Comparison of Immunological Profiles of SARS-CoV-2 Variants in the COVID-19 Pandemic Trends: An Immunoinformatics Approach
Abstract
:1. Introduction
2. Results
2.1. Analysis of the SARS-CoV-2 Spike Glycoprotein Target Sequences
2.2. CTL and HTL Epitope Identification
2.2.1. CTL Epitope Prediction
2.2.2. HTL Epitope Prediction
2.3. Analysis of Linear and Conformational B-Cell Epitopes
2.4. Analysis of Population Coverage
2.5. Binding Interactions of the Vaccine Peptides and the HLA Alleles
3. Discussion
4. Materials and Methods
4.1. Collection of Sequence Dataset
4.2. Sequence Variability Analysis of Spike Glycoprotein
4.3. Phylogenetic Tree Construction
4.4. Prediction of Potential Cytotoxic and Helper T Lymphocyte Epitopes on Spike Glycoprotein of SARS-CoV-2
4.5. B Lymphocyte Epitope Prediction in SARS-CoV-2 S Protein
4.6. Prediction of Protective Antigenic Epitopes
4.7. Conservancy Analysis
4.8. Population Coverage Analysis
4.9. Docking and Simulation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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SARS-CoV-2 Isolate | Length | Molecular Weight (Dalton) | Theoretical PI | Total no of −ve and +ve Aminoacids | Extinction Coefficient (M−1cm−1) | Estimated Half-Life (h) | Instability Index | Aliphatic Index | GRAVY |
---|---|---|---|---|---|---|---|---|---|
Wuhan | 1273 | 141,178.47 | 6.24 | 110/103 | 148,960 | 30 | 33.01 | 84.67 | −0.079 |
England | 1273 | 141,169.51 | 6.32 | 109/103 | 150,450 | 30 | 33.03 | 84.67 | −0.075 |
USA | 1273 | 141,120.43 | 6.32 | 109/103 | 148,960 | 30 | 32.86 | 84.67 | −0.77 |
India | 1273 | 141,280.46. | 6.35 | 109/103 | 150,450 | 30 | 32.82 | 84.45 | −0.078 |
South Africa | 1273 | 141,120.43 | 6.32 | 109/103 | 148,960 | 30 | 32.86 | 84.67 | −0.077 |
SARS-CoV-2 Variant | Epitope | Position | Antigenicity Score | Immunogenicity Score | MHC I Alleles | No of MHC I Binding Alleles | Conservancy at 100% Sequence Identity | Allergenicity | Toxicity |
---|---|---|---|---|---|---|---|---|---|
Wuhan, China | ILDITPCSF | 584–592 | 1.184 | 0.02632 | HLA-B*15:01, HLA-A*01:01, HLA-A*02:06, HLA-B*35:01, HLA-B*08:01, HLA-A*02:01, HLA-A*32:01, HLA-A*24:02, HLA-A*23:01, HLA-A*30:02, HLA-B*58:01, HLA-B*53:01 | 12 | 100% | Non-allergen | Non-toxic |
STQDLFLPF | 50–58 | 0.662 | 0.06828 | HLA-A*32:01, HLA-B*57:01, HLA-B*15:01, HLA-A*26:01, HLA-B*58:01, HLA-B*35:01, HLA-A*30:02, HLA-A*23:01, HLA-A*24:02, HLA-A*01:01, HLA-A*11:01, HLA-B*53:01 | 12 | 100% | Non-allergen | Non-toxic | |
VVFLHVTYV | 1060–1068 | 1.512 | 0.1278 | HLA-A*02:06, HLA-A*02:03, HLA-A*02:01, HLA-A*68:02, HLA-B*51:01, HLA-A*30:01, HLA-A*32:01, HLA-B*08:01, HLA-A*26:01 | 9 | 100% | Non-allergen | Non-toxic | |
GVVFLHVTY | 1059–1067 | 1.410 | 0.20837 | HLA-B*15:01, HLA-A*30:02, HLA-A*26:01, HLA-B*35:01, HLA-A*32:01, HLA-B*57:01, HLA-A*11:01, HLA-A*01:01, HLA-B*58:01 | 9 | 100% | Non-allergen | Non-toxic | |
WTAGAAAYY | 258–266 | 0.662 | 0.15259 | HLA-A*26:01, HLA-A*01:01, HLA-A*30:02, HLA-A*68:01, HLA-B*35:01, HLA-B*15:01, HLA-B*58:01, HLA-B*57:01 | 8 | 100% | Non-allergen | Non-toxic | |
GAAAYYVGY | 261–269 | 0.660 | 0.09963 | HLA-A*30:02, HLA-B*15:01, HLA-B*35:01, HLA-A*26:01, HLA-A*01:01, HLA-A*11:01, HLA-B*58:01 | 7 | 100% | Non-allergen | Non-toxic | |
