scholarly journals T and B cell Epitope analysis of SARS‐CoV‐2 S protein based on immunoinformatics and experimental research

2020 ◽  
Author(s):  
Ziwei Chen ◽  
Pinglang Ruan ◽  
Lili Wang ◽  
Xinmin Nie ◽  
Xuejun Ma ◽  
...  
Keyword(s):  
B Cell ◽  
Experimental Research ◽  
Cell Epitope ◽  
S Protein ◽  
Epitope Analysis ◽  
B Cell Epitope

scholarly journals Potential immune epitope map for structural proteins of SARS-CoV-2

2020 ◽  
Author(s):  
Yengkhom Damayanti Devi ◽  
Himanshu Ballav Goswami ◽  
Sushmita Konwar ◽  
Chandrima Doley ◽  
Anutee Dolley ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Mhc Class I ◽  
Mhc Class Ii ◽  
Cell Epitope ◽  
Class I ◽  
Structural Proteins ◽  
S Protein ◽  
N Protein ◽  
B Cell Epitope

Abstract Researchers around the world are developing more than 145 vaccines (DNA/mRNA/whole-virus/viral-vector/protein-based/repurposed vaccine) against the SARS-CoV-2 and 21 vaccines are in human trials. However, a limited information is available about which SARS-CoV-2 proteins are recognized by human B- and T-cell immune responses. Using a comprehensive computational prediction algorithm and stringent selection criteria, we have predicted and identified potent B- and T-cell epitopes in the structural proteins of SARS-CoV and SARS-CoV-2. The amino acid residues spanning the predicted linear B-cell epitope in the RBD of S protein (370-NSASFSTFKCYGVSPTKLNDLCFTNV-395) have recently been identified for interaction with the CR3022, a previously described neutralizing antibody known to neutralize SARS-CoV-2 through binding to the RBD of the S protein. Intriguingly, most of the amino acid residues spanning the predicted B-cell epitope (aa 331-NITNLCPFGEVFNATRFASVYAWNRK-356, 403-RGDEVRQIAPGQTGKIADYNYKLPD-427 and aa 437- NSNNLDSKVGGNYNYLYRLFRKSNL-461) of the S protein have been experimentally verified to interact with the cross-neutralizing mAbs (S309 and CB6) in an ACE2 receptor-S protein interaction independent-manner. In addition, we found that computationally predicted epitope of S protein (370-395) is likely to function as both linear B-cell and MHC class II epitope. Similarly, 403-27 and 437-461 peptides of S protein were predicted as linear B cell and MHC class I epitope while, 177-196 and 1253-1273 peptides of S protein were predicted as linear and conformational B cell epitope. We found MHC class I epitope 316-GMSRIGMEV-324 predicted as high affinity epitope (HLA-A*02:03, HLA-A*02:01, HLA-A*02:06) common to N protein of both SARS-CoV-2 and SARS-CoV (N317-325) was previously shown to induce interferon-gamma (IFN-γ) in PBMCs of SARS-recovered patients. Interestingly, two MHC class I epitopes, 1041-GVVFLHVTY-1049 (HLA-A*11:01, HLA-A*68:01, HLA-A*03:01) and 1202-FIAGLIAIV-1210 (HLA-A*02:06, HLA-A*68:02) derived from SARS-CoV S protein with epitope conservancy between 85 to 100% with S protein of SARS-CoV-2 was experimentally verified using PBMCs derived from SARS-CoV patients. We observed that HLA-A*02:01, HLA-A*02:03, HLA-A*02:06, HLA-A*11:01, HLA-A*30:01, HLA-A*68:01, HLA-A*68:02, HLA-B*15:01 and HLA-B*35:01 have been predicted to bind to the maximum number of MHC class I epitope (based on the criterion of allele predicted to bind more than 30 epitopes) of S protein of SARS-CoV-2. Similarly, we observed that HLA-A*02:06, HLA-A*30:01, HLA-A*30:02, HLA-A*31:01, HLA-A*32:01, HLA-A*68:01, HLA-A*68:02, HLA-B*15:01 and HLA-B*35:01 are predicted to bind to the maximum number of MHC class I epitope of N protein of SARS-CoV-2. We found that HLA-DRB1*04:01, HLA-DRB1*04:05, HLA-DRB1*13:02, HLA-DRB1*15:01, HLA-DRB3*01:01, HLA-DRB3*02:02, HLA-DRB4*01:01, HLA-DRB5*01:01, HLA-DQA1*04:01, DQB1*04:02, HLA-DPA1*02:01, DPB1*01:01, HLA-DPA1*01:03, DPB1*02:01, HLA-DPA1*01:03, DPB1*04:01, HLA-DPA1*03:01, DPB1*04:02, HLA-DPA1*02:01, DPB1*05:01, HLA-DPA1*02:01, and DPB1*14:01 are predicted to bind to the maximum number of MHC class II epitope of S protein of SARS-CoV-2. Alleles such as HLA-DRB1*04:01, HLA-DRB1*07:01, HLA-DRB1*08:02, HLA-DRB1*09:01, HLA-DRB1*11:01, HLA-DRB1*13:02, HLA-DRB3*02:02, HLA-DRB5*01:01, HLA-DQA1*01:02, DQB1*06:02, DPB1*05:01 and HLA-DPA1*02:01 are found to interact with the maximum number of MHC class II epitope of N protein of SARS-CoV-2. Using the IEDB tool we found the occurrence of HLA alleles with population coverage of around 99% throughout the world. The findings of computational predictions of mega-pool of B- and T-cell epitopes identified in the four main structural proteins of SARS-CoV-2 provides a platform for future experimental validations and the results of present works support the use of RBD or the full-length S and N proteins in an effort towards designing of recombinant protein-based vaccine and a serological diagnostic assay for SARS-CoV-2.

