Design of a Multiepitope Vaccine against Chicken Anemia Virus Disease
Abstract
:1. Introduction
2. Materials and Methods
2.1. Immunoinformatics of Viral Proteins
2.1.1. Retrieval and Filtering of VP1 and VP2 Protein Sequences
2.1.2. CD8+ T-Cell Epitopes and MHC-I Binding Allele Prediction
2.1.3. CD4+ T-Cell Epitopes and MHC-II Binding Allele Prediction
2.1.4. Immunogenicity, Antigenicity, Conservancy, and Allergenicity of Predicted Epitopes
2.1.5. Prediction of Linear B-Cell Epitopes
2.2. Multiepitope Vaccine Construction
2.2.1. Multiepitope Vaccine (MEV) Design
2.2.2. Physicochemical Properties and Secondary Structure Prediction
2.2.3. Prediction of Tertiary Structure, Refinement, and Validation
2.2.4. Conformational B-Cell Epitopes Prediction
2.2.5. Molecular Docking of MEV with TLR3
2.2.6. Molecular Dynamics of the MEV Construct
2.2.7. Reverse Translation, Codon Optimization, and In Silico Cloning of the MEV
2.2.8. Immune Simulation of MEV Construct
3. Results
3.1. Sequence Alignment, Antigenicity, and Membrane Test
3.2. CD8+ T-Cell Epitopes and MHC-I Binding Allele Prediction
3.3. CD4+ T-Cell Epitopes and MHC-II Binding Allele Prediction, Conservancy, and Allergenicity
3.4. Linear B-Cell Epitopes Prediction
3.5. MEV Construction and Validation
3.5.1. MEV Construction and Screening
3.5.2. Physicochemical Properties and Secondary Structure Prediction
3.5.3. Tertiary Structure Prediction, Refinement, and Validation
3.5.4. Conformational B-Cell Epitopes Prediction
3.5.5. Interaction Analysis of MEV Construct and TLR-3
3.5.6. Molecular Dynamics Simulation of the MEV Construct
3.5.7. Reverse Translation, Codon Optimization, and In Silico Cloning
3.5.8. Immune Simulation
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Viral Protein | CD8+ T-Cell Epitopes | Antigenicity Score | Immunogenicity | MHCI-Alleles |
---|---|---|---|---|
VP1 | FQGINFLTE | 0.5863 | 0.2621 | HLA-A*02:06 |
LMTIRFQGV | 1.0143 | 0.2292 | HLA-A*02:06, HLA-A*02:03, HLA-B*08:01, HLA-A*02:01 | |
TMTIRFQGL | 1.1407 | 0.2292 | HLA-B*08:01 | |
KAFHDPRPG | 0.7871 | 0.1189 | HLA-A*30:01 | |
KAFHNPRPG | 0.5687 | 0.0910 | HLA-A*30:01 | |
FHNPRPGAY | 0.6146 | 0.0782 | HLA-A*30:02, HLA-B*35:01 | |
AFHNPRPGA | 0.5667 | 0.0524 | HLA-A*30:01 | |
LTEGLLLPK | 0.5185 | 0.0295 | HLA-A*11:01 | |
VP2 | DPDWYRWNY | 0.9093 | 0.4584 | HLA-B*35:01 |
Viral Protein | CD4+ T-Cell Epitopes | Antigenicity Score | MHCII-Alleles |
