Identification and Analysis of Unstructured, Linear B-Cell Epitopes in SARS-CoV-2 Virion Proteins for Vaccine Development
Abstract
1. Introduction
2. Materials and Methods
2.1. Identification of uBCELs
2.2. Structural and Accessory Analysis of Protein Antigens
2.3. Phylogenetic Analyses
2.4. Epitope Collection in SARS-CoV-2
2.5. Statistical Analyses
3. Results
3.1. SARS-CoV-2 Epitope Catalogue
3.2. Unstructured Epitope Selection to Design Antigenic Peptides and Chimera Proteins
3.3. S Protein uBCEL Analysis
3.4. E Protein Epitope Analysis
3.5. M Protein Epitope Analysis
3.6. N Protein Epitope Analysis
3.7. Assessment of the Agreement between uBCELs in SARS-CoV-2 and Linear B-Cell Epitopes Previously Reported for SARS-CoV
3.8. Epitope Conservation in Bat Coronaviruses
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
BCE | B-cell epitope |
BCEH | B-cell epitope in an alpha-helix section |
E | envelope protein |
IEDB | immune epitope database |
M | membrane protein |
N | nucleocapsid protein |
S | spike protein |
SARS-CoV | Severe Acute Respiratory Syndrome Coronavirus |
SARS-CoV-2 | Severe Acute Respiratory Syndrome Coronavirus 2 |
SDP | specificity determining position |
TMH | transmembrane helix |
uBCE | unstructured B-cell epitope |
uBCEL | unstructured B-cell epitope-containing loop |
UPR | unfolded protein response |
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Protein | uBECL or BCEH a | uBCE b Location | uBCEL or BCEH Location | Flanking SS c | uBCEL Sequence d |
---|---|---|---|---|---|
S | uBCEL-S1 | 21–28 | 16–28 | SP-B1 | vnlttRTQLPPAY |
uBCEL-S2 | 71–81 | 68–85 | B3-B4 | ihvSGTNGTKRFDNpvlp | |
uBCEL-S3 | 404–412 | 402–429 | B25-B26 | irGDEVRQIAPgqtgkiadynyklpddf | |
uBCEL-S4 | 440–445 | 440–450 | B26-B27 | NLDSKVggnyn | |
uBCEL-S5 | 459–470 473–480 | 455–491 | B27-B28 | lfrkSNLKPFERDISTeiYQAGSTPCngvegfncyfp | |
uBCEL-S6 | 615–630 | 615–642 | B38-B39 | VNCTEVPVAIHADQLTptwrvystgsnv | |
uBCEL-S7 | 676–687 | 676–689 | B43-B44 | TQTNSPRRARSVas | |
uBCEL-S8 | 783–797 | 783–803 | H3-B48 | AQVKQIYKTPPIKDFggfnfs | |
uBCEL-S9 | 1125–1131 | 1125–1131 | B60-B61 | NCDVVIG | |
uBCEL-S10 | 1137–1147 | 1136–1147 | B61-H12 | TVYDPLQPELDS | |
uBCEL-S11 | 1240–1246 | 1238–1246 | H15p-H16p | tsCCSCLKG | |
E | BCEH-E1 | 57–68 | 38–75 | H3p | rlcayccnivnvslvkpsfYVYSRVKNLNSSRvpdllv |
M | uBCEL-M1 | 209–215 | 209–222 | B10-Ct | DHSSSSDniallvq |
N | uBCEL-N1 | 16–48 | 18–55 | B1p-B2 | GGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTA |
uBCEL-N2 | 59–78 | 59–78 | B2-H1 | HGKEDLKFPRGQGVPINTNS | |
uBCEL-N3 | 158–170 | 135–170 | B8-B9 | tegalntpkdhigtrnpannaaiVLQLPQGTTLPKG | |
