Mining of linear B cell epitopes of SARS-CoV-2 ORF8 protein from COVID-19 patients

Human norovirus (HuNoV) is the leading cause of nonbacterial gastroenteritis worldwide with the GII.4 genotype accounting for over 80% of infections. The major capsid protein of GII.4 variants is evolving rapidly, resulting in new epidemic variants with altered antigenic potentials that must be considered for the development of an effective vaccine. In this study, we identify and characterize linear blockade B-cell epitopes in HuNoV GII.4. Five unique linear B-cell epitopes, namely P2A, P2B, P2C, P2D, and P2E, were predicted on the surface-exposed regions of the capsid protein. Evolving of the surface-exposed epitopes over time was found to correlate with the emergence of new GII.4 outbreak variants. Molecular dynamic simulation (MD) analysis and molecular docking revealed that amino acid substitutions in the putative epitopes P2B, P2C, and P2D could be associated with immune escape and the appearance of new GII.4 variants by affecting solvent accessibility and flexibility of the antigenic sites and histo-blood group antigens (HBAG) binding. Testing the synthetic peptides in wild-type mice, epitopes P2B (336–355), P2C (367–384), and P2D (390–400) were recognized as GII.4-specific linear blockade epitopes with the blocking rate of 68, 55 and 28%, respectively. Blocking rate was found to increase to 80% using the pooled serum of epitopes P2B and P2C. These data provide a strategy for expanding the broad blockade potential of vaccines for prevention of NoV infection.

Download Full-text

Immunisation With Immunodominant Linear B Cell Epitopes Vaccine of Manganese Transport Protein C Confers Protection against Staphylococcus aureus Infection

PLoS ONE ◽

10.1371/journal.pone.0149638 ◽

2016 ◽

Vol 11 (2) ◽

pp. e0149638 ◽

Cited By ~ 11

Author(s):

Hui-Jie Yang ◽

Jin-Yong Zhang ◽

Chao Wei ◽

Liu-Yang Yang ◽

Qian-Fei Zuo ◽

...

Keyword(s):

Staphylococcus Aureus ◽

B Cell ◽

Protein C ◽

Transport Protein ◽

B Cell Epitopes ◽

Aureus Infection ◽

Manganese Transport ◽

Linear B

Download Full-text

Anaplasma marginale Major Surface Protein 2 CD4+-T-Cell Epitopes Are Evenly Distributed in Conserved and Hypervariable Regions (HVR), Whereas Linear B-Cell Epitopes Are Predominantly Located in the HVR

Infection and Immunity ◽

10.1128/iai.72.12.7360-7366.2004 ◽

2004 ◽

Vol 72 (12) ◽

pp. 7360-7366 ◽

Cited By ~ 35

Author(s):

Jeffrey R. Abbott ◽

Guy H. Palmer ◽

Chris J. Howard ◽

Jayne C. Hope ◽

Wendy C. Brown

Keyword(s):

T Cell ◽

B Cell ◽

Surface Protein ◽

Anaplasma Marginale ◽

T Cell Epitopes ◽

B Cell Epitopes ◽

Major Surface Protein ◽

Hypervariable Regions ◽

Major Surface ◽

Linear B

ABSTRACT Organisms in the genus Anaplasma express an immunodominant major surface protein 2 (MSP2), composed of a central hypervariable region (HVR) flanked by highly conserved regions. Throughout Anaplasma marginale infection, recombination results in the sequential appearance of novel MSP2 variants and subsequent control of rickettsemia by the immune response, leading to persistent infection. To determine whether immune evasion and selection for variant organisms is associated with a predominant response against HVR epitopes, T-cell and linear B-cell epitopes were localized by measuring peripheral blood gamma interferon-secreting cells, proliferation, and antibody binding to 27 overlapping peptides spanning MSP2 in 16 cattle. Similar numbers of MSP2-specific CD4+ T-cell epitopes eliciting responses of similar magnitude were found in conserved and hypervariable regions. T-cell epitope clusters recognized by the majority of animals were identified in the HVR (amino acids [aa] 171 to 229) and conserved regions (aa 101 to 170 and 272 to 361). In contrast, linear B-cell epitopes were concentrated in the HVR, residing within hydrophilic sequences. The pattern of recognition of epitope clusters by T cells and of HVR epitopes by B cells is consistent with the influence of protein structure on epitope recognition.

Download Full-text

Prediction of linear B-cell epitopes using amino acid pair antigenicity scale

Amino Acids ◽

10.1007/s00726-006-0485-9 ◽

2007 ◽

Vol 33 (3) ◽

pp. 423-428 ◽

Cited By ~ 307

Author(s):

J. Chen ◽

H. Liu ◽

J. Yang ◽

K.-C. Chou

Keyword(s):

Amino Acid ◽

B Cell ◽

Amino Acid Pair ◽

B Cell Epitopes ◽

Linear B

Download Full-text

Screening and Identification of Linear B Cell Epitopes Within the Nonstructural Proteins of Enterovirus 71

Viral Immunology ◽

10.1089/vim.2018.0125 ◽

2019 ◽

Vol 32 (2) ◽

pp. 84-88 ◽

Cited By ~ 2

Author(s):

Jianhua Zhang ◽

Huiqi Huang ◽

Lian Xu ◽

Chaonan Lou ◽

Mi Pan

Keyword(s):

B Cell ◽

Enterovirus 71 ◽

Nonstructural Proteins ◽

B Cell Epitopes ◽

Screening And Identification ◽

Linear B

Download Full-text

Neutralizing and Non-Neutralizing Anti-FVIII Antibodies in Black and White Hemophilia A Subjects: A Natural History Profile

Blood ◽

10.1182/blood-2019-124743 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 1131-1131 ◽

Cited By ~ 1

Author(s):

Kathleen P. Pratt ◽

Devi Gunasekera ◽

Pooja Vir ◽

Robert Peters ◽

Siyuan Tan ◽

...

