{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T00:18:05Z","timestamp":1783124285232,"version":"3.54.6"},"reference-count":92,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:00:00Z","timestamp":1778198400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004836","name":"Independent Research Fund Denmark","doi-asserted-by":"publisher","award":["2066-00044B"],"award-info":[{"award-number":["2066-00044B"]}],"id":[{"id":"10.13039\/501100004836","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018693","name":"Horizon Europe","doi-asserted-by":"publisher","award":["101057129"],"award-info":[{"award-number":["101057129"]}],"id":[{"id":"10.13039\/100018693","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011958","name":"Danmarks Frie Forskningsfond","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011958","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"publisher","award":["DNRF170"],"award-info":[{"award-number":["DNRF170"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"H2020 European Research Council","doi-asserted-by":"publisher","award":["101045517"],"award-info":[{"award-number":["101045517"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","thelancet.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["eBioMedicine"],"published-print":{"date-parts":[[2026,6]]},"DOI":"10.1016\/j.ebiom.2026.106310","type":"journal-article","created":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T21:29:09Z","timestamp":1779830949000},"page":"106310","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["Comprehensive longitudinal profiling identifies differential frequency, epitope specificity, and effector function of CD8+ T-cells across COVID-19 disease severities"],"prefix":"10.1016","volume":"128","author":[{"given":"Susana Patricia","family":"Amaya Hernandez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9217-7142","authenticated-orcid":false,"given":"Kamilla Kj\u00e6rgaard","family":"Munk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konstantin","family":"Danilov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad","family":"Kadivar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ditte Stampe","family":"Hersby","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tripti","family":"Tamhane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simone Majken","family":"Stegenborg-Grathwohl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9650-8965","authenticated-orcid":false,"given":"Anders Gorm","family":"Pedersen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne Ortved","family":"Gang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sine Reker","family":"Hadrup","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3382-9432","authenticated-orcid":false,"given":"Sunil Kumar","family":"Saini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ebiom.2026.106310_bib1","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/S0140-6736(20)30183-5","article-title":"Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China","volume":"395","author":"Huang","year":"2020","journal-title":"The Lancet"},{"key":"10.1016\/j.ebiom.2026.106310_bib2","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/s41586-020-2550-z","article-title":"SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls","volume":"584","author":"Le Bert","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.ebiom.2026.106310_bib3","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1007\/s10735-020-09915-3","article-title":"COVID-19 and multiorgan failure: a narrative review on potential mechanisms","volume":"51","author":"Mokhtari","year":"2020","journal-title":"J Mol Histol"},{"key":"10.1016\/j.ebiom.2026.106310_bib4","doi-asserted-by":"crossref","DOI":"10.1016\/j.meegid.2023.105426","article-title":"Genetic susceptibility to severe COVID-19","volume":"110","author":"Cappadona","year":"2023","journal-title":"Infect Genet Evol"},{"key":"10.1016\/j.ebiom.2026.106310_bib5","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/j.cell.2020.08.017","article-title":"Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19","volume":"183","author":"Sekine","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.ebiom.2026.106310_bib6","doi-asserted-by":"crossref","DOI":"10.1084\/jem.20202617","article-title":"Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection","volume":"218","author":"Le Bert","year":"2021","journal-title":"J Exp Med"},{"key":"10.1016\/j.ebiom.2026.106310_bib7","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.108728","article-title":"Early induction of functional SARS-CoV-2-specific T cells associates with rapid viral clearance and mild disease in COVID-19 patients","volume":"34","author":"Tan","year":"2021","journal-title":"Cell Rep"},{"key":"10.1016\/j.ebiom.2026.106310_bib8","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1016\/j.cell.2020.09.038","article-title":"Antigen-specific