RVVVLSFEL | 509–517 | 1.192 | 0.046 | HLA-A*32:01, HLA-A*02:06, HLA-B*57:01, HLA-B*58:01, HLA-A*02:01 | 5 | 100% | Non-allergen | Non-toxic | |
England | WTAGAAAY | 258–266 | 0.826 | 0.15259 | HLA-A*26:01, HLA-A*01:01, HLA-A*30:02, HLA-A*68:01, HLA-B*35:01, HLA-B*15:01, HLA-B*58:01, HLA-B*53:01, HLA-B*57:01 | 9 | 100% | Non-allergen | Non-toxic |
QYIKWPWYI | 1208–1216 | 1.664 | 0.21624 | HLA-A*24:02, HLA-A*23:01, HLA-C*06:02, HLA-C*07:02, HLA-C*14:02, HLA-A*32:01, HLA-C*07:01 | 7 | 100% | Non-allergen | Non-toxic | |
GVYFASTEK | 89–97 | 0.664 | 0.09023 | HLA-A*11:01, HLA-A*30:01, HLA-A*68:01, HLA-A*31:01 | 4 | 100% | Non-allergen | Non-toxic | |
NGVEGFNCY | 481–489 | 1.182 | 0.22039 | HLA-B*35:01, HLA-A*26:01, HLA-C*12:02 | 3 | 100% | Non-allergen | Non-toxic | |
PYRVVVLSF | 507–515 | 1.028 | 0.03138 | HLA-A*23:01, HLA-A*24:02, HLA-C*14:02 | 3 | 100% | Non-allergen | Non-toxic | |
VYAWNRKRI | 350–358 | 0.813 | 0.12625 | HLA-A*24:02, HLA-C*14:02, HLA-A*23:01 | 3 | 100% | Non-allergen | Non-toxic | |
SPRRARSVA | 680–688 | 0.511 | 0.0402 | HLA-B*07:02, HLA-B*08:01 | 2 | 100% | Non-allergen | Non-toxic | |
USA | VVFLHVTYV | 1060–1068 | 1.51 | 0.1278 | HLA-A*02:06, HLA-A*02:03, HLA-A*02:01, HLA-A*68:02, HLA-B*51:01, HLA-A*30:01, HLA-A*30:02, HLA-A*32:01, HLA-B*08:01, HLA-A*26:01, HLA-A*33:01, HLA-A*03:01, HLA-A*31:01, HLA-B*57:01, HLA-B*15:01, HLA-A*68:01 | 16 | 100% | Non-allergen | Non-toxic |
ILDITPCSF | 584–592 | 1.184 | 0.02632 | HLA-B*15:01, HLA-A*01:01, HLA-A*02:06, HLA-B*35:01, HLA-B*08:01, HLA-A*02:01, HLA-A*32:01, HLA-A*24:02, HLA-A*23:01, HLA-A*30:02, HLA-B*58:01, HLA-B*53:01 | 12 | 100% | Non-allergen | Non-toxic | |
GVVFLHVTY | 1059–1067 | 1.140 | 0.20837 | HLA-B*15:01, HLA-A*30:02, HLA-A*26:01, HLA-B*35:01, HLA-A*32:01, HLA-B*57:01, HLA-A*11:01, HLA-B*58:01 | 8 | 100% | Non-allergen | Non-toxic | |
GAAAYYVGY | 1060–1068 | 0.661 | 0.09963 | HLA-A*30:02, HLA-B*15:01, HLA-B*35:01, HLA-A*26:01, HLA-A*01:01, HLA-A*11:01, HLA-B*58:01 | 7 | 100% | Non-allergen | Non-toxic | |
WTAGAAAYY | 258–266 | 0.631 | 0.15259 | HLA-A*26:01, HLA-A*01:01, HLA-A*30:02, HLA-A*68:01, HLA-B*35:01, HLA-B*15:01, HLA-B*58:01 | 7 | 100% | Non-allergen | Non-toxic | |
LPFNDGVYF | 84–92 | 0.559 | 0.11767 | HLA-B*35:01, HLA-B*53:01, HLA-B*51:01, HLA-B*07:02, HLA-A*26:01 | 5 | 100% | Non-allergen | Non-toxic | |
IAIVMVTIM | 1225–1233 | 1.134 | 0.06312 | HLA-B*51:01, HLA-B*35:01 | 2 | 100% | Non-allergen | Non-toxic | |
India | FTISVTTEI | 718–726 | 0.8535 | 0.04473 | HLA-A*68:02; HLA-A*02:06; HLA-A*02:03; HLA-A*02:01; HLA-B*51:01; HLA-A*26:01; HLA-B*58:01; HLA-A*32:01; HLA-B*53:01 | 9 | 100% | Non-allergen | Non-toxic |
VVFLHVTYV | 1060–1068 | 1.512 | 0.1278 | HLA-A*02:06; HLA-A*02:03; HLA-A*02:01; HLA-A*68:02; HLA-B*51:01; HLA-A*30:01; HLA-A*32:01; HLA-B*08:01; HLA-A*26:01 | 9 | 100% | Non-allergen | Non-toxic | |
YQPYRVVVL | 505–513 | 0.5964 | 0.1409 | HLA-B*08:01; HLA-A*02:06; HLA-B*15:01; HLA-A*02:03; HLA-A*02:01; HLA-A*24:02; HLA-B*40:01; HLA-A*23:01 | 8 | 100% | Non-allergen | Non-toxic | |
YSKHTPINL | 204–212 | 1.0547 | 0.9845 | HLA-B*57:01; HLA-A*30:01; HLA-B*08:01; HLA-B*58:01; HLA-A*68:02; HLA-B*51:01; HLA-B*15:01; HLA-A*32:01 | 8 | 100% | Non-allergen | Non-toxic | |