scholarly journals Identification of four linear B-cell epitopes on the SARS-CoV-2 spike protein able to elicit neutralizing antibodies

2020 ◽  
Author(s):  
Lin Li ◽  
Zhongpeng Zhao ◽  
Xiaolan Yang ◽  
WenDong Li ◽  
Shaolong Chen ◽  
...  
Keyword(s):  
B Cell ◽  
Neutralizing Antibodies ◽  
Vaccine Development ◽  
Cell Epitope ◽  
Effective Vaccine ◽  
B Cell Epitopes ◽  
S Protein ◽  
The Public ◽  
B Cell Epitope ◽  
Linear B

SARS-CoV-2 unprecedentedly threatens the public health at worldwide level. There is an urgent need to develop an effective vaccine within a highly accelerated time. Here, we present the most comprehensive S-protein-based linear B-cell epitope candidate list by combining epitopes predicted by eight widely-used immune-informatics methods with the epitopes curated from literature published between Feb 6, 2020 and July 10, 2020. We find four top prioritized linear B-cell epitopes in the hotspot regions of S protein can specifically bind with serum antibodies from horse, mouse, and monkey inoculated with different SARS-CoV-2 vaccine candidates or a patient recovering from COVID-19. The four linear B-cell epitopes can induce neutralizing antibodies against both pseudo and live SARS-CoV-2 virus in immunized wild-type BALB/c mice. This study suggests that the four linear B-cell epitopes are potentially important candidates for serological assay or vaccine development.

scholarly journals SARS-CoV-2-induced humoral immunity through B cell epitope analysis and neutralizing activity in COVID-19 infected individuals in Japan

2020 ◽  
Author(s):  
Shota Yoshida ◽  
Chikako Ono ◽  
Hiroki Hayashi ◽  
Satoshi Shiraishi ◽  
Kazunori Tomono ◽  
...  
Keyword(s):  
B Cell ◽  
Antibody Production ◽  
Vaccine Development ◽  
Hot Spot ◽  
Cell Epitope ◽  
Large Individual ◽  
B Cell Epitopes ◽  
S Protein ◽  
Neutralizing Activity ◽  
B Cell Epitope

AbstractThe aim of this study is to understand adaptive immunity to SARS-CoV-2 through the analysis of B cell epitope and neutralizing activity in coronavirus disease 2019 (COVID-19) patients. We obtained serum from thirteen COVID-19 patients. Most individuals revealed neutralizing activity against SARS-CoV-2 assessed by a pseudotype virus-neutralizing assay. The antibody production against the spike glycoprotein (S protein) or receptor-binding domain (RBD) of SARS-CoV-2 was elevated, with large individual differences, as assessed by ELISA. In the analysis of the predicted the linear B cell epitopes, two regions (671-690 aa. and 1146-1164 aa.), which were located in S1 and S2 but not in the RBD, were highly reactive with the sera from patients. In the further analysis of the B cell epitope within the S protein by utilizing a B cell epitope array, a hot spot in the N-terminal domain of the S protein but not the RBD was observed in individuals with neutralizing activity. Overall, the analysis of antibody production and B cell epitopes of the S protein from patient serum may provide a novel target for the vaccine development against SARS-CoV-2.

