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

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

10.1101/2020.12.13.422550 ◽

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.

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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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Bioinformatic analysis of epitope-based vaccine design against the novel SARS-COV-2

10.21203/rs.3.rs-16262/v1 ◽

2020 ◽

Author(s):

Hongzhi Chen ◽

Xiang Wu

Keyword(s):

B Cell ◽

Nucleocapsid Protein ◽

Vaccine Development ◽

Wide Spectrum ◽

Cell Epitope ◽

Bioinformatic Analysis ◽

Spike Protein ◽

B Cell Epitopes ◽

Surface Accessibility ◽

Binding Peptides

Abstract Background: An outbreak of infection caused by SARS-COV-2 recently has brought great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of an impending pandemic. This study aimed to predict the protective epitopes with bioinformatic methods and resources for vaccine development. Methods: ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DISCTOPE server. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forcasted epitopes were characterized for immunogen potential evaluation.Results: A total of 63 sequential B-cell epitopes on spike protein were predicted and 3 peptides (333-338, 648-663, 1064-1079) exhibited high antigenicity score and good surface accessibility in our modeling. 8 residues within spike protein (Gly184, Gly502, Lys558, Pro561, Pro809, Ser810, Lys811, Pro812) are forcasted as components of discontinuous B-cell epitopes. The bioinformatic analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind class-I and class-II molecule respectively. The peptide (104-112) has a high immunogenicity score and was predicted to bind a wide spectrum of both HLA-1 and HLA-2 molecules. Conclusions: Linear B-cell epitopes (333-338, 648-663, 1064-1079) and discontinuous B-cell epitopes (Gly184, Gly502, Lys558, Pro561, Pro809, Ser810, Lys811, Pro812) on spike protein, T-cell epitope (104-112) within nucleocapsid protein were identified and recommended for developing vaccine against SARS-COV-2.

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The influence of major S protein mutations of SARS-CoV-2 on the potential B cell epitopes

10.1101/2020.08.24.264895 ◽

2020 ◽

Author(s):

Xianlin Yuan ◽

liangping li

Keyword(s):

B Cell ◽

Large Scale ◽

Population Change ◽

Vaccine Development ◽

Rna Virus ◽

Neutralizing Antibody ◽

Spike Protein ◽

Common Variants ◽

B Cell Epitopes ◽

S Protein

AbstractSARS-CoV-2 has rapidly transmitted worldwide and results in the COVID-19 pandemic. Spike glycoprotein on surface is a key factor of viral transmission, and has appeared a lot of variants due to gene mutations, which may influence the viral antigenicity and vaccine efficacy. Here, we used bioinformatic tools to analyze B-cell epitopes of prototype S protein and its 9 common variants. 12 potential linear and 53 discontinuous epitopes of B-cells were predicted from the S protein prototype. Importantly, by comparing the epitope alterations between prototype and variants, we demonstrate that B-cell epitopes and antigenicity of 9 variants appear significantly different alterations. The dominant D614G variant impacts the potential epitope least, only with moderately elevated antigenicity, while the epitopes and antigenicity of some mutants(V483A, V367F, etc.) with small incidence in the population change greatly. These results suggest that the currently developed vaccines should be valid for a majority of SARS-CoV-2 infectors. This study provides a scientific basis for large-scale application of SARS-CoV-2 vaccines and for taking precautions against the probable appearance of antigen escape induced by genetic variation after vaccination.Author SummaryThe global pandemic of SARS-CoV-2 has lasted for more than half a year and has not yet been contained. Until now there is no effective treatment for SARS-CoV-2 caused disease (COVID-19). Successful vaccine development seems to be the only hope. However, this novel coronavirus belongs to the RNA virus, there is a high mutation rate in the genome, and these mutations often locate on the Spike proteins of virus, the gripper of the virus entering the cells. Vaccination induce the generation of antibodies, which block Spike protein. However, the Spike protein variants may change the recognition and binding of antibodies and make the vaccine ineffective. In this study, we predict neutralizing antibody recognition sites (B cell epitopes) of the prototype S protein of SARS-COV2, along with several common variants using bioinformatics tools. We discovered the variability in antigenicity among the mutants, for instance, in the more widespread D614G variant the change of epitope was least affected, only with slight increase of antigenicity. However, the antigenic epitopes of some mutants change greatly. These results could be of potential importance for future vaccine design and application against SARS-CoV2 variants.

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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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Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment

Pathogens ◽

10.3390/pathogens9050324 ◽

2020 ◽

Vol 9 (5) ◽

pp. 324 ◽

Cited By ~ 43

Author(s):

Takahiko Koyama ◽

Dilhan Weeraratne ◽

Jane L. Snowdon ◽

Laxmi Parida

Keyword(s):

Rna Polymerase ◽

B Cell ◽

Genetic Drift ◽

Vaccine Development ◽

Cell Epitope ◽

Spike Protein ◽

Immune Recognition ◽

T Cell Epitopes ◽

Antibody Treatment ◽

B Cell Epitope

New coronavirus (SARS-CoV-2) treatments and vaccines are under development to combat COVID-19. Several approaches are being used by scientists for investigation, including (1) various small molecule approaches targeting RNA polymerase, 3C-like protease, and RNA endonuclease; and (2) exploration of antibodies obtained from convalescent plasma from patients who have recovered from COVID-19. The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. As the disease has grown to become a pandemic, B-cell and T-cell epitopes predicted from SARS coronavirus have been reported. Using the epitope information along with variants of the virus, we have found several variants which might cause drifts. Among such variants, 23403A>G variant (p.D614G) in spike protein B-cell epitope is observed frequently in European countries, such as the Netherlands, Switzerland, and France, but seldom observed in China.

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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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