WTAGAAAYY | 258–266 | 0.6306 | 0.1525 | HLA-A*26:01; HLA-A*01:01; HLA-A*30:02; HLA-A*68:01; HLA-B*35:01; HLA-B*15:01; HLA-B*58:01 | 7 | 100% | Non-allergen | Non-toxic | |
LPFNDGVYF | 84–92 | 0.5593 | 0.11767 | HLA-B*35:01; HLA-B*53:01; HLA-B*51:01; HLA-B*07:02; HLA-A*26:01 | 5 | 100% | Non-allergen | Non-toxic | |
GAAAYYVGY | 261–269 | 0.6604 | 0.9963 | HLA-A*30:02; HLA-B*15:01; HLA-B*35:01; HLA-A*26:01; HLA-A*01:01 | 5 | 100% | Non-allergen | Non-toxic | |
South Africa | IAIPINFTI | 712–720 | 1.5131 | 0.27703 | HLA-B*51:01; HLA-B*58:01; HLA-B*57:01; HLA-A*02:06; HLA-A*68:02; HLA-B*53:01; HLA-A*32:01; HLA-A*02:01; HLA-A*23:01; HLA-B*35:01; HLA-A*24:02 | 11 | 100% | Non-allergen | Non-toxic |
FTISVTTEI | 718–726 | 0.8534 | 0.04473 | HLA-A*68:02; HLA-A*02:06; HLA-A*02:03; HLA-A*02:01; HLA-B*51:01; HLA-A*26:01; HLA-B*58:01; HLA-A*32:01; HLA-B*53:01 | 9 | 100% | Non-allergen | Non-toxic | |
YQPYRVVVL | 505–513 | 0.5964 | 0.1409 | HLA-B*08:01; HLA-A*02:06; HLA-B*15:01; HLA-A*02:03; HLA-A*02:01; HLA-A*24:02; HLA-B*40:01 HLA-A*23:01 | 8 | 100% | Non-allergen | Non-toxic | |
WTAGAAAYY | 258–266 | 0.6306 | 0.15259 | HLA-A*26:01; HLA-A*01:01; HLA-A*30:02; HLA-A*68:01; HLA-B*35:01; HLA-B*15:01; HLA-B*58:01 | 7 | 100% | Non-allergen | Non-toxic | |
YSKHTPINL | 204–212 | 1.0547 | 0.09845 | HLA-B*57:01; HLA-A*30:01; HLA-B*08:01; HLA-B*58:01; HLA-A*68:02; HLA-B*51:01; HLA-A*32:01 | 7 | 100% | Non-allergen | Non-toxic | |
LPFNDGVYF | 84–92 | 0.5593 | 0.11767 | HLA-B*35:01; HLA-B*53:01; HLA-B*51:01; HLA-B*07:02; HLA-A*26:01 | 5 | 100% | Non-allergen | Non-toxic | |
GVVFLHVTY | 1059–1067 | 1.4104 | 0.20837 | HLA-B*15:01; HLA-A*30:02; HLA-A*26:01; HLA-B*35:01; HLA-A*32:01 | 5 | 100% | Non-allergen | Non-toxic |
Sl. No. | Peptide | MHC II Binding Allele | Start | End | Method | Percentile Rank | Vaxijen Score | Allergenicity | Toxicity |
---|---|---|---|---|---|---|---|---|---|
Wuhan Isolate | |||||||||
1 | MFVFLVLLPLVSSQC | HLA-DRB1*01:01 | 1 | 15 | Consensus | 0.24 | Antigen (0.5741) | Non-allergen | Non-toxic |
2 | MFVFLVLLPLVSSQC | HLA-DPA1*03:01/DPB1*04:02 | 1 | 15 | Consensus | 0.34 | Antigen (0.5741) | Non-allergen | Non-toxic |
3 | VLLPLVSSQCVNLTT | HLA-DRB4*01:01 | 6 | 20 | Consensus | 1.5 | Antigen (0.8957) | Non-allergen | Non-toxic |
4 | LHSTQDLFLPFFSNV | HLA-DPA1*01:03/DPB1*02:01 | 48 | 62 | Consensus | 1.4 | Antigen (0.2110) | Allergen | Non-toxic |
5 | LFLPFFSNVTWFHAI | HLA-DPA1*01:03/DPB1*04:01 | 54 | 68 | NetMHCIIpan | 0.81 | Antigen (0.2477) | Non-allergen | Non-toxic |
6 | KTQSLLIVNNATNVV | HLA-DRB3*02:02 | 113 | 127 | NetMHCIIpan | 0.17 | Antigen (0.6303) | Allergen | Non-toxic |
7 | SFVIRGDEVRQIAPG | HLA-DRB3*01:01 | 399 | 413 | Consensus | 0.51 | Antigen (0.5882) | Non-allergen | Non-toxic |
8 | GNYNYLYRLFRKSNL | HLA-DRB1*11:01 | 447 | 461 | Consensus | 0.22 | Non-antigen (0.1808) | Allergen | Non-toxic |
9 | PYRVVVLSFELLHAP | HLA-DPA1*03:01/DPB1*04:02 | 507 | 521 | Consensus | 0.25 | Antigen (0.8161) | Non-allergen | Non-toxic |
10 | FNFNGLTGTGVLTES | HLA-DRB1*09:01 | 541 | 555 | Consensus | 0.75 | Antigen (0.7797) | Non-allergen | Non-toxic |
