Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble
Abstract
:1. Introduction
2. Results
2.1. Analysis of ASFV Protein Space
2.2. Identification of ASFV Putative-Exposed Proteins
2.3. Selection of B-Cell Epitopes
2.4. De Novo Predicted B-Cell Epitopes
2.5. Selection of CD4+ T-Cell Epitopes
2.6. De Novo Predicted CD4+ T-Cell Epitopes
2.7. Selection of CD8+ T-Cell Epitopes
3. Discussion
4. Materials and Methods
4.1. Collection of ASFV Proteomes
4.2. Collection of Experimentally Validated ASFV Epitopes
4.3. Clustering of ASFV Proteins and Generation of Multiple Sequence Alignments
4.4. Generating an ASFV Invariable Proteome
4.5. Prediction of CD8+ T-Cell Epitopes
4.6. Prediction of CD4+ T-Cell Epitopes
4.7. Prediction of B-Cell Epitopes
4.8. In-House Scripts and BLAST Searches
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Epitope | Protein Name (ORF) | Protein ID 1 | Sus scrofa Hit (id %) 2 | Microbiota Hit (id %) 2 |
---|---|---|---|---|
FPENSHNIQTAGKQD | p72 (B646L) | E0WMM0 | XP_020938976.1 (40.0%) | WP_008983921.1 (53.3%) |
YCEYPGERLYENVRFDVNGNSLDEYSSDVTTL | p72 (B646L) | E0WMM0 | XP_020953642.1 (25.0%) | WP_091148772.1 (34.4%) |
VCKVDKDCGSGEHCV | p22 (KP177R) | E0WMB7 | XP_020923036.1 (66.7%) | WP_046972048.1 (60.0%) |
AAIEEEDIQFINPYQD | p54 (E183L) | E0WM75 | XP_020932305.1 (50.0%) | WP_042346777.1 (68.8%) |
Epitope | Protein Name (ORF) | Protein ID 1 | Sus scrofa Hit (id %) 2 | Microbiota Hit (id %) 2 |
---|---|---|---|---|
LATCGKAGNFCECSNYSTS | CD2 homolog (E402R) | E0WMJ6 | XP_003483701.1 (47.4%) | WP_007633917.1 (47.4%) |
KKQQPPKKVCKVDKDCGSGEHC | p22 (KP177R) | E0WMB7 | XP_020923055.1 (40.9%) | WP_137027291.1 (63.6%) |
FFQPVYPRHYGECLSP | p54 (E183L) | E0WM75 | XP_020934554.1 (50.0%) | WP_018576392.1 (56.3%) |
GFEYNKVRPHTGTPTLGNKLT | p72 (B646L) | E0WMM0 | XP_020939243.1 (42.9%) | WP_143542922.1 (47.6%) |
HKPHQSKPILTDENDTQRTC | p72 (B646L) | E0WMM0 | XP_020932317.1 (35.0%) | WP_169883328.1 (45.0%) |
HTNPKFLSQHFPENSHNIQTAGKQDITPITD | p72 (B646L) | E0WMM0 | XP_020933726.1 (32.3%) | WP_042032899.1 (38.7%) |
QMGAHGQLQTFPRNGYDWDNQTPLE | p72 (B646L) | E0WMM0 | XP_020956625.1 (28.0%) | WP_075838746.1 (36.0%) |
SFQDRDTALPDACSSISDI | p72 (B646L) | E0WMM0 | XP_020950058.1 (42.1%) | WP_165776787.1 (57.9%) |
TWNISDQNPHQHRDWHK | p72 (B646L) | E0WMM0 | XP_003123199.2 (41.2%) | WP_077451423.1 (58.8%) |
VTHTNNNHHDEKLMS | p72 (B646L) | E0WMM0 | XP_020946598.1 (46.7%) | WP_072834091.1 (53.3%) |
TSPLLSHNLSTREGIKQ | p17 (D117L) | E0WM57 | XP_020947378.1 (47.1%) | WP_021704232.1 (58.8%) |
GVCKNKVFEKHPLIKKNDY | MGF_110-9L | E0WMD4 | XP_020922529.1 (47.4%) | WP_124535981.1 (63.2%) |
AGRGIPLGNPHVKPNIEQELIKS | p49 (B438L) | E0WML4 | XP_013850764.1 (30.4%) | WP_168007327.1 (56.5%) |
