Identification of CD8+ Immunogenic Peptides for Vaccine Design against Nipah Virus in Humans
Abstract
Background: Nipah virus is a pathogenic virus of ruinous zoonotic potential with inflated rate of mortality in humans.
Methods: Considering the emerging threat of this pandemic virus, the present investigation amid to design vaccine by using the bioinformatics tools such as host and virus codon usage analysis, CD8+ peptide prediction, immunogenicity/allergenicity/toxicity, MHC-I allele binding prediction and subsequent population coverage and MHC-I-peptide docking analysis.
Results: In this study (conducted in 2022 at School of Biotechnology, Katra, India), a set of 11 peptides of the structural proteins of Nipah Virus were predicted and recognized by the set of MHC-I alleles that are expressed in 92% of the global human population.
Conclusion: The strong interactions between these peptides and the MHC-I protein suggest them as strong peptide candidates for the development of vaccine against Nipah Virus.
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2. Ochani RK, Batra S, Shaikh A, Asad A (2019). Nipah virus-the rising epidemic: a review. Infez Med, 27(2):117–27.
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25. Khandia R, Singhal S, Kumar U, et al (2019). Analysis of Nipah virus codon usage and adaptation to hosts. Front Mi-crobiol, 10:886.
26. Andreatta M, Nielsen M (2016). Gapped se-quence alignment using artificial neural networks: application to the MHC class I system. Bioinformatics, 32(4):511–7.
27. Wang L, Harcourt BH, Yu M, et al (2001). Molecular biology of Hendra and Nipah viruses, Microbes Infect, 3 (4):279–287.
28. Chadha MS, Comer JA, Lowe L, et al (2006). Nipah virus associated encephalitis out-break, Siliguri, India. Emerg Infect Dis, 12 (2): 235–240.
29. Gurley ES, Montgomery JM, Hossain MJ, et al (2007). Person-to person transmission of Nipah virus in a Bangladeshi com-munity. Emerg Infect Dis, 13 (7): 1031–1037.
30. Aditi, Shariff M (2019). Nipah virus in-fection: A review. Epidemiol Infect, 147: e95.
2. Ochani RK, Batra S, Shaikh A, Asad A (2019). Nipah virus-the rising epidemic: a review. Infez Med, 27(2):117–27.
3. Chua KB, Goh KJ, Wong KT, et al (1999). Fatal encephalitis due to Nipah virus among pig-farmers in Malaysia. Lan-cet,354(9186):1257–9.
4. Carrasco-Hernandez R, Jácome R, López Vidal Y, et al (2017). Are RNA viruses candidate agents for the next global pandemic? A review. ILAR J,58(3):343-58.
5. Martinez-Gil L, Vera-Velasco NM, Mingar-ro I (2017). Exploring the human-Nipah virus protein-protein interactome. J Vi-rol, 91(23):e01461-17.
6. Sharma V, Kaushik S, Kumar R, et al (2019). Emerging trends of Nipah virus: A re-view. Rev Med Virol,29(1):e2010.
7. Sudeep AB, Yadav PD, Gokhale MD, et al (2021). Detection of Nipah virus in Pteropusmedius in 2019 outbreak from Ernakulam district, Kerala, India. BMC Infect Dis,21(1):162.
8. Gurley ES, Montgomery JM, Hossain MJ, et al (2007). Person-to-person transmission of Nipah virus in a Bangladeshi com-munity. Emerg Infect Dis, 13(7):1031-7.
9. Skowron K, Bauza-Kaszewska J, Grudlewska-Buda K, et al (2022). Nipah virus–Another threat from the world of zoonotic viruses. Front Microbiol, 12:811157.
10. Arunkumar G, Devadiga S, McElroy AK, et al (2019). Adaptive Immune Responses in Humans During Nipah Virus Acute and Convalescent Phases of Infection. Clin Infect Dis, 69(10):1752–6.