scholarly journals SARS-CoV-2-induced humoral immunity through B cell epitope analysis in COVID-19 infected individuals

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shota Yoshida ◽  
Chikako Ono ◽  
Hiroki Hayashi ◽  
Shinya Fukumoto ◽  
Satoshi Shiraishi ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
B Cell ◽  
Antibody Titer ◽  
Antibody Production ◽  
Cell Epitope ◽  
University Hospital ◽  
B Cell Epitopes ◽  
S Protein ◽  
B Cell Epitope

AbstractThe aim of this study is to understand adaptive immunity to SARS-CoV-2 through the analysis of B cell epitope and neutralizing activity in coronavirus disease 2019 (COVID-19) patients. We obtained serum from forty-three COVID-19 patients from patients in the intensive care unit of Osaka University Hospital (n = 12) and in Osaka City Juso Hospital (n = 31). Most individuals revealed neutralizing activity against SARS-CoV-2 assessed by a pseudotype virus-neutralizing assay. The antibody production against the spike glycoprotein (S protein) or receptor-binding domain (RBD) of SARS-CoV-2 was elevated, with large individual differences, as assessed by ELISA. We observed the correlation between neutralizing antibody titer and IgG, but not IgM, antibody titer of COVID-19 patients. In the analysis of the predicted the linear B cell epitopes, hot spots in the N-terminal domain of the S protein were observed in the serum from patients in the intensive care unit of Osaka University Hospital. Overall, the analysis of antibody production and B cell epitopes of the S protein from patient serum may provide a novel target for the vaccine development against SARS-CoV-2.

scholarly journals Identification of four linear B-cell epitopes on the SARS-CoV-2 spike protein able to elicit neutralizing antibodiesIdentification of four linear B-cell epitopes on the SARS-CoV-2 spike protein able to elicit neutralizing antibodies

2021 ◽  
Author(s):  
Lin Li ◽  
Zhongpeng Zhao ◽  
Xiaolan Yang ◽  
Wendong Li ◽  
Shaolong Chen ◽  
...  
Keyword(s):  
B Cell ◽  
Neutralizing Antibodies ◽  
Vaccine Development ◽  
Cell Epitope ◽  
Spike Protein ◽  
Effective Vaccine ◽  
B Cell Epitopes ◽  
S Protein ◽  
B Cell Epitope ◽  
Linear B

Abstract SARS-CoV-2 unprecedentedly threatens the public health at worldwide level. There is an urgent need to develop an effective vaccine within a highly accelerated time. Here, we present the most comprehensive S-protein-based linear B-cell epitope candidate list by combining epitopes predicted by eight widely-used immune-informatics methods with the epitopes curated from literature published between Feb 6, 2020 and July 10, 2020. We find four top prioritized linear B-cell epitopes in the hotspot regions of S protein can specifically bind with pooled serum antibodies from horses, mice, and monkeys inoculated with different SARS-CoV-2 vaccine candidates or five patients recovering from COVID-19. The four linear B-cell epitopes can induce neutralizing antibodies against both pseudo and live SARS-CoV-2 virus in immunized wild-type BALB/c mice. This study suggests that the four linear B-cell epitopes are potentially important candidates for serological assay or vaccine development.

B-cell epitope mapping of YscF, a T3SS needle protein of Yersinia spp., with the panel of immune sera from vaccinated models

2020 ◽  
Author(s):  
Zaytsev Sergey ◽  
Motin Vladimir ◽  
Khizhnyakova Mariya ◽  
Feodorova Valentina Anatolievna ◽  
Elena Lyapina ◽  
...  
Keyword(s):  
B Cell ◽  
Epitope Mapping ◽  
Cell Epitope ◽  
B Cell Epitope ◽  
Needle Protein
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