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Article

In Silico Prediction of Human Leukocytes Antigen (HLA) Class II Binding Hepatitis B Virus (HBV) Peptides in Botswana

1
Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana
2
Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
3
Department of Applied Biology and Biochemistry, Faculty of Applied Sciences, National University of Science and Technology, Bulawayo 0000, Zimbabwe
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Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone 0000, Botswana
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Centre for Proteomic and Genomic Research, Cape Town 7925, South Africa
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Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone 0000, Botswana
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Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Independent Researcher, P.O. Box 497, Wits, Johannesburg 2050, South Africa
9
Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
*
Author to whom correspondence should be addressed.
Viruses 2020, 12(7), 731; https://doi.org/10.3390/v12070731
Received: 12 June 2020 / Accepted: 3 July 2020 / Published: 6 July 2020
(This article belongs to the Special Issue Hepatitis B Virus: From Diagnostics to Treatments)
Hepatitis B virus (HBV) is the primary cause of liver-related malignancies worldwide, and there is no effective cure for chronic HBV infection (CHB) currently. Strong immunological responses induced by T cells are associated with HBV clearance during acute infection; however, the repertoire of epitopes (epi) presented by major histocompatibility complexes (MHCs) to elicit these responses in various African populations is not well understood. In silico approaches were used to map and investigate 15-mers HBV peptides restricted to 9 HLA class II alleles with high population coverage in Botswana. Sequences from 44 HBV genotype A and 48 genotype D surface genes (PreS/S) from Botswana were used. Of the 1819 epi bindings predicted, 20.2% were strong binders (SB), and none of the putative epi bind to all the 9 alleles suggesting that multi-epitope, genotype-based, population-based vaccines will be more effective against HBV infections as opposed to previously proposed broad potency epitope-vaccines which were assumed to work for all alleles. In total, there were 297 unique epi predicted from the 3 proteins and amongst, S regions had the highest number of epi (n = 186). Epitope-densities (Depi) between genotypes A and D were similar. A number of mutations that hindered HLA-peptide binding were observed. We also identified antigenic and genotype-specific peptides with characteristics that are well suited for the development of sensitive diagnostic kits. This study identified candidate peptides that can be used for developing multi-epitope vaccines and highly sensitive diagnostic kits against HBV infection in an African population. Our results suggest that viral variability may hinder HBV peptide-MHC binding, required to initiate a cascade of immunological responses against infection. View Full-Text
Keywords: hepatitis B virus (HBV); HLA class II alleles; T-cell epitopes; in silico; immunoinformatics; candidate multi-epitope vaccines (MEV); escape mutation; Botswana; Africa hepatitis B virus (HBV); HLA class II alleles; T-cell epitopes; in silico; immunoinformatics; candidate multi-epitope vaccines (MEV); escape mutation; Botswana; Africa
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MDPI and ACS Style

Choga, W.T.; Anderson, M.; Zumbika, E.; Phinius, B.B.; Mbangiwa, T.; Bhebhe, L.N.; Baruti, K.; Kimathi, P.O.; Seatla, K.K.; Musonda, R.M.; Bell, T.G.; Moyo, S.; Blackard, J.T.; Gaseitsiwe, S. In Silico Prediction of Human Leukocytes Antigen (HLA) Class II Binding Hepatitis B Virus (HBV) Peptides in Botswana. Viruses 2020, 12, 731. https://doi.org/10.3390/v12070731

AMA Style

Choga WT, Anderson M, Zumbika E, Phinius BB, Mbangiwa T, Bhebhe LN, Baruti K, Kimathi PO, Seatla KK, Musonda RM, Bell TG, Moyo S, Blackard JT, Gaseitsiwe S. In Silico Prediction of Human Leukocytes Antigen (HLA) Class II Binding Hepatitis B Virus (HBV) Peptides in Botswana. Viruses. 2020; 12(7):731. https://doi.org/10.3390/v12070731

Chicago/Turabian Style

Choga, Wonderful T., Motswedi Anderson, Edward Zumbika, Bonolo B. Phinius, Tshepiso Mbangiwa, Lynnette N. Bhebhe, Kabo Baruti, Peter O. Kimathi, Kaelo K. Seatla, Rosemary M. Musonda, Trevor G. Bell, Sikhulile Moyo, Jason T. Blackard, and Simani Gaseitsiwe. 2020. "In Silico Prediction of Human Leukocytes Antigen (HLA) Class II Binding Hepatitis B Virus (HBV) Peptides in Botswana" Viruses 12, no. 7: 731. https://doi.org/10.3390/v12070731

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