11. Anwar AM, Soudy M, Mohamed R (2019).vhcub: Virus-host codon usage co-adaptation analysis. F1000Res,8:2137.
12. Doytchinova IA, Flower DR (2007).VaxiJen: a server for prediction of protective an-tigens, tumour antigens and subunit vac-cines. BMC Bioinformatics, 8:4.
13. Gasteiger E, Hoogland C, Gattiker A, et al (2005). Protein identification and analy-sis tools on the ExPASy server. In: Walker, J.M. (eds) The Proteomics Protocols Handbook. Springer Protocols Hand-books. Humana Press.
14. Larsen M V, Lundegaard C, Lamberth K, et al (2007). Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics, 8:424.
15. Dimitrov I, Naneva L, Doytchinova I, et al (2014). AllergenFP: allergenicity predic-tion by descriptor fingerprints. Bioinfor-matics, 30(6):846–51.
16. Gupta S, Kapoor P, Chaudhary K, et al (2013).In silico approach for predicting toxicity of peptides and proteins. PLoS One, 8(9):e73957.
17. Dhanda SK, Vir P, Raghava GPS (2013). Designing of interferon-gamma induc-ing MHC class-II binders. Biol Direct, 8:30.
18. Lundegaard C, Lund O, Nielsen M (2008). Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. Bioin-formatics, 24(11):1397–8.
19. Bui HH, Sidney J, Dinh K, et al (2006). Pre-dicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics,7:153.
20. Waterhouse A, Bertoni M, Bienert S, et al (2018). SWISS-MODEL: homology mod-elling of protein structures and com-plexes. Nucleic Acids Res, 46(W1):W296–303.
21. Bienert S, Waterhouse A, De Beer TAP, et al (2017). The SWISS-MODEL Reposito-ry—new features and functionality. Nu-cleic Acids Res, 45(D1):D313–D319.
22. Trott O, Olson AJ (2010). AutoDockVina: improving the speed and accuracy of docking with a new scoring function, ef-ficient optimization, and multithreading. J Comput Chem,31(2):455–61.
23. Bowers KJ, Chow E, Xu H, et al (2006). Pro-ceedings of the 2006 ACM/IEEE Conference on Supercomputing. ACM New York, NY, USA.
24. MadhaviSastry G, Adzhigirey M, Day T, et al (2013). Protein and ligand prepara-tion: parameters, protocols, and influ-ence on virtual screening enrichments. J Comput Aided Mol Des, 27(3):221–34.
25. Khandia R, Singhal S, Kumar U, et al (2019). Analysis of Nipah virus codon usage and adaptation to hosts. Front Mi-crobiol, 10:886.
26. Andreatta M, Nielsen M (2016). Gapped se-quence alignment using artificial neural networks: application to the MHC class I system. Bioinformatics, 32(4):511–7.
27. Wang L, Harcourt BH, Yu M, et al (2001). Molecular biology of Hendra and Nipah viruses, Microbes Infect, 3 (4):279–287.
28. Chadha MS, Comer JA, Lowe L, et al (2006). Nipah virus associated encephalitis out-break, Siliguri, India. Emerg Infect Dis, 12 (2): 235–240.
29. Gurley ES, Montgomery JM, Hossain MJ, et al (2007). Person-to person transmission of Nipah virus in a Bangladeshi com-munity. Emerg Infect Dis, 13 (7): 1031–1037.
30. Aditi, Shariff M (2019). Nipah virus in-fection: A review. Epidemiol Infect, 147: e95.
| Files | ||
| Issue | Vol 53 No 12 (2024) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijph.v53i12.17331 | |
| Keywords | ||
| Zoonotic virus Nipah virus Vaccine design Immunogenicpeptides Molecular dynamics | ||
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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
How to Cite
1.
Suden P, Singh I, Chopra C, Mehta M, Chandra R, Bhushan I. Identification of CD8+ Immunogenic Peptides for Vaccine Design against Nipah Virus in Humans. Iran J Public Health. 2024;53(12):2789-2801.
