Bioinformatics Prediction of SARS-CoV-2 Epitopes as Vaccine Candidates for the Colombian Population
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials
2.2. Literature Search of HLAs Frequencies
2.3. HLAs Selection for Epitope Prediction
2.4. T-Cell Epitope Prediction
2.5. Peptide-Protein Docking Studies
2.6. Interactions Analysis and Molecular Dynamics
3. Results
3.1. Literature Search of HLAs Frequencies
3.2. HLAs Selection for Epitope Prediction
3.2.1. HLA I
3.2.2. HLA II
3.3. T-Cell Epitope Prediction
3.4. Peptide-Protein Docking Studies
3.5. Interactions Analysis and Molecular Dynamics
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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Search | Query |
---|---|
HLA Class I | (“MHC Class I” OR “MHC I” OR “HLA Class I” OR “HLA I” OR “HLA-A” OR “HLA-B” OR “HLA-C”) AND “Colombia” |
HLA Class II | Query #1: (“MHC Class II” OR “MHC II” OR “HLA Class II” OR “HLA II”) AND “Colombia” Query #2: (“DRB1” OR “DRB3” OR “DRB4” OR “DRB5” OR “DQB1” OR “DQA1”) AND “HLA” AND “Colombia” Query #3: (“DPA1” OR “DPB1”) AND “HLA” AND “Colombia” |
Protein | Length | NCBI Reference Sequence |
---|---|---|
Spike protein (S) | 1273 aa | YP_009724390.1 |
Envelope protein (E) | 75 aa | YP_009724392.1 |
Membrane glycoprotein (M) | 222 aa | YP_009724393.1 |
Nucleocapsid phosphoprotein (N) | 419 aa | YP_009724397.2 |
HLA I | Results |
---|---|
PubMed | 78 |
Web of Science | 116 |
Science Direct | 292 |
HLA II | Results of Query #1 | Results of Query #2 | Results of Query #3 |
---|---|---|---|
PubMed | 77 | 105 | 6 |
Web of Science | 106 | 106 | 6 |
Science Direct | 345 | 266 | 40 |
Ethnic Groups | HLA-A | HLA-B | HLA-C | |||
---|---|---|---|---|---|---|
Allele | Frequency (%) | Allele | Frequency (%) | Allele | Frequency (%) | |
Colombia-Bogotá (n = 1463) | A*24:02 | 20.8 | B*35:43 | 8.6 | C*04:01 | 14.9 |
A*02:01 | 16.1 | B*40:02 | 8.4 | C*01:02 | 11.4 | |
A*01:01 | 6.1 | B*44:03 | 5.6 | C*07:02 | 9.7 | |
A*03:01 | 6.1 | B*51:01 | 5.6 | C*07:01 | 8.9 | |
A*68:01 | 5.2 | B*07:02 | 5.0 | C*03:04 | 8.2 | |
A*29:02 | 4.5 | B*35:01 | 4.5 | C*05:01 | 5.1 | |
A*11:01 | 4.3 | B*14:02 | 4.0 | C*06:02 | 5.1 | |
A*31:01 | 4.0 | B*44:02 | 3.9 | C*16:01 | 5.1 | |
A*23:01 | 3.3 | B*18:01 | 3.5 | C*08:02 | 4.9 | |
A*02:22 | 3.2 | B*08:01 | 3.2 | C*12:03 | 4.5 |
Ethnic Groups | HLA-A | HLA-B | HLA-C | |||
---|---|---|---|---|---|---|
Allele | Frequency | Allele | Frequency | Allele | Frequency | |
Arhuaco (n = 17) | A*24:02 | 0.441 | B*35:43 | 0.441 | C*01:02 | 0.382 |
Embera (n = 14) | A*24:02 | 0.536 | B*39:05 | 0.429 | C*07:02 | 0.464 |
Inga (n = 16) | A*24:02 | 0.367 | B*40:02 | 0.286 | C*01:02 | 0.367 |
Kogi (n = 15) | A*24:02 | 0.433 | B*35:43 | 0.429 | C*01:02 | 0.571 |
North Chimila (n = 47) | A*24:02 | 0.457 | B*51:10 | 0.404 | C*15:02 | 0.468 |
North Wiwa El Encanto (n = 52) | A*24:02 | 0.433 | B*35:43 | 0.385 | C*01:02 | 0.51 |
Waunana (n = 20) | A*24:02 | 0.6 | B*40:02 | 0.25 | C*03:04 | 0.35 |