11 | DIPIGAGICASYQTQ | HLA-DQA1*05:01/DQB1*03:01 | 633 | 677 | Consensus | 1.2 | Antigen (1.1088) | Non-allergen | Non-toxic |
12 | IAIPTNFTISVTTEI | HLA-DRB1*07:01 | 712 | 726 | Consensus | 0.47 | Antigen (0.7719) | Allergen | Non-toxic |
133 | CSNLLLQYGSFCTQL | HLA-DRB1*15:01 | 749 | 763 | Consensus | 0.58 | Antigen (0.6336) | Non-allergen | Non-toxic |
14 | WYIWLGFIAGLIAIV | HLA-DQA1*05:01/DQB1*03:01 | 1214 | 1228 | Consensus | 0.58 | Antigen (0.5770) | Non-allergen | Non-toxic |
15 | IWLGFIAGLIAIVMV | HLA-DQA1*05:01/DQB1*03:01 | 1216 | 1230 | Consensus | 0.51 | Antigen (0.6150) | Non-allergen | Non-toxic |
England Variant | |||||||||
16 | FVFLVLLPLVSSQCV | HLA-DRB1*01:01 | 2 | 16 | Consensus | 0.24 | Antigen (0.7185) | Non-allergen | Non-toxic |
17 | KTQSLLIVNNATNVV | HLA-DRB1*13:02 | 113 | 127 | Consensus | 0.01 | Antigen (0.6303) | Allergen | Non-toxic |
18 | YRVVVLSFELLHAPA | HLA-DPA1*01:03/DPB1*04:01 | 508 | 522 | NetMHCIIpan | 0.95 | Antigen (0.7072) | Non-allergen | Non-toxic |
19 | VVLSFELLHAPATVC | HLA-DRB1*01:01 | 511 | 525 | Consensus | 0.03 | Antigen (0.8618) | Non-allergen | Non-toxic |
20 | DIPIGAGICASYQTQ | HLA-DQA1*05:01/DQB1*03:01 | 663 | 677 | Consensus | 1.2 | Antigen (1.1088) | Non-allergen | Non-toxic |
21 | PRRARSVASQSIIAY | HLA-DPA1*02:01/DPB1*14:01 | 681 | 695 | NetMHCIIpan | 1.2 | Non-antigen (0.2408) | Non-allergen | Non-toxic |
22 | YIWLGFIAGLIAIVM | HLA-DQA1*05:01/DQB1*03:01 | 1215 | 1229 | Consensus | 0.51 | Antigen (0.6090) | Non-allergen | Non-toxic |
USA Variant | |||||||||
23 | SSGWTAGAAAYYVGY | HLA-DQA1*05:01/DQB1*03:01 | 255 | 269 | Consensus | 0.94 | Antigen (0.6604) | Non-allergen | Non-toxic |
24 | SGWTAGAAAYYVGYL | HLA-DQA1*05:01/DQB1*03:01 | 256 | 270 | Consensus | 1.2 | Antigen (0.6604) | Non-allergen | Non-toxic |
25 | VVVLSFELLHAPATV | HLA-DPA1*03:01/DPB1*04:02 | 510 | 524 | Consensus | 0.9 | Antigen (0.8083) | Non-allergen | Non-toxic |
26 | DIPIGAGICASYQTQ | HLA-DQA1*05:01/DQB1*03:01 | 663 | 677 | Consensus | 1.2 | Antigen (1.1088) | Non-allergen | Non-toxic |
27 | IAIPTNFTISVTTEI | HLA-DRB1*07:01 | 712 | 726 | Consensus | 0.47 | Antigen (0.7719) | Allergen | Non-toxic |
28 | RSFIEDLLFNKVTLA | HLA-DPA1*02:01/DPB1*05:01 | 815 | 829 | Consensus | 1.4 | Non-antigen (−0.0341) | Allergen | Non-toxic |
29 | GWTFGAGAALQIPFA | HLA-DRB1*09:01 | 885 | 899 | Consensus | 0.35 | Non-antigen (0.4665) | Non-allergen | Non-toxic |
30 | PREGVFVSNGTHWFV | HLA-DRB1*13:02 | 1090 | 1104 | Consensus | 1.2 | Antigen (1.0165) | Non-allergen | Non-toxic |
31 | REGVFVSNGTHWFVT | HLA-DRB3*02:02 | 1091 | 1105 | NetMHCIIpan | 0.2 | Antigen (1.0165) | Non-allergen | Non-toxic |
32 | SGNCDVVIGIVNNTV | HLA-DRB1*13:02 | 1123 | 1137 | Consensus | 1.3 | Antigen (0.5968) | Non-allergen | Non-toxic |
33 | CDVVIGIVNNTVYDP | HLA-DRB1*13:02 | 1126 | 1140 | Consensus | 0.7 | Antigen (0.7320) | Non-allergen | Non-toxic |
34 | WYIWLGFIAGLIAIV | HLA-DQA1*05:01/DQB1*03:01 | 1214 | 1228 | Consensus | 0.58 | Antigen (0.5770) | Non-allergen | Non-toxic |
Indian Variant | |||||||||
35 | MFVFLVLLPLVSSQC | HLA-DRB1*01:01 | 1 | 15 | Consensus | 0.24 | Antigen (0.5741) | Non-allergen | Non-toxic |
36 | DLFLPFFSNVTWFHA | HLA-DRB1*04:01 | 53 | 67 | Consensus | 1.1 | Non-antigen (0.2472) | Non-allergen | Non-toxic |
