In Silico Characterization of Epitopes from Human Rotavirus VP7 Genotype G9 Design for Vaccine Development
Abstract
Acute gastroenteritis caused by Rotavirus remains the leading cause of child mortality worldwide. Rotavirus genotype G9 circulates in humans throughout the world. Antibodies against the outer glycoproteins VP7 and VP4 Rotavirus capsid are the main neutralization antibodies in the vaccine assessment. This study aimed to select an epitope to evoke T and B cells' response, as a favorable candidate for vaccine development using in Silico evaluation. In the present study, Rotavirus genotypes were determined in 100 stools specimens collected from children with acute diarrhea. The results showed predominant G genotype, G9 (38.5%) followed by G2 (22.9%), G1 (16.5%), G12 (11.4%), G4 (6.4%), and G3 (4.3%). The G9 was dominant in this study and other regions of Iran; thus, this study was conducted to select an epitope from Rotavirus genotype G9 as a promising epitope candidate for future vaccine development. For this reason, several works including a complete sequence of VP7 G9, phylogenetic analysis, Prediction of Protein Structure, Physicochemical Properties of Protein and Epitope prediction were carried out. The outcomes of this study revealed that the complete sequence of VP7 (G9) was comprised of 1062 nt with 326 amino acids (accession number MH824633). The selected epitope contained amino acid sequence of STLCLYYPTEASTQIGDTEWKN with the best score for T and B cells response. Based on data of computational biology, the selected epitope can optimistically have considered as an epitope candidate for rotavirus vaccine development.
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13. Lee S-W, Markham PF, Coppo MJ, Legione AR, Markham JF, Noormohammadi AH, et al. Attenuated vaccines can recombine to form virulent field viruses. Science 2012;337(6091):188.
14. Simonsen L, Viboud C, Elixhauser A, Taylor RJ, Kapikian A. More on RotaShield and intussusception: the role of age at the time of vaccination. J Infect Dis 2005;192(Supp1):S36-S43.
15. Li Z, Cui K, Wang H, Liu F, Huang K, Duan Z, et al. A milk-based self-assemble Rotavirus VP6–ferritin nanoparticle vaccine elicited protection against the viral infection. J Nanobiotechnology 2019;17(1):13.
16. Esona MD, Mijatovic-Rustempasic S, Yen C, Parashar UD, Gentsch JR, Bowen MD, et al. Detection of PCV-2 DNA in stool samples from infants vaccinated with RotaTeq®. Hum Vaccin Immunother 2014;10(1):25-32.
17. O'Leary ST, Parashar UD, Crane LA, Allison MA, Stokley S, Beaty BL, et al. Adoption of Rotavirus vaccine by US physicians: progress and challenges. American journal of preventive medicine. 2013;44(1):56-62.
18. Jin-Yuan W, Yan Z, Guang-Ming Z, Guo-Fa M, Shan Y, Na Yn, et al. Isolation and characterization of a new candidate human inactivated Rotavirus vaccine strain from hospitalized children in Yunnan, China: 2010-2013. World J Clin Cases 2018; 6(11): 426–40.
19. Nick ST, Mohebbi SR, Ghaemi A, Hosseini SM. Human rotavirus in Iran; molecular epidemiology, genetic diversity and recent updates on vaccine advances. Gastroenterology and hepatology from bed to bench. 2019;12(2):98..
20. Azaran A, Makvandi M, Teimoori A, Ebrahimi S, Heydari F, Nikfar R. Distribution of Rotavirus Genotypes Circulating in Ahvaz, Iran in 2016. Iranian biomedical journal 2018; 22(2):107.
21. Jalilvand S, Afchangi A, Mohajel N, Roohvand F, Shoja Z. Diversity of VP7 genes of G1 Rotaviruses isolated in Iran, 2009–2013. Infect Genet Evol 2016;37:275-9.
22. Moure UAE, Banga-Mingo V, Gody JC, Mwenda JM, Fandema J, Waku-Kouomou D, et al. Emergence of G12 and G9 rotavirus genotypes in the Central African Republic, January 2014 to February 2016. BMC Res Notes2018;11(1):5.
23. Emslie KR, Miller JM, Slade MB, Dormitzer PR, Greenberg HB, Williams KL. Expression of the rotavirus SA11 protein VP7 in the simple eukaryote Dictyostelium discoideum. J Virol 1995;69(3):1747-54.