adaptive immunity to SARS-CoV-2 in acute COVID-19 and associations with age and disease severity","volume":"183","author":"Rydyznski Moderbacher","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.ebiom.2026.106310_bib9","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1038\/s41591-021-01386-7","article-title":"CD8+ T cells contribute to survival in patients with COVID-19 and hematologic cancer","volume":"27","author":"Bange","year":"2021","journal-title":"Nat Med"},{"key":"10.1016\/j.ebiom.2026.106310_bib10","doi-asserted-by":"crossref","first-page":"1764","DOI":"10.1016\/j.immuni.2022.08.008","article-title":"SARS-CoV-2-specific T cells in the changing landscape of the COVID-19 pandemic","volume":"55","author":"Bertoletti","year":"2022","journal-title":"Immunity"},{"key":"10.1016\/j.ebiom.2026.106310_bib11","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1038\/s41467-021-21111-9","article-title":"Rapid decline of neutralizing antibodies against SARS-CoV-2 among infected healthcare workers","volume":"12","author":"Marot","year":"2021","journal-title":"Nat Commun"},{"key":"10.1016\/j.ebiom.2026.106310_bib12","doi-asserted-by":"crossref","DOI":"10.1002\/cti2.1319","article-title":"Decline in neutralising antibody responses, but sustained T-cell immunity, in COVID-19 patients at 7 months post-infection","volume":"10","author":"Chen","year":"2021","journal-title":"Clin Transl Immunology"},{"key":"10.1016\/j.ebiom.2026.106310_bib13","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1093\/infdis\/jiaa618","article-title":"Dynamics of neutralizing antibody titers in the months after severe acute respiratory syndrome coronavirus 2 infection","volume":"223","author":"Crawford","year":"2021","journal-title":"J Infect Dis"},{"key":"10.1016\/j.ebiom.2026.106310_bib14","doi-asserted-by":"crossref","first-page":"1336","DOI":"10.1038\/s41590-020-0782-6","article-title":"Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19","volume":"21","author":"Peng","year":"2020","journal-title":"Nat Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib15","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/j.jiph.2022.01.007","article-title":"Immune response to SARS-CoV-2 variants: a focus on severity, susceptibility, and preexisting immunity","volume":"15","author":"Alefishat","year":"2022","journal-title":"J Infect Public Health"},{"key":"10.1016\/j.ebiom.2026.106310_bib16","article-title":"Systemic and lower respiratory tract immunity to SARS-CoV-2 omicron and variants in pediatric severe COVID-19 and Mis-C","volume":"10","author":"Tang","year":"2022","journal-title":"Vaccines (Basel)"},{"key":"10.1016\/j.ebiom.2026.106310_bib17","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.abg5021","article-title":"Integrated longitudinal immunophenotypic, transcriptional, and repertoire analyses delineate immune responses in patients with COVID-19","volume":"6","author":"Notarbartolo","year":"2021","journal-title":"Sci Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib18","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1016\/j.immuni.2021.05.010","article-title":"Longitudinal analysis reveals that delayed bystander CD8+ T cell activation and early immune pathology distinguish severe COVID-19 from mild disease","volume":"54","author":"Bergamaschi","year":"2021","journal-title":"Immunity"},{"key":"10.1016\/j.ebiom.2026.106310_bib19","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.abf7550","article-title":"SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8 + T cell activation in COVID-19 patients","volume":"6","author":"Saini","year":"2021","journal-title":"Sci Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib20","doi-asserted-by":"crossref","first-page":"3410","DOI":"10.1038\/s41467-020-17240-2","article-title":"Immunological and inflammatory profiles in mild and severe cases of COVID-19","volume":"11","author":"Song","year":"2020","journal-title":"Nat Commun"},{"key":"10.1016\/j.ebiom.2026.106310_bib21","doi-asserted-by":"crossref","first-page":"D405","DOI":"10.1093\/nar\/gku938","article-title":"The immune epitope database (IEDB) 3.0","volume":"43","author":"Vita","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.ebiom.2026.106310_bib22","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1038\/s41590-021-00902-8","article-title":"Robust SARS-CoV-2-specific T cell immunity is maintained at 6 months following primary infection","volume":"22","author":"Zuo","year":"2021","journal-title":"Nat Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib23","doi-asserted-by":"crossref","DOI":"10.1126\/science.abf4063","article-title":"Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection","volume":"371","author":"Dan","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.ebiom.2026.106310_bib24","doi-asserted-by":"crossref","first-page":"2010","DOI":"10.1093\/infdis\/jiab543","article-title":"Durability