37 | KTQSLLIVNNATNVV | HLA-DRB1*13:02 | 113 | 127 | Consensus | 0.01 | Antigen (0.6303) | Allergen | Non-toxic |
38 | REFVFKNIDGYFKIY | HLA-DRB5*01:01 | 190 | 204 | Consensus | 0.17 | Non-antigen (−0.1712) | Allergen | Non-toxic |
39 | TRFASVYAWNRKRIS | HLA-DPA1*02:01/DPB1*14:01 | 232 | 246 | Consensus | 0.52 | Non-antigen (0.4963) | Allergen | Non-toxic |
40 | NYNYLYRLFRKSNLK | HLA-DRB1*11:01 | 448 | 462 | Consensus | 0.42 | Non-antigen (0.1089) | Allergen | Non-toxic |
41 | PYRVVVLSFELLHAP | HLA-DPA1*01:03/DPB1*02:01 | 507 | 521 | Consensus | 0.36 | Antigen (0.8161) | Non-allergen | Non-toxic |
42 | AIPINFTISVTTEIL | HLA-DRB1*07:01 | 713 | 727 | Consensus | 0.29 | Antigen (1.1305) | Non-allergen | Non-toxic |
43 | LQIPFAMQMAYRFNG | HLA-DRB4*01:01 | 894 | 908 | Consensus | 0.73 | Antigen (0.7205) | Non-allergen | Non-toxic |
44 | QQLIRAAEIRASANL | HLA-DPA1*02:01/DPB1*14:01 | 1010 | 1024 | NetMHCIIpan | 0.2 | Non-antigen (0.1269) | Allergen | Non-toxic |
45 | REGVFVSNGTHWFVT | HLA-DRB3*02:02 | 1091 | 1195 | NetMHCIIpan | 0.2 | Non-antigen (0.4461) | Allergen | Non-toxic |
46 | IWLGFIAGLIAIVMV | HLA-DQA1*05:01/DQB1*03:01 | 1216 | 1230 | Consensus | 0.51 | Antigen (0.6150) | Non-allergen | Non-toxic |
South African Variant | |||||||||
47 | MFVFLVLLPLVSSQC | HLA-DRB1*01:01 | 1 | 15 | Consensus | 0.24 | Antigen (0.5741) | Non-allergen | Non-toxic |
48 | FVFLVLLPLVSSQCV | HLA-DRB1*01:01 | 2 | 16 | Consensus | 0.24 | Antigen (0.7185) | Non-allergen | Non-toxic |
49 | LHSTQDLFLPFFSNV | HLA-DPA1*01:03/DPB1*02:01 | 48 | 62 | Consensus | 1.4 | Non-antigen (0.2110) | Allergen | Non-toxic |
50 | KTQSLLIVNNATNVV | HLA-DRB1*13:02 | 113 | 127 | Consensus | 0.01 | Antigen (0.6303) | Allergen | Non-toxic |
51 | REFVFKNIDGYFKIY | HLA-DRB5*01:01 | 190 | 204 | Consensus | 0.17 | Non-antigen (−0.1712) | Allergen | Non-toxic |
52 | NITRFQTLLALHRSY | HLA-DRB5*01:01 | 234 | 248 | Consensus | 0.32 | Non-antigen (0.1775) | Non-allergen | Non-toxic |
53 | ATRFASVYAWNRKRI | HLA-DRB5*01:01 | 344 | 358 | Consensus | 0.49 | Non-antigen (0.3489) | Allergen | Non-toxic |
54 | NYNYLYRLFRKSNLK | HLA-DRB1*11:01 | 448 | 462 | Consensus | 0.42 | Non-antigen (0.1089) | Allergen | Non-toxic |
55 | PYRVVVLSFELLHAP | HLA-DPA1*02:01/DPB1*01:01 | 507 | 521 | Consensus | 0.3 | Antigen (0.8161) | Non-allergen | Non-toxic |
56 | IAIPTNFTISVTTEI | HLA-DRB1*07:01 | 712 | 726 | Consensus | 0.47 | Antigen (0.7719) | Non-allergen | Non-toxic |
57 | TSGWTFGAGAALQIP | HLA-DRB1*09:01 | 883 | 897 | Consensus | 0.34 | Non-antigen (−0.0178) | Non-allergen | Non-toxic |
58 | ALQIPFAMQMAYRFN | HLA-DRB4*01:01 | 893 | 907 | Consensus | 0.81 | Antigen (1.0112) | Allergen | Non-toxic |
59 | QQLIRAAEIRASANL | HLA-DPA1*02:01/DPB1*14:01 | 1010 | 1024 | NetMHCIIpan | 0.2 | Non-antigen (0.1269) | Allergen | Non-toxic |
60 | REGVFVSNGTHWFVT | HLA-DRB3*02:02 | 1091 | 1105 | NetMHCIIpan | 0.2 | Non-antigen (0.4461) | Non-allergen | Non-toxic |
61 | CDVVIGIVNNTVYDP | HLA-DRB1*13:02 | 1126 | 1140 | Consensus | 0.7 | Antigen (0.7320) | Non-allergen | Non-toxic |
62 | YIWLGFIAGLIAIVM | HLA-DQA1*05:01/DQB1*03:01 | 1215 | 1229 | Consensus | 0.51 | Antigen (0.6090) | Non-allergen | Non-toxic |
Position | Epitope Sequence | Score | Antigenicity |