Wayuu (n = 15) | A*24:02 | 0.2 | B*40:02 | 0.2 | C*04:01 | 0.25 |
Zenu (n = 16) | A*24:02 | 0.417 | B*40:02 | 0.25 | C*15:02 | 0.25 |
Ticuna Arara (n = 17) | A*24:02 | 0.5 | B*39:03 | 0.286 | C*07:02 | 0.429 |
Ticuna Tarapaca (n = 19) | A*24:02 | 0.526 | B*40:02 | 0.447 | C*03:04 | 0.529 |
HLA II Alleles | WAFs (%) | n |
---|---|---|
Mestizo | ||
DQB1*03:02 | 22.47 | 1737 |
DQB1*03:01 | 19.23 | 1737 |
DQB1*02:01 | 14.45 | 1737 |
DRB1*04:07 | 12.39 | 1737 |
DQB1*05:01 | 11.63 | 1737 |
DQB1*04:02 | 10.76 | 1737 |
DRB1*07:01 | 9.29 | 1925 |
DQB1*06:02 | 7.03 | 1737 |
DRB1*15:01 | 6.28 | 1925 |
DRB1*08:02 | 6.25 | 1737 |
DRB1*03:01 | 5.74 | 1925 |
DRB1*13:01 | 5.09 | 1925 |
African Colombian | ||
DQA1*01:02 | 23.42 | 234 |
DQA1*05:01 | 19.86 | 140 |
DQB1*02:01 | 19.79 | 182 |
DQA1*01:01 | 18.04 | 234 |
DQB1*05:01 | 17.69 | 182 |
DQB1*06:02 | 16.21 | 182 |
DQB1*03:01 | 15.88 | 182 |
DRB1*15:03 | 13.47 | 182 |
DQA1*03:01 | 12.77 | 94 |
DQB1*04:02 | 12.37 | 182 |
DQA1*04:01 | 11.29 | 140 |
DRB1*03:01 | 10.98 | 182 |
DRB1*03:02 | 9.17 | 182 |
DRB1*07:01 | 8.56 | 182 |
DRB1*08:01 | 8.30 | 42 |
DQA1*02:01 | 8.04 | 234 |
DRB1*08:04 | 6.00 | 42 |
DRB1*13:04 | 6.00 | 42 |
DQB1*03:02 | 5.94 | 182 |
DRB1*13:02 | 5.65 | 182 |
DRB1*01:01 | 5.14 | 140 |
Colombian Amerindians | ||
DPB1*04:02 | 49.99 | 668 |
DQA1*03:01 | 46.27 | 1573 |
DPB1*14:01 | 45.67 | 668 |
DRB4*01:00 | 44.23 | 1300 |
DQB1*03:02 | 43.49 | 2633 |
DRB4*01:01 | 38.10 | 34 |
DQA1*05:01 | 35.05 | 2084 |
DRB1*04.03 | 32.30 | 48 |
DQB1*03:01 | 32.06 | 2633 |
DQA1*05:00 | 19.62 | 321 |
DQB1*04:02 | 18.53 | 2537 |
DRB5*01:00 | 18.20 | 77 |
DRB3*01:01 | 18.11 | 1573 |
DRB1*14:02 | 18.01 | 2173 |
DQA1*04:01 | 17.59 | 2348 |
DRB1*04:07 | 17.32 | 2829 |
DRB5*02:00 | 17.11 | 1257 |
DRB1*16:02 | 14.48 | 2777 |
DRB1*08:022 | 14.29 | 42 |
DRB1*04:11 | 14.19 | 2691 |
DRB1*08:02 | 10.47 | 2701 |
DRB1*08:04 | 7.32 | 2091 |
DRB1*04:04 | 7.23 | 2722 |
Type | HLA I and HLA II Alleles |
---|---|
HLA-A | HLA-A*24:02, HLA-A*02:01, HLA-A*01:01, HLA-A*03:01, HLA-A*68:01, HLA-A*29:02, HLA-A*11:01, HLA-A*31:01, HLA-A*23:01, and HLA-A*02:22. |
HLA-B | HLA-B*35:43, HLA-B*40:02, HLA-B*44:03, HLA-B*51:01, HLA-B*07:02, HLA-B*35:01, HLA-B*14:02, HLA-B*44:02, HLA-B*18:01, HLA-B*08:01, HLA-B*39:05, HLA-B*51:10, and HLA-B*39:03. |
HLA-C | HLA-C*04:01, HLA-C*01:02, HLA-C*07:02, HLA-C*07:01, HLA-C*03:04, HLA-C*05:01, HLA-C*06:02, HLA-C*16:01, HLA-C*08:02, HLA-C*12:03, and HLA-C*15:02. |
HLA-DRB1 | DRB1*01:01, DRB1*03:01, DRB1*03:02, DRB1*04:03, DRB1*04:04, DRB1*04:07, DRB1*04:11, DRB1*07:01, DRB1*08:01, DRB1*08:02, DRB1*08:04, DRB1*08:22, DRB1*13:01, DRB1*13:02, DRB1*13:04, DRB1*14:02, DRB1*15:01, DRB1*15:03, and DRB1*16:02. |
Epitopes | Estimated Coverage for Colombian Population (WAF) | Experiments (IEDB) | IEDB ID |
---|---|---|---|
Spike Protein (S) | |||
HLA 1 | |||
VYDPLQPEL | HLA-A = 50.85%, HLA-B = 34.39%, HLA-C = 82.07%. | ML: (+). TC-IFNg: (−). | 71996 |