24. McCrae M, McCorquodale J. Expression of a major bovine rotavirus neutralisation antigen (VP7c) in Escherichia. Gene 1987;55(1):9-18.
25. Pêra FF, Mutepfa DL, Khan AM, Els JH, Mbewana S, van Dijk AA, et al. Engineering and expression of a human rotavirus candidate vaccine in Nicotiana benthamiana. Virol J 2015;12(1):205.
26. Blutt SE, Crawford SE, Warfield KL, Lewis DE, Estes MK, Conner ME. The VP7 outer capsid protein of rotavirus induces polyclonal B-cell activation. Virol J 2004;78(13):6974-81.
27. Hart C, Cunliffe N. Rotavirus in antigenic variation. Academic Press London Alam NH, Ashraf H Treatment of infectious diarrhea in children Paediatr Drugs. 2003;5(3):151-65.
28. Jiang V, Jiang B, Tate J, Parashar UD, Patel MM. Performance of rotavirus vaccines in developed and developing countries. Hum Vaccin 2010;6(7):532-42.
29. Nandy A, Basak S. A brief review of computer-assisted approaches to rational design of peptide vaccines. Int J Mol Sci 2016;17(5):666.
2. Control CfD, Prevention. Rotavirus surveillance--worldwide, 2001-2008. MMWR Morb Mortal Wkly Rep 2008;57(46):1255-7.
3. Surendran S. Rotavirus infection: molecular changes and pathophysiology. Exp Clin Sci J 2008;7(62):154.
4. Alfieri A, Parazzi M, Takiuchi E, Médici K, Alfieri A. Frequency of group A Rotavirus in diarrhoeic calves in Brazilian cattle herds, 1998–2002. Trop Anim Health Prod 2006;38(7-8):521-6.
5. Chen F, Knutson TP, Ciarlet M, Sturos M, Marthaler DG. Complete genome characterization of a Rotavirus B (RVB) strain identified in Alpine goat kids with enteritis reveals inter-species transmission with RVB bovine strains. J Gen Virol 2018;99(4):457-63.
6. Ogden KM, Tan Y, Akopov A, Stewart LS, McHenry R, Fonnesbeck CJ, et al. Multiple introductions and antigenic mismatch with vaccines may contribute to increased predominance of G12P [8] Rotaviruses in the United States. J Virol 2019;93(1):e01476-18.
7. João ED, Strydom A, O’Neill HG, Cuamba A, Cassocera M, et al. Rotavirus A strains obtained from children with acute gastroenteritis in Mozambique, 2012-2013: G and P genotypes and phylogenetic analysis of VP7 and partial VP4 genes. Arch Virol 2018;163(1):153-65.
8. Mukherjee A, Ghosh S, Bagchi P, Dutta D, Chattopadhyay S, Kobayashi N, et al. Full genomic analyses of human Rotavirus G4P [4], G4P [6], G9P [19] and G10P [6] strains from North-eastern India: evidence for interspecies transmission and complex reassortment events. Clin Microbiol Infect 2011;17(9):1343-6.
9. Do LP, Nakagomi T, Otaki H, Agbemabiese CA, Nakagomi O, Tsunemitsu H. Phylogenetic inference of the porcine Rotavirus A origin of the human G1 VP7 gene. Infect Genet Evol 2016;40:205-13.
10. Emamghorashi F, Rajabi S, Shadman A. Frequency of Rotavirus infection in children with acute gastroenteritis in Jahrom, South of Iran. Iran J Med Sci 2015; 33(2):84-7.
11. Jalilvand S, Roohvand F, Arashkia A, Shoja Z. Update on Epidemiology and Circulating Genotypes of Rotavirus in Iranian Children With Severe Diarrhea: 1986-2015. International Journal of Travel Medicine and Global Health 2018; 6(1):7-10.
12. Azaran A, Makvandi M, Samarbafzadeh A, Neisi N, Hoseinzadeh M, Rasti M, et al. Study on Rotavirus Infection and Its Genotyping in Children Below 5 Years in South West Iran. Iran J Pediatr 2016;26(2):e2080-e.
13. Lee S-W, Markham PF, Coppo MJ, Legione AR, Markham JF, Noormohammadi AH, et al. Attenuated vaccines can recombine to form virulent field viruses. Science 2012;337(6091):188.