---|---|---|---|
Wuhan Isolate | |||
14–28 | QCVNLTTRTQLPPAY | 0.772 | 1.4548 |
109–114 | TLDSKT | 0.529 | 1.1073 |
1033–1039 | VLGQSKR | 0.523 | 1.6008 |
England Isolate | |||
392–429 | FTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDF | 0.695 | 0.5786 |
576–585 | VRDPQTLEIL | 0.644 | 0.5446 |
872–928 | QYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFN | 0.649 | 0.5394 |
USA Isolate | |||
392–429 | FTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDF | 0.695 | 0.5786 |
553–565 | TESNKKFLPFQQF | 0.666 | 0.5056 |
872–928 | QYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFN | 0.649 | 0.5394 |
576–585 | VRDPQTLEIL | 0.644 | 0.5449 |
Indian Isolate | |||
239–265 | QTLLALHRSYLTPGDSSSGWTAGAAAY | 0.816 | 0.4822 |
14–27 | QCVNLTTRTQLPPA | 0.771 | 1.4983 |
64–83 | WFHAGASSGTNGTKRFDNPV | 0.763 | 0.4097 |
169–190 | EYVSQPFLMDLEGKQGNFKNLR LIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCT | 0.75 | 0.7830 |
118–167 | RFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFK | 0.732 | 0.3023 |
South African Isolate | |||
239–265 | QTLLALHRSYLTPGDSSSGWTAGAAAY | 0.815 | 0.4822 |
14–27 | QCVNLTTRTQLPPA | 0.769 | 1.4983 |
64–83 | WFHAIHVSGTNGTKRFDNPV | 0.763 | 0.4100 |
169–190 | EYVSQPFLMDLEGKQGNFKNLR | 0.75 | 0.7830 |
118–167 | LIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCT | 0.731 | 0.1177 |
328–378 | RFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFK | 0.728 | 0.3023 |
Residue Position | Residue Name | Contact Number | Propensity Score | DiscotopeScore |
---|---|---|---|---|
Wuhan Isolate | ||||
181 | GLY | 6 | 0.026 | −0.667 |
183 | GLN | 19 | 1.817 | −0.577 |
444 | LYS | 9 | 1.701 | 0.47 |
447 | GLY | 5 | 1.651 | 0.886 |
449 | TYR | 4 | −0.223 | −0.667 |
496 | GLY | 3 | 0.343 | −0.041 |
501 | ASN | 27 | 3.051 | −0.405 |
679 | ASN | 15 | 1.01 | −0.831 |
684 | ALA | 11 | 1.663 | 0.206 |
1144 | GLU | 7 | 0.215 | −0.615 |
1145 | LEU | 4 | −0.092 | −0.541 |
England Isolate | ||||
72 | GLY | 11 | 0.723 | −0.625 |
75 | GLY | 10 | 1.381 | 0.072 |
147 | LYS | 10 | 1.503 | 0.18 |
148 | ASN | 13 | 1.34 | −0.309 |
149 | ASN | 17 | 1.084 | −0.996 |
152 | TRP | 14 | 2.444 | 0.553 |
498 | GLN | 6 | 0.354 | −0.377 |
499 | PRO | 9 | 1.027 | −0.126 |
1142 | GLN | 7 | 0.467 | −0.392 |
1144 | GLU | 3 | 1.177 | 0.697 |
1145 | LEU | 5 | 0.608 | −0.037 |
1147 | SER | 6 | 0.413 | −0.325 |
1148 | PHE | 5 | 0.591 | −0.052 |
USA Isolate | ||||
72 | GLY | 11 | 0.718 | −0.629 |
75 | GLY | 10 | 1.379 | 0.071 |
147 | LYS | 10 | 1.502 | 0.179 |
148 | ASN | 13 | 1.336 | −0.313 |
150 | LYS | 10 | 2.307 | 0.891 |
152 | TRP | 14 | 2.443 | 0.552 |
154 | GLU | 2 | −0.24 | −0.442 |
444 | LYS | 9 | 0.883 | −0.253 |
447 | GLY | 6 | 0.901 | 0.107 |
496 | GLY | 4 | 0.289 | −0.204 |
498 | GLN | 6 | 1.323 | 0.481 |
499 | PRO | 9 | 1.995 | 0.731 |
501 | ASN | 24 | 3.012 | −0.095 |
1141 | LEU | 3 | −0.549 | −0.831 |
1142 | GLN | 7 | 0.466 | −0.393 |
1145 | LEU | 5 | 0.608 | −0.037 |
1147 | SER | 6 | 0.412 | −0.325 |
1148 | PHE | 5 | 0.59 | −0.053 |
1149 | LYS | 5 | 0.797 | 0.13 |
Indian Isolate | ||||
147 | LYS | 10 | 4.318 | −0.682 |
149 | ASN | 9 | 4.399 | −0.101 |
153 | MET | 18 | 1.485 | −7.515 |
424 | LYS | 24 | 4.315 | −7.685 |
