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

Abstract

SARS-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.

Immunodominant and Neutralizing Linear B-Cell Epitopes Spanning the Spike and Membrane Proteins of Porcine Epidemic Diarrhea Virus

“…( 39 ). Moreover, the epitopes S1B-15, S1B-16, and S1B-17, which are located within the COE domain, also mirror the three most dominant epitopes within the SARS-CoV-2 S RBD identified in our previous work ( 37 ). Additionally, the C-terminal endodomain of the S protein is another main site accommodating an immunodominant B-cell epitope of SARS-CoV-2 ( 37 , 39 – 41 ) as well as the neutralizing epitope 2C10 with the GPRLQPY motif (epitope S2B-33 in this study) of PEDV ( 25 ).…”

“…Interestingly, although PEDV (alphacoronavirus) and SARS-CoV-2 (betacoronavirus) belong to different genus, the landscape of immunodominant epitopes on the S protein of these two coronaviruses remarkably resembles. The following epitopes including i) S1B-1, ii) S1B-19 (19.1 and 19.3), iii) S2B-22, and iv) S2B-29 and S2B-30.2 are located at the following regions: i) the N-terminus next to the signal sequence; ii) CTD, upstream region of the S1/S2 cleavage site; iii) FP region; and iv) upstream region of the HR2, respectively, which have also been indicated to be the main sites of immunodominant epitopes on the SARS-CoV-2 S protein recently reported by our group ( 37 ) and Li et al. ( 39 ).…”

“…Our immunoinformatics methods allowed us to identify important B-cell epitopes from diverse sequences of PEDV. Moreover, we have employed the prediction methods developed in this study in identifying B-cell epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ( 37 ), and we have proven that our immunoinformatics-based method is potent and useful in facilitating the identification of immunodominant epitopes with less time and cost compared with conventional methods.…”

Bioinformatic analysis of B and T cell epitopes from SARS-CoV-2 Spike, Membrane and Nucleocapsid proteins as a strategy to assess possible cross-reactivity between emerging variants, including Omicron, and other human coronaviruses

“…For the specific case of spike protein, we were able to compile a total of 116 potential B cell epitopes, of which 61 were epitopes previously reported in silico (ERIS) 52,[54][55][56][57][58][59] by other research groups (Supplementary Table 1), on the other hand, we compiled 19 experimentally confirmed epitopes (ECE) [57][58][59][60] (Supplementary Table 3) also reported by others. Using BepiPred 1.0 and 2.0, our study predicted 36 epitopes that were selected based on their score and surface accessibility, and which we have denominated epitopes predicted in this study (which was not certified by peer review) is the author/funder.…”

“…Following the same workflow that was used for S protein, we performed the analysis for the membrane (M) and nucleocapsid (N) protein sequences. For M protein, we were able to collect a total of 18 potential B cell epitopes (Supplementary Table 1), of which 9 are defined as ERIS 36,52,54,57,60 . In addition, we found in the literature 2 ECE 57 , as shown in Supplementary Tables 1 and 3.…”