uBCEL-N4 | 173–208 | 173–213 | B9-H2p | AEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPArmagn | |
uBCEL-N5 | 235–247 | 235–247 | H2p-H3p | SGKGQQQQGQTVT | |
uBCEL-N6 | 276–287 | 276–287 | H4-H5 | RRGPEQTQGNFG | |
uBCEL-N7 | 339–344 | 339–344 | B11-H9 | LDDKDP | |
uBCEL-N8 | 363–383 | 363–383 | H10-H11p | FPPTEPKKDKKKKADETQALP |
uBCEL | Change(s) | n | Date of First Isolation | Geolocation |
---|---|---|---|---|
uBCEL-S2 | I68- | 11 | 15/03/2020 | USA: WA |
N74K | 2 | 20/01/2020 | Brasil; China | |
D80Y | 2 | 31/03/2020 | USA: WA | |
uBCEL-S5 | G476S | 7 | 10/03/2020 | USA: WA |
V483A | 11 | 05/03/2020 | USA: WA | |
uBCEL-S7 | Q677H | 2 | 19/03/2020 | USA: UT |
uBCEL-S8 | T791I | 6 | 26/02/2020 | Taiwan |
BCEH-E1 | P71L | 2 | 19/03/2020 | USA: WA |
uBCEL-N2 | P67S | 2 | 17/03/2020 | USA: NY; USA: WA |
uBCEL-N3 | A152S | 2 | 13/03/2020 | USA: UT |
uBCEL-N4 | S180I | 2 | 31/03/2020 | USA: WA |
S183Y | 4 | 17/03/2020 | USA | |
R185C | 5 | 15/03/2020 | USA | |
R185L | 2 | 19/03/2020 | USA | |
S188L | 3 | 18/03/2020 | USA | |
S188P | 2 | 13/03/2020 | Taiwan | |
S190I | 3 | 17/03/2020 | USA: NY | |
S196L | 6 | 29/02/2020 | USA | |
S197L | 17 | 26/02/2020 | Greece; Spain; USA | |
S202N | 7 | 30/01/2020 | China; USA | |
R203K,G204R | 62 | 27/02/2020 | Czech Republic; Greece; India; Israel; Peru; Spain; Sri Lanka; Taiwan; USA | |
T205I | 10 | 29/01/2020 | China; USA | |
A208G | 4 | 16/03/2020 | USA: WA; USA: NY | |
uBCEL-N7 | P344S | 2 | ?/01/2020 | Japan |
uBCEL-N8 | E367- | 2 | 16/03/2020 | SA: UT; USA: WA |
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Corral-Lugo, A.; López-Siles, M.; López, D.; McConnell, M.J.; Martin-Galiano, A.J. Identification and Analysis of Unstructured, Linear B-Cell Epitopes in SARS-CoV-2 Virion Proteins for Vaccine Development. Vaccines 2020, 8, 397. https://doi.org/10.3390/vaccines8030397
Corral-Lugo A, López-Siles M, López D, McConnell MJ, Martin-Galiano AJ. Identification and Analysis of Unstructured, Linear B-Cell Epitopes in SARS-CoV-2 Virion Proteins for Vaccine Development. Vaccines. 2020; 8(3):397. https://doi.org/10.3390/vaccines8030397
Chicago/Turabian StyleCorral-Lugo, Andrés, Mireia López-Siles, Daniel López, Michael J. McConnell, and Antonio J. Martin-Galiano. 2020. "Identification and Analysis of Unstructured, Linear B-Cell Epitopes in SARS-CoV-2 Virion Proteins for Vaccine Development" Vaccines 8, no. 3: 397. https://doi.org/10.3390/vaccines8030397
APA StyleCorral-Lugo, A., López-Siles, M., López, D., McConnell, M. J., & Martin-Galiano, A. J. (2020). Identification and Analysis of Unstructured, Linear B-Cell Epitopes in SARS-CoV-2 Virion Proteins for Vaccine Development. Vaccines, 8(3), 397. https://doi.org/10.3390/vaccines8030397