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

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.

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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

10.21203/rs.3.rs-348597/v1 ◽

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.

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Immunodominant linear B cell epitopes in the spike and membrane proteins of SARS-CoV-2 identified by immunoinformatics prediction and immunoassay

Scientific Reports ◽

10.1038/s41598-021-99642-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kanokporn Polyiam ◽

Waranyoo Phoolcharoen ◽

Namphueng Butkhot ◽

Chanya Srisaowakarn ◽

Arunee Thitithanyanont ◽

...

Keyword(s):

B Cell ◽

Cleavage Site ◽

Vaccine Development ◽

Cell Epitope ◽

Epitope Prediction ◽

E Proteins ◽

B Cell Epitopes ◽

C Terminus ◽

B Cell Epitope ◽

Linear B

AbstractSARS-CoV-2 continues to infect an ever-expanding number of people, resulting in an increase in the number of deaths globally. With the emergence of new variants, there is a corresponding decrease in the currently available vaccine efficacy, highlighting the need for greater insights into the viral epitope profile for both vaccine design and assessment. In this study, three immunodominant linear B cell epitopes in the SARS-CoV-2 spike receptor-binding domain (RBD) were identified by immunoinformatics prediction, and confirmed by ELISA with sera from Macaca fascicularis vaccinated with a SARS-CoV-2 RBD subunit vaccine. Further immunoinformatics analyses of these three epitopes gave rise to a method of linear B cell epitope prediction and selection. B cell epitopes in the spike (S), membrane (M), and envelope (E) proteins were subsequently predicted and confirmed using convalescent sera from COVID-19 infected patients. Immunodominant epitopes were identified in three regions of the S2 domain, one region at the S1/S2 cleavage site and one region at the C-terminus of the M protein. Epitope mapping revealed that most of the amino acid changes found in variants of concern are located within B cell epitopes in the NTD, RBD, and S1/S2 cleavage site. This work provides insights into B cell epitopes of SARS-CoV-2 as well as immunoinformatics methods for B cell epitope prediction, which will improve and enhance SARS-CoV-2 vaccine development against emergent variants.

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

10.1101/2020.07.22.212761 ◽

2020 ◽

Cited By ~ 1

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.

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Identification of Protective Peptides of Fasciola Hepatica-Derived Cathepsin L1 (FhCL1) in Vaccinated Sheep by a Linear B-cell Epitope Mapping Approach

10.21203/rs.3.rs-28171/v1 ◽

2020 ◽

Author(s):

Leandro Buffoni Perazzo ◽

Laura Garza-Cuartero ◽

Raúl Pérez-Caballero ◽

Rafael Zafra ◽

F. Javier Martínez-Moreno ◽

...

Keyword(s):

B Cell ◽

Development Strategy ◽

Epitope Mapping ◽

Vaccine Development ◽

Fasciola Hepatica ◽

Control Strategies ◽

Cell Epitope ◽

Immunodominant Antigen ◽

B Cell Epitope ◽

Linear B

Abstract Background Fasciolosis is one of the most important parasitic diseases of livestock. The need for better control strategies gave rise to the identification of various vaccine candidates. The recombinant form of a member of the cysteine protease family, cathepsin L1 of Fasciola hepatica (FhCL1) has been a vaccine target for the past few decades since it has been shown to behave as an immunodominant antigen. However, when FhCL1 was used as vaccine, it has been observed to elicit significant protection in some trials, whereas no protection was provided in others.Methods In order to improve vaccine development strategy, we conducted a linear B-cell epitope mapping of FhCL1 in vaccinated-protected, vaccinated but not protected, and unvaccinated-infected sheep.Results Our study showed that the pattern and dynamic of peptide recognition varied noticeably between protected and non-protected animals, and that the regions 55–63 and 77–84, which are within the propeptide, and regions 102–114 and 265–273 of FhCL1 were specifically recognised only by vaccinated-protected animals with significant decrease in fluke burden. In addition, these animals also showed significant production of specific IgG2, whereas none was observed in non-protected and infected animals.Conclusions We have identified forty-two residues of FhCL1 that contributed to protective immunity against infection with F. hepatica in sheep. Our results provide indications in relation to key aspects of the immune response. Given the variable outcomes of vaccination trials conducted in ruminants to date, this study adds new insights to improve strategies of vaccine development.