460 | ASN | 18 | 2.804 | −6.196 |
461 | LEU | 17 | 3.048 | −5.452 |
462 | LYS | 16 | 3.219 | −4.781 |
501 | TYR | 15 | 1.556 | −5.944 |
563 | GLN | 11 | 1.367 | −4.133 |
679 | ASN | 10 | 3.455 | −1.545 |
809 | PRO | 11 | 4.234 | −1.266 |
1158 | ASN | 10 | 4.027 | −0.973 |
1159 | HIS | 10 | 4.027 | −0.973 |
1160 | THR | 8 | 3.607 | −0.393 |
1161 | SER | 7 | 3.308 | −0.192 |
South African Isolate | ||||
146 | HIS | 14 | 3.276 | 3.724 |
147 | LYS | 11 | 4.084 | −1.416 |
148 | ASN | 8 | 4.194 | 0.194 |
149 | ASN | 9 | 4.399 | −0.101 |
150 | LYS | 8 | 4.194 | 0.194 |
151 | SER | 13 | 4.108 | −2.392 |
152 | TRP | 18 | 3.747 | −5.253 |
409 | GLN | 20 | 2.989 | −7.011 |
414 | GLN | 18 | 2.979 | −6.021 |
424 | LYS | 9 | 4.399 | −0.101 |
498 | GLN | 21 | 3.461 | −7.039 |
499 | PRO | 20 | 3.536 | −6.464 |
501 | ASN | 15 | 2.768 | −4.732 |
679 | ASN | 9 | 3.115 | −1.385 |
680 | SER | 9 | 3.115 | −1.385 |
809 | PRO | 11 | 4.234 | −1.266 |
810 | SER | 13 | 3.958 | −0.542 |
811 | LYS | 12 | 3.646 | −2.354 |
1155 | TYR | 11 | 2.84 | −2.66 |
1156 | PHE | 12 | 3.55 | −2.45 |
1157 | LYS | 10 | 3.353 | −1.647 |
1158 | ASN | 10 | 4.027 | −0.973 |
1159 | HIS | 10 | 4.027 | −0.973 |
1160 | THR | 8 | 3.607 | −0.393 |
1160 | THR | 8 | 3.607 | −0.393 |
1161 | SER | 7 | 3.308 | −0.192 |
Epitope | Country | Population Coverage |
---|---|---|
Wuhan Strain | ||
ILDITPCSF STQDLFLPF VVFLHVTYV GVVFLHVTY WTAGAAAYY GAAAYYVGY | World | 93.65% |
South Asia | 88.23% | |
India | 80.22% | |
England | 97.08% | |
France | 96.42% | |
Italy | 95.12% | |
Sweden | 92.66% | |
United States | 95.3 | |
South Africa | 87.07% | |
England Isolate | ||
NGVEGFNCY QYIKWPWYI WTAGAAAYY VYAWNRKRI GVYFASTEK SPRRARSVA PYRVVVLSF | World | 94.15% |
South Asia | 92.78% | |
India | 89.3% | |
England | 97.62% | |
France | 97.36% | |
Italy | 95.84% | |
Sweden | 96.12% | |
United States | 93.76% | |
South Africa | 96.49% | |
USA Isolate | ||
VVFLHVTYV IAIVMVTIM LPFNDGVYF IAIPTNFTI | World | 91.98% |
South Asia | 81.6% | |
India | 73.8% | |
England | 95.97% | |
France | 96.2% | |
Italy | 93.59% | |
Sweden | 98.77% | |
United States | 94.9% | |
South Africa | 83.62% | |
Indian Isolate | ||
FTISVTTEI VVFLHVTYV YQPYRVVVL YSKHTPINL WTAGAAAYY LPFNDGVYF GAAAYYVGY | World | 97.98% |
South Asia | 91.95% | |
India | 85.34% | |
England | 99.71% | |
France | 99.21% | |
Italy | 97.97% | |
Sweden | 99.82% | |
United States | 98.07% | |
South Africa | 90.51% | |
South African Isolate | ||
IAIPINFTI FTISVTTEI YQPYRVVVL WTAGAAAYY YSKHTPINL GVVFLHVTY LPFNDGVYF | World | 97.48% |
South Asia | 91.95% | |
India | 85.34% | |
England | 99.71% | |
France | 99.21% | |
Italy | 97.97% | |
Sweden | 99.82% | |
United States | 98.07% | |
South Africa | 90.51% |
S.No. | Potential Peptide for Vaccine | Binding Alleles | Attractive vdW | Repulsive vdW | ACE | HB | Global Energy |
---|---|---|---|---|---|---|---|
Wuhan Isolate | |||||||
1. | ILDITPCSF | HLA-B*51:01 | −28.64 | 7.59 | −9.54 | −2.23 | −58.28 |
HLA-B*08:01 | −24.90 | 5.90 | −8.27 | −3.92 | −50.66 | ||
HLA-A*02:06 | −24.14 | 10.32 | −9.30 | −2.48 | −49.01 | ||
2. | STQDLFLPF | HLA-A*32:01 | −19.73 | 14.97 | −11.66 | −1.83 | −44.18 |
HLA-B*57:01 | −29.53 | 21.42 | −3.31 | −3.03 | −40.05 | ||