FPKDFNASSVPLTSAEKDHSLRGDNS | p49 (B438L) | E0WML4 | NP_999435.1 (50.0%) | WP_007759066.1 (46.2%) |
GQAEYFDTSKQTISRHNNYIPKYTGGIGDS | p49 (B438L) | E0WML4 | XP_020939832.1 (33.3%) | WP_095912160.1 (36.7%) |
LADYRSDPPLWESDLPRHNRYSDNILN | p49 (B438L) | E0WML4 | XP_020954566.1 (25.9%) | WP_143667676.1 (55.6%) |
LNPQHKNIGYGDAQDLEPYS | p49 (B438L) | E0WML4 | XP_013849660.1 (30.0%) | WP_085490987.1 (60.0%) |
PSFDNDVKRRNKDTVWARFGV | Trans-prenyltransferase (B318L) | E0WML3 | XP_005674076.1 (38.1%) | WP_142159516.1 (47.6%) |
GINNLGEKIYTCEPFKTSF | Transmembrane protein B169L | E0WML5 | XP_003354140.1 (42.1%) | WP_095898538.1 (63.2%) |
KYLERQDLELLGYSPT | Transmembrane protein C257L | E0WMK4 | XP_003356508.3 (68.8%) | WP_111879816.1 (62.5%) |
DEPIVQNPFLENFWKPEQKTFNQSGLFEESS | Uncharacterized protein B475L | E0WML6 | XP_020932571.1 (29.0%) | WP_078933170.1 (38.7%) |
FRDAQNPPSSFTLGGHCQA | Uncharacterized protein E146L | E0WM78 | NP_001121958.1 (52.6%) | WP_147756634.1 (47.4%) |
EASYDTMRTKLMKFSGINKEKENN | Uncharacterized protein M1249L | E0WMJ8 | XP_020928637.1 (41.7%) | WP_022932625.1 (41.7%) |
GKQEAELITTEYLNIKKQWELQEKNACA | Uncharacterized protein M1249L | E0WMJ8 | XP_020951797.1 (50.0%) | WP_134792973.1 (46.4%) |
ISAYSSPGLFGEDIID | Uncharacterized protein M1249L | E0WMJ8 | XP_020934753.1 (50.0%) | WP_041516260.1 (56.3%) |
LSQPELVHDYYNNYKDQY | Uncharacterized protein M1249L | E0WMJ8 | XP_020923164.1 (38.9%) | WP_133014505.1 (55.6%) |
NPVEQKFLQHAEQREKEQMILQ | Uncharacterized protein M1249L | E0WMJ8 | XP_020946579.1 (50.0%) | WP_085491731.1 (45.5%) |
Epitope | Protein (ORF) | Protein ID 1 | Mean Flex. 2 | Mean RSA 3 | Sus scrofa Hit (id %) 4 | Microbiota Hit (id %) 4 |
---|---|---|---|---|---|---|
KPHQSKPILTDENDTQRT | p72 (B646L) | E0WMM0 | 1.7 | 50.1 | XP_020932317.1 (38.9%) | WP_169883328.1 (50.0%) |
NIQTAGKQDITPITD | p72 (B646L) | E0WMM0 | 1.8 | 56.8 | XP_020933726.1 (66.7%) | WP_001886209.1 (53.3%) |
Epitope | No. HLA Alleles 1 | Protein Name (ORF) | Protein ID 2 | Sus scrofa Hit (id %) 3 | Microbiota Hit (id %) 3 |
---|---|---|---|---|---|
GLGFILIVIFIYLLLITLQQMLTRHI | 5 | Uncharacterized protein (B117L) | E0WM34 | XP_003360623.1 (46.2%) | WP_119317083.1 (53.9%) |
MNIYLVWFLYILLGNLILAVIY | 4 | ASFV_G_ACD_01990 | E0WMB3 | XP_003124218.1 (59.1%) | WP_155703379.1 (68.2%) |
LSLICVFSHFFEELYITKP | 3 | Probable methyltransferase (EP424R) | E0WMJ3 | XP_013843985.2 (42.1%) | WP_010770249.1 (52.6%) |
WYLKYVIAYILLLTMLVIGLIYRIIVLIYRSIQAQK | 3 | ASFV_G_ACD_01940 | E0WMA9 | XP_013836670.2 (33.3%) | WP_100215420.1 (55.6%) |
AINFLLLQNGSAVLRYS | 2 | p72 (B646L) | E0WMM0 | NP_999474.1 (52.9%) | WP_113638931.1 (64.7%) |