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The Computational Prediction Methods for Linear B-cell Epitopes

Current Bioinformatics ◽

10.2174/1574893613666181112145706 ◽

2019 ◽

Vol 14 (3) ◽

pp. 226-233 ◽

Cited By ~ 2

Author(s):

Cangzhi Jia ◽

Hongyan Gong ◽

Yan Zhu ◽

Yixia Shi

Keyword(s):

B Cell ◽

Structural Information ◽

Cell Epitope ◽

Epitope Prediction ◽

Computational Prediction ◽

Extraction Methods ◽

B Cell Epitopes ◽

B Cell Epitope ◽

Reliable Methods ◽

Linear B

Background: B-cell epitope prediction is an essential tool for a variety of immunological studies. For identifying such epitopes, several computational predictors have been proposed in the past 10 years. Objective: In this review, we summarized the representative computational approaches developed for the identification of linear B-cell epitopes. </P><P> Methods: We mainly discuss the datasets, feature extraction methods and classification methods used in the previous work. Results: The performance of the existing methods was not very satisfying, and so more effective approaches should be proposed by considering the structural information of proteins. Conclusion: We consider existing challenges and future perspectives for developing reliable methods for predicting linear B-cell epitopes.

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Identification and Analysis of Unstructured, Linear B-Cell Epitopes in SARS-CoV-2 Virion Proteins for Vaccine Development

Vaccines ◽

10.3390/vaccines8030397 ◽

2020 ◽

Vol 8 (3) ◽

pp. 397

Author(s):

Andrés Corral-Lugo ◽

Mireia López-Siles ◽

Daniel López ◽

Michael J. McConnell ◽

Antonio J. Martin-Galiano

Keyword(s):

B Cell ◽

Vaccine Development ◽

Cell Epitope ◽

Vaccine Failure ◽

B Cell Epitopes ◽

Secondary Structure Formation ◽

Phylogenetic Comparison ◽

B Cell Epitope ◽

Pandemic Strains ◽

Mutational Processes

The efficacy of SARS-CoV-2 nucleic acid-based vaccines may be limited by proteolysis of the translated product due to anomalous protein folding. This may be the case for vaccines employing linear SARS-CoV-2 B-cell epitopes identified in previous studies since most of them participate in secondary structure formation. In contrast, we have employed a consensus of predictors for epitopic zones plus a structural filter for identifying 20 unstructured B-cell epitope-containing loops (uBCELs) in S, M, and N proteins. Phylogenetic comparison suggests epitope switching with respect to SARS-CoV in some of the identified uBCELs. Such events may be associated with the reported lack of serum cross-protection between the 2003 and 2019 pandemic strains. Incipient variability within a sample of 1639 SARS-CoV-2 isolates was also detected for 10 uBCELs which could cause vaccine failure. Intermediate stages of the putative epitope switch events were observed in bat coronaviruses in which additive mutational processes possibly facilitating evasion of the bat immune system appear to have taken place prior to transfer to humans. While there was some overlap between uBCELs and previously validated SARS-CoV B-cell epitopes, multiple uBCELs had not been identified in prior studies. Overall, these uBCELs may facilitate the development of biomedical products for SARS-CoV-2.

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Corrigendum: Leishmania infantum Virulence Factor A2 Protein: Linear B-Cell Epitope Mapping and Identification of Three Main Linear B-Cell Epitopes in Vaccinated and Naturally Infected Dogs

Frontiers in Immunology ◽

10.3389/fimmu.2018.02245 ◽

2018 ◽

Vol 9 ◽

Author(s):

Monique Paiva Campos ◽

Fabiano Borges Figueiredo ◽

Fernanda Nazaré Morgado ◽

Alinne Rangel dos Santos Renzetti ◽

Sara Maria Marques de Souza ◽

...