---|---|---|---|
VP1 | AFRKAFHDPRPGTYS | 0.5598 | HLA-DRB5*01:01 |
FLTEGLLLPKNSTAG | 0.5757 | HLA-DRB1*01:01, HLA-DPA1*03:01 | |
FRKAFHDPRPGTYSV | 0.6011 | HLA-DRB5*01:01 | |
FRKAFHNPRPGAYSV | 0.5000 | HLA-DRB5*01:01 | |
IRFQGINFLTEGLIL | 0.7592 | HLA-DPA1*01:03, HLA-DPA1*03:01, HLA-DPA1*02:01 | |
LLMTIRFQGVIFLTE | 0.8222 | HLA-DRB1*04:05, HLA-DRB1*01:01, HLA-DRB1*15:01, HLA-DPA1*02:01, HLA-DPA1*03:01, HLA-DPA1*01:03 | |
PNPNLLMTIRFQGVI | 0.8698 | HLA-DRB4*01:01, HLA-DPA1*03:01, HLA-DPA1*01:03, HLA-DRB1*11: 01, HLA-DRB1*01:01 | |
PNPQSTMTIRFQGLI | 0.8712 | HLA-DRB4*01:01 | |
PQSTMTIRFQGLIFL | 0.7590 | HLA-DRB1*15:01, HLA-DRB4*01:01, HLA-DPA1*02:01, HLA-DPA1*03:01 | |
QSTMTIRFQGLIFLT | 0.8821 | HLA-DRB1*15:01, HLA-DRB4*01:01, HLA-DPA1*02:01, HLA-DPA1*03:01 | |
TMTIRFQGLIFLTEG | 0.8422 | HLA-DRB1*04:05, HLA-DRB1*15:01, HLA-DRB4*01:01, HLA-DPA1*02:01, HLA-DPA1*03:01 | |
VP2 | DPDWYRWNYNHSIAV | 0.7586 | HLA-DRB1*13:02, HLA-DRB3*01:01 |
QRDPDWYRWNYNHSI | 0.8368 | HLA-DRB1*07:01, HLA-DRB3*01:01 | |
RDPDWYRWNYNHSIA | 0.8539 | HLA-DRB1*07:01, HLA-DRB3*01:01 |
Viral Protein | B-Cell Epitopes | Antigenicity Score | ABCpred Score |
---|---|---|---|
VP1 | AFRKAFHNPRPGTYSVRL | 0.6040 | 0.84 |
GYAFRKAFHNPRPGTYSV | 0.5284 | 0.71 | |
KAFHNPRPGTYSVRLPNP | 0.6401 | 0.89 | |
LTEGLLLPKNSTAGGYAF | 0.6674 | 0.77 | |
NPQSTMTIRFQGLIFLTE | 0.8296 | 0.65 | |
QSTMTIRFQGINFLTEGL | 0.8772 | 0.77 | |
RKAFHNPRPGTYSVRLPN | 0.7101 | 0.86 | |
RLPNPNLLMTIRFQGVIF | 0.5641 | 0.74 | |
STAGGYAFRKAFHNPRPG | 0.6224 | 0.65 | |
YAFRKAFHDPRPGTYSVR | 0.6751 | 0.74 | |
YAFRKAFHNPRPGAYSVR | 0.8513 | 0.78 | |
YAFRKAFHNPRPGTYSVR | 0.7547 | 0.88 | |
VP2 | GNPSLQRDPDWYRWNYNH | 0.5966 | 0.80 |
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Fatoba, A.J.; Adeleke, V.T.; Maharaj, L.; Okpeku, M.; Adeniyi, A.A.; Adeleke, M.A. Design of a Multiepitope Vaccine against Chicken Anemia Virus Disease. Viruses 2022, 14, 1456. https://doi.org/10.3390/v14071456
Fatoba AJ, Adeleke VT, Maharaj L, Okpeku M, Adeniyi AA, Adeleke MA. Design of a Multiepitope Vaccine against Chicken Anemia Virus Disease. Viruses. 2022; 14(7):1456. https://doi.org/10.3390/v14071456
Chicago/Turabian StyleFatoba, Abiodun Joseph, Victoria T. Adeleke, Leah Maharaj, Moses Okpeku, Adebayo A. Adeniyi, and Matthew A. Adeleke. 2022. "Design of a Multiepitope Vaccine against Chicken Anemia Virus Disease" Viruses 14, no. 7: 1456. https://doi.org/10.3390/v14071456