YQPYRVVVL | HLA-A = 43.43%, HLA-B = 18.49%, HLA-C = 82.07%. | TC-QB: (+). | 1334394 |
TLDSKTQSL | HLA-A = 25.42%, HLA-B = 15.04%, HLA-C = 82.07%. | TC-A: (+). TC-QB: (+). TC-IFNg: (−). | 1075075 |
VRDPQTLEI | HLA-A = 24.09%, HLA-B = 7.42%, HLA-C = 57.39%. | - | |
FTISVTTEI | HLA-A = 19.34%, HLA-B = 14.84%, HLA-C = 57.5%. | TC-A: (+). | 1317060 |
HLA 2 | |||
RAAEIRASANLAATK | HLA-DRB1 = 48.88%. | ML: (+). TC-IFNg: (−). | 533447 |
TPINLVRDLPQGFSA | HLA-DRB1 = 33.7%. | ML: (+). | 1330624 |
FGGFNFSQILPDPSK | HLA-DRB1 = 33.47%. | - | |
KHTPINLVRDLPQGF | HLA-DRB1 = 31.59%. | TC-A: (+). TC-IFNg: (+). TC-IL5: (−). | 1309123 |
Envelope Protein (E) | |||
HLA 1 | |||
YVYSRVKNL | HLA-A = 19.34%, HLA-B = 27.01%, HLA-C = 82.07%. | TC-A: (+). TC-QB: (+). | 1075128 |
LAILTALRL | HLA-B = 6.19%, HLA-C = 22.09%. | - | |
VSLVKPSFY | HLA-A = 14.9%, HLA-B = 8.65%, HLA-C = 27.97%. | - | |
VTLAILTAL | HLA-A = 16.13%, HLA-C = 33.47%. | - | |
RVKNLNSSR | HLA-A = 19.54%. | - | |
HLA 2 | |||
KPSFYVYSRVKNLNS | HLA-DRB1 = 43.18%. | - | |
VYSRVKNLNSSRVPD | HLA-DRB1 = 55.99%. | - | |
VKPSFYVYSRVKNLN | HLA-DRB1 = 43.18%. | - | |
YSRVKNLNSSRVPDL | HLA-DRB1 = 37.1%. | - | |
SFYVYSRVKNLNSSR | HLA-DRB1 = 61.92%. | - | |
PSFYVYSRVKNLNSS | HLA-DRB1 = 55.74%. | - | |
FYVYSRVKNLNSSRV | HLA-DRB1 = 42.58%. | TC-IFNg: (+). TC-TNF: (+). TC-IL5: (−). TC-A: (−). | 1310430 |
LVKPSFYVYSRVKNL | HLA-DRB1 = 26.5%. | - | |
YVYSRVKNLNSSRVP | HLA-DRB1 = 51.81%. | - | |
Membrane Protein (M) | |||
HLA 1 | |||
ITVATSRTL | HLA-C = 47.52%. | - | |
Nucleocapsid Protein (N) | |||
HLA 1 | |||
QFAPSASAF | HLA-A = 49.12%, HLA-B = 25.14%, HLA-C = 47.85%. | - | |
QRNAPRITF | HLA-A = 47.09%, HLA-B = 19.77%, HLA-C = 24.33%. | TC-IFNg: (+). TC-QB: (+). TC-TNF: (−). TC-A: (−). | 1309136 |
SPDDQIGYY | HLA-A = 3.24%, HLA-B = 25.38%, HLA-C = 26%. | TC-A: (+). TC-IFNg: (−). | 1310816 |
HLA 2 | |||
GTWLTYTGAIKLDDK | HLA-DRB1 = 40.37%. | TC-IFNg: (+). TC-A: (+). TC-TNF: (+). | 1310464 |
NFKDQVILLNKHIDA | HLA-DRB1 = 24.69%. | - | |
TKAYNVTQAFGRRGP | HLA-DRB1 = 52.85%. | - |
Epitopes | SARS-CoV-2 Protein | IFN Epitope Server | Worldwide Coverage (%) [IEDB] |
---|---|---|---|
YQPYRVVVL | S | 0.29285355 | 96.62 |
RAAEIRASANLAATK | S | 0.29346657 | ND |
QFAPSASAF | N | 0.82212984 | 77.60 |
SPDDQIGYY | N | 0.24883001 | 80.12 |
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Montes-Grajales, D.; Olivero-Verbel, J. Bioinformatics Prediction of SARS-CoV-2 Epitopes as Vaccine Candidates for the Colombian Population. Vaccines 2021, 9, 797. https://doi.org/10.3390/vaccines9070797
Montes-Grajales D, Olivero-Verbel J. Bioinformatics Prediction of SARS-CoV-2 Epitopes as Vaccine Candidates for the Colombian Population. Vaccines. 2021; 9(7):797. https://doi.org/10.3390/vaccines9070797
Chicago/Turabian StyleMontes-Grajales, Diana, and Jesus Olivero-Verbel. 2021. "Bioinformatics Prediction of SARS-CoV-2 Epitopes as Vaccine Candidates for the Colombian Population" Vaccines 9, no. 7: 797. https://doi.org/10.3390/vaccines9070797