet Gynecol 2020 2020/03/29. DOI: 10.1016/j.ajog.2020.03.021.
[6] Muniyappa R and Gubbi S. (2020).COVID-19 Pandemic, Corona Viruses, and Diabetes Mellitus. Am J Physiol Endocrinol Metab 2020 2020/04/02. DOI: 10.1152/ajpendo.00124.2020.
[7] Han X, Cao Y, Jiang N, et al. (2020). Novel Coronavirus Pneumonia (COVID-19) Progression Course in 17 Discharged Patients: Comparison of Clinical and Thin-Section CT Features During Recovery. Clin Infect Dis 2020 2020/04/01. DOI: 10.1093/cid/ciaa271.
[8] Bal A, Destras G, Gaymard A, et al. (2020). Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino-acid deletion in nsp2 (Asp268Del). Clin Microbiol Infect 2020 2020/04/03. DOI: 10.1016/ j.cmi.2020.03.020.
[9] Capobianchi MR, Rueca M, Messina F, et al. (2020).Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy. Clin Microbiol Infect 2020 2020/04/02. DOI: 10.1016/ j.cmi.2020.03.025.
[10]Petrosillo N, Viceconte G, Ergonul O, et al. (2020). COVID-19, SARS, and MERS: are they
closely related? Clin Microbiol Infect 2020 2020/04/03. DOI: 10.1016/j.cmi.2020.03.026.
[11] Zeng H, Xu C, Fan J, et al. (2020). Antibodies in Infants Born to Mothers With COVID-19 Pneumonia. JAMA 2020 2020/03/28. DOI: 10.1001/jama.2020.4861.
[12]Ibrahim IM, Abdelmalek DH, Elshahat ME, et al. (2020). COVID-19 spike-host cell receptor GRP78 binding site prediction. J Infect 2020 2020/03/15. DOI: 10.1016/ j.jinf. 2020 .02 . 026.
[13]Tilocca B, Soggiu A, Musella V, et al. (2020). Molecular basis of COVID-19 relationships in different species: a one health perspective. Microbes Infect 2020 2020/03/21. DOI: 10.1016/j.micinf.2020.03.002.
[14]Udugama B, Kadhiresan P, Kozlowski HN, et al. (2020). Diagnosing COVID-19: The Disease and Tools for Detection. ACS Nano 2020 2020/04/01. DOI: 10.1021/acsnano.0c02624.
[15]Long C, Xu H, Shen Q, et al. (2020). Diagnosis of the Coronavirus disease (COVID-19): RRT-PCR or CT? Eur J Radiol 2020; 126: 108961. 2020/04/02. DOI: 10.1016/j. ejrad. 2020 . 108961.
[16] Hase R, Kurita T, Muranaka E, et al. (2020). A case of imported COVID-19 diagnosed by PCR-positive lower respiratory specimen but with PCR-negative throat swabs. Infect Dis (Lond) 2020: 1-4. 2020/04/03. DOI: 10.1080/ 23744235 .2020.1744711.
[17]Chan JF, Yip CC, To KK, et al. (2020). Improved molecular diagnosis of COVID-19 by the novel, highly sensitive, and specific COVID-19-RdRp/Hel real-time reverse transcription-polymerase chain reaction assay validated in vitro and with clinical specimens. J Clin Microbiol 2020 2020/03/07. DOI: 10.1128/JCM.00310-20.
[18]Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, et al. (2006)
The immune epitope database (IEDB) 3.0. Nucleic Acids Res 43: D405-D412
[19] Reche P, Flower DR, Fridkis-Hareli M, Hoshino Y.(2015).Peptide-Based immuno thera- peutics and vaccines 2015. J Immunol Res 2015.
[20] Emini EA, Hughes JV, Perlow D, Boger J (1985) Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol 55: 836-839.
[21] Kolaskar AS, Tongaonkar PC. A semi-empirical method for prediction of
antigenic determinants on protein antigens. FEBS letters (1990) 276: 172-174.
[22] Andreatta M, Nielsen M. Gapped sequence alignment using artificial neural networks: application to the MHC class I system. Bioinformatics (2015) 32: 511-517.
[23] Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, et al. (2003).
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Science. 12: 1007.
[24] Wang P, Sidney J, Dow C, Mothe B, Sette A, et al. (2008). A systematic assessment of MHC class II peptide binding predictions and evaluation of the approach. PLoS Comput Biol 4: e1000048.
[25] Bui HH, Sidney J, Dinh K, Southwood S, Newman MJ, et al. (2006). Predicting
population coverage of T-cell epitope based
diagnostics and vaccines. BMC bioinformatics.7: 153.
[26] Källberg M, Wang H, Wang S, Peng J, Wang Z, et al. (2012). Template-based protein structure modeling using the RaptorX web server. Nature protocols 7: 1511-1522.
[27]Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004). UCSF Chimera-a visualization system.
[28] Mitchell LA, Tingle AJ, Décarie D, Shukin R (1999). Identification of rubella virus T-cell epitopes recognized in anamnestic response to RA27/3 vaccine: associations with a boost in neutralizing antibody titer. Vaccine 17: 2356-2365
[29] Broere F, Apasov SG, Sitkovsky MV, van Eden W (2011) A2 T cell subsets and
T cell-mediated immunity. Principles of Immunopharmacology 15-27.