ATRLVAVRAQQLAINGSTMLKKK | 2 | DNA-directed RNA polymerase subunit 6 homolog (C147L) | E0WMK7 | XP_020956260.1 (30.4%) | WP_093129025.1 (56.5%) |
GLNFQAVRYEMIMSLPLDIP | 2 | Putative ATP-dependent RNA helicase (D1133L) | E0WM56 | XP_013834167.2 (55.0%) | WP_096721649.1 (60%) |
HYPASFHYTMLEALIIDN | 2 | Putative ATP-dependent RNA helicase (D1133L) | E0WM56 | XP_005666131.2 (38.9%) | WP_167872395.1 (55.6%) |
ISIITFLSLRKRKKHVEEI | 2 | CD2 homolog (E402R) | E0WMJ6 | XP_020951930.1 (42.1%) | WP_039931062.1 (52.6%) |
MYFQQTRSILIKNDAVFILNLG | 2 | ASFV_G_ACD_01870 | E0WMA2 | XP_020949404.1 (54.6%) | WP_069997539.1 (40.9%) |
NAFVDYIISNFNHAVTCRKP | 2 | Transmembrane protein (B66L) | E0WM38 | XP_020936233.1 (40.0%) | WP_128359657.1 (45.0%) |
NNILVEILSFKNYYSSNTSLLSIKT | 2 | MGF_360-21R | E0WMB1 | XP_020924396.1 (40.0%) | WP_117888406.1 (44.0%) |
NVIFLKVISNTAVSVFWRD | 2 | Uncharacterized protein (C62L) | E0WMK8 | XP_020958320.1 (52.6%) | WP_094566288.1 (52.6%) |
PTPLIPSMAMSIPRMINKRKKRIQFLTFLTNLFLYN | 2 | Uncharacterized protein (A118R) | E0WMH4 | XP_020945397.1 (30.6%) | WP_165296256.1 (50.0%) |
Predicted Epitope | No. SLA Alleles 1 | Protein (ORF) | Protein ID 2 | TAP IC50 3 | Sus scrofa Hit (id %) 4 | Microbiota Hit (id %)4 |
---|---|---|---|---|---|---|
MAMQKLFTY | 29 | Putative DNA-directed RNA polymerase subunit 5 homolog (D205R) | E0WM58 | −0.94 | NP_001037992.1 (66.7%) | WP_025027576.1 (77.8%) |
KRHENIWML | 27 | Uncharacterized protein D339L | E0WM55 | −2.81 | XP_013850843.2 (55.6%) | WP_130548297.1 (77.8%) |
CTQPARVTY | 22 | DNA-directed RNA polymerase subunit beta (EP1242L) | E0WMJ1 | 0.17 | XP_003127876.2 (66.7%) | WP_164721234.1 (77.8%) |
NIMPGLVSY | 21 | Ribonucleoside-diphosphate reductase (F334L) | E0WMI2 | 0.65 | XP_020927225.1 (55.6%) | WP_157084930.1 (77.8%) |
ANPSEGWKY | 10 | DNA topoisomerase 2 (P1192R) | E0WM62 | 0.23 | XP_020958373.1 (55.6%) | WP_117029589.1 (77.8%) |
EEFNYLWVY | 7 | Uncharacterized protein G1340L | E0WM39 | −2.05 | NP_999483.1 (66.7%) | WP_083089560.1 (77.8%) |
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Ros-Lucas, A.; Correa-Fiz, F.; Bosch-Camós, L.; Rodriguez, F.; Alonso-Padilla, J. Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble. Pathogens 2020, 9, 1078. https://doi.org/10.3390/pathogens9121078
Ros-Lucas A, Correa-Fiz F, Bosch-Camós L, Rodriguez F, Alonso-Padilla J. Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble. Pathogens. 2020; 9(12):1078. https://doi.org/10.3390/pathogens9121078
Chicago/Turabian StyleRos-Lucas, Albert, Florencia Correa-Fiz, Laia Bosch-Camós, Fernando Rodriguez, and Julio Alonso-Padilla. 2020. "Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble" Pathogens 9, no. 12: 1078. https://doi.org/10.3390/pathogens9121078