Keyword(s):

B Cell ◽

Virulence Factor ◽

Leishmania Infantum ◽

Epitope Mapping ◽

Cell Epitope ◽

B Cell Epitopes ◽

B Cell Epitope ◽

Linear B

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Novel differential linear B-cell epitopes to identify Zika and dengue virus infections in patients

10.1101/639542 ◽

2019 ◽

Author(s):

Siti Naqiah Amrun ◽

Wearn-Xin Yee ◽

Farhana Abu Bakar ◽

Bernett Lee ◽

Yiu-Wing Kam ◽

...

Keyword(s):

B Cell ◽

Neutralizing Antibodies ◽

Cell Epitope ◽

Structural Similarity ◽

Amino Acid Residues ◽

Virus Infections ◽

Protein Amino Acid ◽

B Cell Epitopes ◽

Diagnostic Standards ◽

Linear B

AbstractBackgroundRecent Zika virus (ZIKV) outbreaks challenged existing laboratory diagnostic standards, especially for serology-based methods. Due to the genetic and structural similarity of ZIKV with other flaviviruses, this results in cross-reactive antibodies which confounds serological interpretations.MethodsPlasma from Singapore ZIKV patients was screened longitudinally for antibody responses and neutralizing capacities against ZIKV. Samples from healthy controls, ZIKV and DENV patients were further assessed using ZIKV and DENV peptides of precursor membrane (prM), envelope (E) or non-structural 1 (NS1) viral proteins in a peptide-based ELISA for epitope identification. Identified epitopes were re-validated and diagnostically evaluated using sera of patients with DENV, bacteria or unknown infections from Thailand.ResultsLong-lasting ZIKV-neutralizing antibodies were elicited during ZIKV infection. Thirteen potential linear B-cell epitopes were identified and of these, four common flavivirus, three ZIKV-specific, and one DENV-specific differential epitopes had more than 50% sensitivities and specificities. Notably, ZIKV-specific peptide 26 on domain I/II of E protein (amino acid residues 271-288) presented 80% sensitivity and 85.7% specificity. Importantly, the differential epitopes also showed significance in differentiating non-flavivirus patient samples.ConclusionsLinear B-cell epitope candidates to differentiate ZIKV and DENV infections were identified, providing the first step towards the design of a much-needed serology-based assay.

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

Scientific Reports ◽

10.1038/s41598-021-85202-9 ◽

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.

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Advances in In-silico B-cell Epitope Prediction

Current Topics in Medicinal Chemistry ◽

10.2174/1568026619666181130111827 ◽

2019 ◽

Vol 19 (2) ◽

pp. 105-115 ◽

Cited By ~ 5

Author(s):

Pingping Sun ◽

Sijia Guo ◽

Jiahang Sun ◽

Liming Tan ◽

Chang Lu ◽

...

Keyword(s):

B Cell ◽

In Silico ◽

Vaccine Development ◽

Cell Epitope ◽

Disease Diagnosis ◽

Diagnostic Tools ◽

Accurate Identification ◽

B Cell Epitopes ◽

B Cell Epitope ◽

In Silico Methods

Identification of B-cell epitopes in target antigens is one of the most crucial steps for epitopebased vaccine development, immunodiagnostic tests, antibody production, and disease diagnosis and therapy. Experimental methods for B-cell epitope mapping are time consuming, costly and labor intensive; in the meantime, various in-silico methods are proposed to predict both linear and conformational B-cell epitopes. The accurate identification of B-cell epitopes presents major challenges for immunoinformaticians. In this paper, we have comprehensively reviewed in-silico methods for B-cell epitope identification. The aim of this review is to stimulate the development of better tools which could improve the identification of B-cell epitopes, and further for the development of therapeutic antibodies and diagnostic tools.

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