14. Simonsen L, Viboud C, Elixhauser A, Taylor RJ, Kapikian A. More on RotaShield and intussusception: the role of age at the time of vaccination. J Infect Dis 2005;192(Supp1):S36-S43.
15. Li Z, Cui K, Wang H, Liu F, Huang K, Duan Z, et al. A milk-based self-assemble Rotavirus VP6–ferritin nanoparticle vaccine elicited protection against the viral infection. J Nanobiotechnology 2019;17(1):13.
16. Esona MD, Mijatovic-Rustempasic S, Yen C, Parashar UD, Gentsch JR, Bowen MD, et al. Detection of PCV-2 DNA in stool samples from infants vaccinated with RotaTeq®. Hum Vaccin Immunother 2014;10(1):25-32.
17. O'Leary ST, Parashar UD, Crane LA, Allison MA, Stokley S, Beaty BL, et al. Adoption of Rotavirus vaccine by US physicians: progress and challenges. American journal of preventive medicine. 2013;44(1):56-62.
18. Jin-Yuan W, Yan Z, Guang-Ming Z, Guo-Fa M, Shan Y, Na Yn, et al. Isolation and characterization of a new candidate human inactivated Rotavirus vaccine strain from hospitalized children in Yunnan, China: 2010-2013. World J Clin Cases 2018; 6(11): 426–40.
19. Nick ST, Mohebbi SR, Ghaemi A, Hosseini SM. Human rotavirus in Iran; molecular epidemiology, genetic diversity and recent updates on vaccine advances. Gastroenterology and hepatology from bed to bench. 2019;12(2):98..
20. Azaran A, Makvandi M, Teimoori A, Ebrahimi S, Heydari F, Nikfar R. Distribution of Rotavirus Genotypes Circulating in Ahvaz, Iran in 2016. Iranian biomedical journal 2018; 22(2):107.
21. Jalilvand S, Afchangi A, Mohajel N, Roohvand F, Shoja Z. Diversity of VP7 genes of G1 Rotaviruses isolated in Iran, 2009–2013. Infect Genet Evol 2016;37:275-9.
22. Moure UAE, Banga-Mingo V, Gody JC, Mwenda JM, Fandema J, Waku-Kouomou D, et al. Emergence of G12 and G9 rotavirus genotypes in the Central African Republic, January 2014 to February 2016. BMC Res Notes2018;11(1):5.
23. Emslie KR, Miller JM, Slade MB, Dormitzer PR, Greenberg HB, Williams KL. Expression of the rotavirus SA11 protein VP7 in the simple eukaryote Dictyostelium discoideum. J Virol 1995;69(3):1747-54.
24. McCrae M, McCorquodale J. Expression of a major bovine rotavirus neutralisation antigen (VP7c) in Escherichia. Gene 1987;55(1):9-18.
25. Pêra FF, Mutepfa DL, Khan AM, Els JH, Mbewana S, van Dijk AA, et al. Engineering and expression of a human rotavirus candidate vaccine in Nicotiana benthamiana. Virol J 2015;12(1):205.
26. Blutt SE, Crawford SE, Warfield KL, Lewis DE, Estes MK, Conner ME. The VP7 outer capsid protein of rotavirus induces polyclonal B-cell activation. Virol J 2004;78(13):6974-81.
27. Hart C, Cunliffe N. Rotavirus in antigenic variation. Academic Press London Alam NH, Ashraf H Treatment of infectious diarrhea in children Paediatr Drugs. 2003;5(3):151-65.
28. Jiang V, Jiang B, Tate J, Parashar UD, Patel MM. Performance of rotavirus vaccines in developed and developing countries. Hum Vaccin 2010;6(7):532-42.
29. Nandy A, Basak S. A brief review of computer-assisted approaches to rational design of peptide vaccines. Int J Mol Sci 2016;17(5):666.
| Files | ||
| Issue | Vol 18, No 6 (2019) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijaai.v18i6.2179 | |
| PMID | 32245310 | |
| Keywords | ||
| Computational biology Rotavirus Vaccines | ||
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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
How to Cite
1.
Jalilian S, Teimoori A, Makvandi M. In Silico Characterization of Epitopes from Human Rotavirus VP7 Genotype G9 Design for Vaccine Development. Iran J Allergy Asthma Immunol. 2019;18(6):664-670.
