{"doi":"10.1016/j.celrep.2023.113596","title":"The HLA-II immunopeptidome of SARS-CoV-2","abstract":"Targeted synthetic vaccines have the potential to transform our response to viral outbreaks, yet the design of these vaccines requires a comprehensive knowledge of viral immunogens. Here, we report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides that are naturally processed and loaded onto human leukocyte antigen-II (HLA-II) complexes in infected cells. We identify over 500 unique viral peptides from canonical proteins as well as from overlapping internal open reading frames. Most HLA-II peptides colocalize with known CD4 + T cell epitopes in coronavirus disease 2019 patients, including 2 reported immunodominant regions in the SARS-CoV-2 membrane protein. Overall, our analyses show that HLA-I and HLA-II pathways target distinct viral proteins, with the structural proteins accounting for most of the HLA-II peptidome and nonstructural and noncanonical proteins accounting for the majority of the HLA-I peptidome. These findings highlight the need for a vaccine design that incorporates multiple viral elements harboring CD4 + and CD8 + T cell epitopes to maximize vaccine effectiveness.","journal":"Cell Reports","year":2023,"id":342006,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":15,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9542,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":249892,"name":"Da‐Yuan Chen","orcid":"0000-0002-1957-3330","position":1,"is_corresponding":false},{"id":44969,"name":"Siranush Sarkizova","orcid":"0000-0003-2530-8610","position":2,"is_corresponding":false},{"id":371257,"name":"Hannah B. Taylor","orcid":"0000-0003-2146-8764","position":3,"is_corresponding":false},{"id":28893,"name":"Matteo Gentili","orcid":"0000-0002-6970-8133","position":4,"is_corresponding":false},{"id":1030768,"name":"Gabrielle M. Hernandez","orcid":"0009-0005-0494-0467","position":5,"is_corresponding":false},{"id":555102,"name":"Leah R. Pearlman","orcid":null,"position":6,"is_corresponding":false},{"id":554217,"name":"Matthew R. Bauer","orcid":"0000-0001-6309-3548","position":7,"is_corresponding":false},{"id":104737,"name":"Charles M. Rice","orcid":"0000-0003-3087-8079","position":8,"is_corresponding":false},{"id":2216,"name":"Karl R. Clauser","orcid":"0000-0002-1052-9456","position":9,"is_corresponding":false},{"id":409,"name":"Nir Hacohen","orcid":"0000-0002-2349-2656","position":10,"is_corresponding":false},{"id":2226,"name":"Steven A. Carr","orcid":"0000-0002-7203-4299","position":11,"is_corresponding":false},{"id":554219,"name":"Jennifer G. Abelin","orcid":"0000-0001-5262-7241","position":12,"is_corresponding":false},{"id":232300,"name":"Mohsan Saeed","orcid":"0000-0001-8505-7054","position":13,"is_corresponding":false},{"id":7155,"name":"Pardis C. Sabeti","orcid":"0000-0002-9843-1890","position":14,"is_corresponding":false},{"id":554216,"name":"Shira Weingarten-Gabbay","orcid":"0000-0001-7579-0236","position":0,"is_corresponding":true}],"reference_count":89,"raw_metadata":null,"created_at":"2026-07-19T01:11:08.077724Z","pmid":"38117652","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}