of SARS-CoV-2\u2013Specific T-Cell responses at 12 months postinfection","volume":"224","author":"Lu","year":"2021","journal-title":"J Infect Dis"},{"key":"10.1016\/j.ebiom.2026.106310_bib25","article-title":"Longitudinal analysis shows durable and broad immune memory after SARS-CoV-2 infection with persisting antibody responses and memory B and T cells","volume":"2","author":"Cohen","year":"2021","journal-title":"Cell Rep Med"},{"key":"10.1016\/j.ebiom.2026.106310_bib26","doi-asserted-by":"crossref","first-page":"W449","DOI":"10.1093\/nar\/gkaa379","article-title":"NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data","volume":"48","author":"Reynisson","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.ebiom.2026.106310_bib27","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adm8951","article-title":"Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set","volume":"10","author":"Kristensen","year":"2024","journal-title":"Sci Adv"},{"key":"10.1016\/j.ebiom.2026.106310_bib28","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1038\/nprot.2006.121","article-title":"Generation of peptide\u2013MHC class I complexes through UV-mediated ligand exchange","volume":"1","author":"Rodenko","year":"2006","journal-title":"Nat Protoc"},{"key":"10.1016\/j.ebiom.2026.106310_bib29","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1007\/978-1-59745-450-6_28","article-title":"High-throughput T-cell epitope discovery through MHC peptide exchange","volume":"524","author":"Hadrup","year":"2009","journal-title":"Methods Mol Biol"},{"key":"10.1016\/j.ebiom.2026.106310_bib30","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.aau9039","article-title":"Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells","volume":"4","author":"Saini","year":"2019","journal-title":"Sci Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib31","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1038\/nbt.3662","article-title":"Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes","volume":"34","author":"Bentzen","year":"2016","journal-title":"Nat Biotechnol"},{"key":"10.1016\/j.ebiom.2026.106310_bib32","doi-asserted-by":"crossref","first-page":"861","DOI":"10.21105\/joss.00861","article-title":"UMAP: uniform manifold approximation and projection","volume":"3","author":"McInnes","year":"2018","journal-title":"J Open Source Softw"},{"key":"10.1016\/j.ebiom.2026.106310_bib33","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1002\/cyto.a.22625","article-title":"FlowSOM: using self-organizing maps for visualization and interpretation of cytometry data","volume":"87","author":"Van Gassen","year":"2015","journal-title":"Cytometry Part A"},{"key":"10.1016\/j.ebiom.2026.106310_bib35","series-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"10.1016\/j.ebiom.2026.106310_bib36","series-title":"Proceedings of International Workshop on Set Visualization and Reasoning. Edinburgh, United Kingdom: CEUR Workshop Proceedings","first-page":"84","article-title":"A case study in fitting area-proportional euler diagrams with ellipses using eulerr","author":"Larsson","year":"2018"},{"key":"10.1016\/j.ebiom.2026.106310_bib37","series-title":"rstatix: Pipe-Friendly Framework for Basic Statistical Tests","author":"Kassambara","year":"2025"},{"key":"10.1016\/j.ebiom.2026.106310_bib38","doi-asserted-by":"crossref","DOI":"10.18637\/jss.v076.i01","article-title":"Stan: a probabilistic programming language","volume":"76","author":"Carpenter","year":"2017","journal-title":"J Stat Softw"},{"key":"10.1016\/j.ebiom.2026.106310_bib39","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1111\/j.1467-9531.2007.00181.x","article-title":"2. Average predictive comparisons for models with nonlinearity, interactions, and variance components","volume":"37","author":"Gelman","year":"2007","journal-title":"Sociol Methodol"},{"key":"10.1016\/j.ebiom.2026.106310_bib40","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat Commun"},{"key":"10.1016\/j.ebiom.2026.106310_bib41","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2024","journal-title":"Nat Biotechnol"},{"key":"10.1016\/j.ebiom.2026.106310_bib42","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1038\/nprot.2009.97","article-title":"Mapping identifiers for the integration of genomic datasets with the R\/Bioconductor package biomaRt","volume":"4","author":"Durinck","year":"2009","journal-title":"Nat Protoc"},{"key":"10.1016\/j.ebiom.2026.106310_bib43","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"10.1016\/j.ebiom.2026.106310_bib44","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.ebiom.2026.106310_bib45","author":"Korotkevich"},{"key":"10.1016\/j.ebiom.2026.106310_bib46","doi-asserted-by":"crossref","DOI":"10.1126\/science.abi9591","article-title":"KIR+CD8+ T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19","volume":"376","author":"Li","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.ebiom.2026.106310_bib47","doi-asserted-by":"crossref","first-page":"2593","DOI":"10.1038\/s41467-021-22811-y","article-title":"Identification and characterization of a SARS-CoV-2 specific CD8+ T cell response with immunodominant features","volume":"12","author":"Gangaev","year":"2021","journal-title":"Nat Commun"},{"key":"10.1016\/j.ebiom.2026.106310_bib48","doi-asserted-by":"crossref","first-page":"7543","DOI":"10.1038\/s41467-022-35281-7","article-title":"Identification of human progenitors of exhausted CD8+ T cells associated with elevated IFN-\u03b3 response in early phase of viral infection","volume":"13","author":"Cai","year":"2022","journal-title":"Nat Commun"},{"key":"10.1016\/j.ebiom.2026.106310_bib49","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ebiom.2026.106310_bib50","author":"Blighe"},{"key":"10.1016\/j.ebiom.2026.106310_bib51","doi-asserted-by":"crossref","first-page":"47","DOI":"10.12688\/f1000research.22139.1","article-title":"scRepertoire: an R-based toolkit for single-cell immune receptor analysis","volume":"9","author":"Borcherding","year":"2020","journal-title":"F1000Res"},{"key":"10.1016\/j.ebiom.2026.106310_bib52","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.abe0240","article-title":"Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome","volume":"5","author":"R\u00f6ltgen","year":"2020","journal-title":"Sci Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib53","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/s41392-020-00301-9","article-title":"Disease severity dictates SARS-CoV-2-specific neutralizing antibody responses in COVID-19","volume":"5","author":"Chen","year":"2020","journal-title":"Signal Transduct Target Ther"},{"key":"10.1016\/j.ebiom.2026.106310_bib54","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1038\/nm.2446","article-title":"A human memory T cell subset with stem cell\u2013like properties","volume":"17","author":"Gattinoni","year":"2011","journal-title":"Nat Med"},{"key":"10.1016\/j.ebiom.2026.106310_bib55","doi-asserted-by":"crossref","DOI":"10.1038\/s41590-026-02421-w","article-title":"Metabolic quiescence of naive-like memory T cells precedes and maintains antigen-specific T cell memory","volume":"27","author":"Frischholz","year":"2026","journal-title":"Nat Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib56","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1038\/s41590-021-01084-z","article-title":"An immunodominant NP105\u2013113-B\u221707:02 cytotoxic T cell response controls viral replication and is associated with less severe COVID-19 disease","volume":"23","author":"Peng","year":"2022","journal-title":"Nat Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib57","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1038\/s41586-023-06331-x","article-title":"A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection","volume":"620","author":"Augusto","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.ebiom.2026.106310_bib58","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1007\/s40265-021-01480-7","article-title":"BNT162b2 mRNA COVID-19 vaccine: first approval","volume":"81","author":"Lamb","year":"2021","journal-title":"Drugs"},{"key":"10.1016\/j.ebiom.2026.106310_bib59","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1056\/NEJMoa2035389","article-title":"Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine","volume":"384","author":"Baden","year":"2021","journal-title":"N Engl J Med"},{"key":"10.1016\/j.ebiom.2026.106310_bib60","doi-asserted-by":"crossref","first-page":"864","DOI":"10.1016\/j.immuni.2023.03.005","article-title":"Spheromers reveal robust T cell responses to the Pfizer\/BioNTech vaccine and attenuated peripheral CD8+ T cell responses post SARS-CoV-2 infection","volume":"56","author":"Gao","year":"2023","journal-title":"Immunity"},{"key":"10.1016\/j.ebiom.2026.106310_bib61","doi-asserted-by":"crossref","first-page":"679","DOI":"10.3390\/vaccines12060679","article-title":"Assessing predictive value of SARS-CoV-2 epitope-specific CD8+ T-Cell response in patients with severe symptoms","volume":"12","author":"Mart\u00edn-Mart\u00edn","year":"2024","journal-title":"Vaccines (Basel)"},{"key":"10.1016\/j.ebiom.2026.106310_bib62","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1038\/s41564-022-01106-y","article-title":"SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals","volume":"7","author":"Lang-Meli","year":"2022","journal-title":"Nat Microbiol"},{"key":"10.1016\/j.ebiom.2026.106310_bib63","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.cell.2016.05.035","article-title":"Mitochondrial dynamics controls T cell fate through metabolic