Keyword(s):

B Cell ◽

Hemophilia A ◽

African Ancestry ◽

Full Length ◽

Inhibitory Antibody ◽

B Cell Epitopes ◽

Black African ◽

Coagulation Inhibitors ◽

Antibody Titers ◽

Linear B

The most common complication in hemophilia A (HA) treatment, affecting 25-30% of severe HA patients, is the development of alloimmune inhibitors that foreclose the ability of infused factor VIII (FVIII) to participate in coagulation. Inhibitors confer significant pathology on affected individuals and present major complexities in their management. Inhibitors are more common in African American patients, and it has been hypothesized that this is a consequence of haplotype (H)-treatment product mismatch. F8 gene haplotypes H1-H5 are defined by combinations of nonsynonymous SNPs encoding FVIII sequence variants D1241E, M2238V and R484H. F8 haplotypes H2-H5 are more prevalent in individuals with black African ancestry, while >90% of the white population has the H1 haplotype. This study used a validated Luminex-based assay to determine total anti-FVIII antibody titers in plasma from 395 HA (189 black, 206 white) and 23 non-HA control subjects, measuring their binding to recombinant full-length H1 and H2 and B-domain-deleted (BDD) H1/H2, H3 and H4 FVIII proteins. Inhibitor titers were determined using a chromogenic Bethesda assay with the Nijmegen modification. Linear B-cell epitopes recognized by antibodies in human plasma samples were characterized using commercial peptide microarrays with imprinted 15-mer peptides spanning the FVIII A1, A2, C1 and C2 domains, with binding interactions detected using fluorescent-labeled anti-human IgG antibodies. Neither total nor inhibitory antibody titers correlated with F8 haplotype. FVIII peptides with the D1241E and M3348V polymorphisms showed low antibody reactivity, indicating they do not comprise linear B-cell epitopes. Similarly, antibodies from subjects with H3 and H5 haplotypes, who were necessarily infused with FVIII products having a different haplotype than that of their endogenous, (dysfunctional) F8 sequence, did not show haplotype-correlated differential binding to the three BDD-FVIII or full-length FVIII proteins, indicating the polymorphic M2238V or D1241E sites do not correspond to immunodominant, conformational B-cell epitopes. Interestingly, the BDD-FVIII proteins were significantly more reactive with antibodies in plasma than were two commercial full-length recombinant FVIII products. Overall, results of this study indicated that low-titer FVIII-reactive antibodies are readily detected in most HA subjects and in a majority of healthy non-HA controls. The observed stronger immunoreactivity of BDD-FVIII suggests that B-domain removal exposes novel B-cell epitopes, perhaps through conformational rearrangements of FVIII domains. Disclosures Pratt: Bloodworks NW: Patents & Royalties: inventor on patents related to FVIII immunogenicity; Grifols, Inc: Research Funding. Peters:Sanofi: Employment. Mann:Haematologic Technologies: Other: Owner; Stago: Consultancy; Novo Nordisk: Consultancy; Takeda: Consultancy; Shire: Consultancy; Baxalta: Consultancy.

Download Full-text

Immunodominant and neutralizing linear B cell epitopes spanning the spike and membrane proteins of Porcine Epidemic Diarrhea Virus

10.1101/2021.10.05.463270 ◽

2021 ◽

Author(s):

Kanokporn Polyiam ◽

Marasri Ruengjitchatchawalya ◽

Phenjun Mekvichitsaeng ◽

Kampon Kaeoket ◽

Tawatchai Hoonsuwan ◽

...

Keyword(s):

B Cell ◽

Porcine Epidemic Diarrhea Virus ◽

M Protein ◽

B Cell Epitopes ◽

Diarrhea Virus ◽

M Proteins ◽

Porcine Epidemic Diarrhea ◽

Neutralizing Epitopes ◽

Immunodominant Epitopes ◽

Linear B

AbstractPorcine Epidemic Diarrhea Virus (PEDV) is the causative agent of PED, an enteric disease that causes high mortality rates in piglets. PEDV is an alphacoronavirus that has high genetic diversity. Insights into neutralizing B cell epitopes of all genetically diverse PEDV strains are of importance, particularly for designing a vaccine that can provide broad protection against PEDV. In this work, we aimed to explore the landscape of linear B cell epitopes on the spike (S) and membrane (M) proteins of global PEDV strains. All amino acid sequences of the PEDV S and M proteins were retrieved from the NCBI database and grouped. Immunoinformatics-based methods were next developed and used to identify putative linear B cell epitopes from 14 and 5 consensus sequences generated from distinct groups of the S and M proteins, respectively. ELISA testing predicted peptides with PEDV-positive sera revealed 9 novel immunodominant epitopes on the S protein. Importantly, 7 of these novel immunodominant epitopes and other subdominant epitopes were demonstrated to be neutralizing epitopes by neutralization-inhibition assay. Additionally, our study shows the first time that M protein is also the target of neutralizing antibodies as 7 neutralizing epitopes in the M protein were identified. Conservancy analysis revealed that epitopes in the S1 subunit are more variable than those in the S2 subunit and M protein. In this study, we offer the immunoinformatics approach for linear B cell epitope identification and a more complete profile of linear B cell epitopes across the PEDV S and M proteins, which may contribute to the development of a greater PEDV vaccine as well as peptide-based immunoassays.

Download Full-text