The Immune Epitope Database (IEDB): 2024 update.

Over the past 20 years, the Immune Epitope Database (IEDB, iedb.org) has established itself as the foremost resource for immune epitope data. The IEDB catalogs published epitopes and their contextual experimental data in a freely searchable public resource.

Next-generation IEDB tools: a platform for epitope prediction and analysis.

The Next-Generation (NG) IEDB Tools website (https://nextgen-tools.iedb.org) provides users with a redesigned interface to many of the algorithms for epitope prediction and analysis that were originally released on the legacy IEDB Tools website.

PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins.

Background: Numerous tools exist for biological sequence comparisons and search. One case of particular interest for immunologists is finding matches for linear peptide T cell epitopes, typically between 8 and 15 residues in length, in a large set of protein sequences. Both to find exact matches or matches that account for residue substitutions.

T cell reactivity to Bordetella pertussis is highly diverse regardless of childhood vaccination.

The incidence of whooping cough due to Bordetella pertussis (BP) infections has increased recently. It is believed that the shift from whole-cell pertussis (wP) vaccines to acellular pertussis (aP) vaccines may be contributing to this rise. While T cells are key in controlling and preventing disease, nearly all knowledge relates to antigens in aP vaccines.

Genome-wide characterization of T cell responses to reveals broad reactivity and similar polarization irrespective of childhood vaccination profiles.

The incidence of whooping cough (pertussis), the respiratory disease caused by (BP) has increased in recent years, and it is suspected that the switch from whole-cell pertussis (wP) to acellular pertussis (aP) vaccines may be a contributing factor to the rise in morbidity. While a growing body of evidence indicates that T cells play a role in the control and prevention of symptomatic disease, nearly all data on human BP-specific T cells is related to the four antigens contained in the aP vaccines, and data detailing T cell responses to additional non-aP antigens, are lacking. Here, we derived a full-genome map of human BP-specific CD4+ T cell responses using a high-throughput Activation Induced Marker (AIM) assay, to screen a peptide library spanning over 3000 different BP ORFs.

Immunodominant MHC-II (Major Histocompatibility Complex II) Restricted Epitopes in Human Apolipoprotein B.

Background: CD (cluster of differentiation) 4 T-cell responses to APOB (apolipoprotein B) are well characterized in atherosclerotic mice and detectable in humans. CD4 T cells recognize antigenic peptides displayed on highly polymorphic HLA (human leukocyte antigen)-II. Immunogenicity of individual APOB peptides is largely unknown in humans.

Bioinformatic Analysis Underpinning the Frequent Occurrence of Immune Thrombocytopenic Purpura in COVID-19 Patients.

Background: Secondary immune thrombocytopenic purpura (ITP) associated with coronavirus disease 2019 (COVID-19) is a rare but serious complication of the pandemic. Diagnostic criteria include clinical and laboratory findings. Early treatment is often effective, but rare severe bleeding and death can occur.

Lack of evidence of significant homology of SARS-CoV-2 spike sequences to myocarditis-associated antigens.

Background: COVID-19 mRNA vaccines have proven to be highly safe and effective. Myocarditis is an adverse event associated with mRNA vaccination, especially in young male subjects. These events are rare and, in the majority of cases, resolve quickly.

Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals.

Understanding adaptive immunity to SARS-CoV-2 is important for vaccine development, interpreting coronavirus disease 2019 (COVID-19) pathogenesis, and calibration of pandemic control measures. Using HLA class I and II predicted peptide "megapools," circulating SARS-CoV-2-specific CD8 and CD4 T cells were identified in ∼70% and 100% of COVID-19 convalescent patients, respectively. CD4 T cell responses to spike, the main target of most vaccine efforts, were robust and correlated with the magnitude of the anti-SARS-CoV-2 IgG and IgA titers.