HLA-B*15:01 | −3.50 | 0.00 | 0.36 | 0.00 | −8.53 | ||
3. | VVFLHVTYV | HLA-B*51:01 | −29.19 | 10.45 | −1.43 | −3.35 | −51.05 |
HLA-A*02:03 | −18.26 | 2.58 | −9.10 | −4.13 | −42.85 | ||
4. | GVVFLHVTY | HLA-B*35:01 | −36.19 | 7.98 | −8.72 | −1.99 | −66.28 |
HLA-A*01:01 | −32.13 | 6.50 | −7.59 | −2.76 | −55.83 | ||
HLA-B*15:01 | −9.36 | 2.62 | 0.96 | −0.20 | −3.98 | ||
5. | WTAGAAAYY | HLA-B*35:01 | −27.77 | 4.34 | −2.83 | −3.28 | −54.98 |
HLA-A*01:01 | −30.65 | 13.59 | −7.64 | −4.80 | −53.52 | ||
6. | GAAAYYVGY | HLA-A*30:02 | −25.83 | 3.78 | −4.26 | −4.52 | −51.90 |
HLA-B*15:01 | −20.22 | 7.80 | −0.58 | −0.99 | −24.32 | ||
England Isolate | |||||||
7. | QYIKWPWYI | HLA-A*23:01 | −25.46 | 8.91 | −13.16 | −0.95 | −57.28 |
HLA-C*06:02 | −29.14 | 16.66 | −4.45 | −3.18 | −50.48 | ||
8. | GVYFASTEK | HLA-A*30:01 | −21.73 | 4.79 | 2.52 | −3.41 | −28.36 |
9. | NGVEGFNCY | HLA-B*35:01 | −37.69 | 6.42 | 2.02 | −2.25 | −46.33 |
10. | PYRVVVLSF | HLA-A*23:01 | −25.49 | 9.71 | −11.33 | −2.48 | −65.01 |
HLA-C*14:02 | −25.48 | 5.04 | −1.94 | −0.95 | −41.16 | ||
11. | VYAWNRKRI | HLA-A*23:01 | −22.44 | 4.18 | −4.02 | −3.34 | −46.75 |
12. | SPRRARSVA | HLA-B*07:02 | −25.14 | 8.95 | 3.94 | −1.97 | −18.83 |
USA Isolate | |||||||
13. | IAIVMVTIM | HLA-B*51:01 | −30.57 | 25.38 | −16.59 | −0.98 | −59.86 |
14. | LPFNDGVYF | HLA-B*35:01 | −35.26 | 47.18 | −3.06 | −3.78 | −30.68 |
Indian Isolate | |||||||
15. | YQPYRVVVL | HLA-B*08:01 | −36.00 | 10.43 | −7.97 | −2.46 | −62.85 |
16. | YSKHTPINL | HLA-A*68:02 | −22.93 | 6.44 | −10.43 | −2.56 | −59.11 |
17. | FTISVTTEI | HLA-A*68:02 | −29.71 | 11.47 | −7.29 | −2.07 | −53.01 |
18. | WTAGAAAYY | HLA-A*26:01 | −31.19 | 8.71 | −0.08 | −1.66 | −44.75 |
19. | GAAAYYVGY | HLA-A*30:02 | −19.74 | 5.30 | −9.59 | −2.21 | −43.65 |
South African Isolate | |||||||
20. | IAIPINFTI | HLA-B*51:01 | −22.76 | 6.82 | −13.73 | −0.80 | −54.96 |
21. | FTISVTTEI | HLA-B*51:01 | −22.68 | 11.47 | −7.29 | −7.29 | −53.01 |
22. | QLTPTWRVY | HLA-B*35:01 | −19.09 | 8.37 | −10.39 | 0.00 | −44.39 |
23. | YSKHTPINL | HLA-B*57:01 | −24.90 | 3.82 | −1.65 | −1.65 | −41.72 |
24. | YQPYRVVVL | HLA-B*08:01 | −21.47 | 10.07 | −9.41 | −0.98 | −38.80 |
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Mallavarpu Ambrose, J.; Priya Veeraraghavan, V.; Kullappan, M.; Chellapandiyan, P.; Krishna Mohan, S.; Manivel, V.A. Comparison of Immunological Profiles of SARS-CoV-2 Variants in the COVID-19 Pandemic Trends: An Immunoinformatics Approach. Antibiotics 2021, 10, 535. https://doi.org/10.3390/antibiotics10050535
Mallavarpu Ambrose J, Priya Veeraraghavan V, Kullappan M, Chellapandiyan P, Krishna Mohan S, Manivel VA. Comparison of Immunological Profiles of SARS-CoV-2 Variants in the COVID-19 Pandemic Trends: An Immunoinformatics Approach. Antibiotics. 2021; 10(5):535. https://doi.org/10.3390/antibiotics10050535
Chicago/Turabian StyleMallavarpu Ambrose, Jenifer, Vishnu Priya Veeraraghavan, Malathi Kullappan, Poongodi Chellapandiyan, Surapaneni Krishna Mohan, and Vivek Anand Manivel. 2021. "Comparison of Immunological Profiles of SARS-CoV-2 Variants in the COVID-19 Pandemic Trends: An Immunoinformatics Approach" Antibiotics 10, no. 5: 535. https://doi.org/10.3390/antibiotics10050535