programming","volume":"166","author":"Buck","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.ebiom.2026.106310_bib64","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1016\/j.cell.2017.04.004","article-title":"Metabolic instruction of immunity","volume":"169","author":"Buck","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.ebiom.2026.106310_bib65","doi-asserted-by":"crossref","DOI":"10.1172\/JCI143729","article-title":"Hypoxia-inducible factor activity promotes antitumor effector function and tissue residency by CD8+ T cells","volume":"131","author":"Liikanen","year":"2021","journal-title":"J Clin Investig"},{"key":"10.1016\/j.ebiom.2026.106310_bib66","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1038\/s42003-023-04730-4","article-title":"Metabolic dysregulation impairs lymphocyte function during severe SARS-CoV-2 infection","volume":"6","author":"Gurshaney","year":"2023","journal-title":"Commun Biol"},{"key":"10.1016\/j.ebiom.2026.106310_bib67","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/s41590-020-00808-x","article-title":"SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition","volume":"22","author":"Nelde","year":"2021","journal-title":"Nat Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib68","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1007\/s00262-016-1851-4","article-title":"Uncoupling protein 2 regulates metabolic reprogramming and fate of antigen-stimulated CD8+ T cells","volume":"65","author":"Chaudhuri","year":"2016","journal-title":"Cancer Immunol Immunother"},{"key":"10.1016\/j.ebiom.2026.106310_bib69","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/s41590-021-01122-w","article-title":"The T cell immune response against SARS-CoV-2","volume":"23","author":"Moss","year":"2022","journal-title":"Nat Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib70","doi-asserted-by":"crossref","first-page":"e240","DOI":"10.1016\/S2666-5247(21)00025-2","article-title":"Dynamics of SARS-CoV-2 neutralising antibody responses and duration of immunity: a longitudinal study","volume":"2","author":"Chia","year":"2021","journal-title":"Lancet Microbe"},{"key":"10.1016\/j.ebiom.2026.106310_bib71","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1016\/S0140-6736(20)31604-4","article-title":"Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1\/2, single-blind, randomised controlled trial","volume":"396","author":"Folegatti","year":"2020","journal-title":"The Lancet"},{"key":"10.1016\/j.ebiom.2026.106310_bib72","doi-asserted-by":"crossref","DOI":"10.1172\/JCI149150","article-title":"First-dose mRNA vaccination is sufficient to reactivate immunological memory to SARS-CoV-2 in subjects who have recovered from COVID-19","volume":"131","author":"Mazzoni","year":"2021","journal-title":"Journal of Clinical Investigation"},{"key":"10.1016\/j.ebiom.2026.106310_bib73","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.adh0687","article-title":"SARS-CoV-2 vaccination enhances the effector qualities of spike-specific T cells induced by COVID-19","volume":"8","author":"Cai","year":"2023","journal-title":"Sci Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib74","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1186\/s12967-023-03996-w","article-title":"Global landscape of SARS-CoV-2 mutations and conserved regions","volume":"21","author":"Abbasian","year":"2023","journal-title":"J Transl Med"},{"key":"10.1016\/j.ebiom.2026.106310_bib75","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2021.103353","article-title":"The impact of viral mutations on recognition by SARS-CoV-2 specific T cells","volume":"24","author":"de Silva","year":"2021","journal-title":"iScience"},{"key":"10.1016\/j.ebiom.2026.106310_bib76","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1186\/s12967-020-02515-5","article-title":"Correlation of the two most frequent HLA haplotypes in the Italian population to the differential regional incidence of Covid-19","volume":"18","author":"Pisanti","year":"2020","journal-title":"J Transl Med"},{"key":"10.1016\/j.ebiom.2026.106310_bib77","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2021.641900","article-title":"Association of HLA class I genotypes with severity of coronavirus disease-19","volume":"12","author":"Shkurnikov","year":"2021","journal-title":"Front Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib78","article-title":"Human Leukocyte Antigen (HLA) class I susceptible alleles against COVID-19 increase both infection and severity rate","volume":"12","author":"Ishii","year":"2020","journal-title":"Cureus"},{"key":"10.1016\/j.ebiom.2026.106310_bib79","doi-asserted-by":"crossref","first-page":"2325","DOI":"10.1038\/s41423-021-00750-4","article-title":"Activation or exhaustion of CD8+ T cells in patients with COVID-19","volume":"18","author":"Rha","year":"2021","journal-title":"Cell Mol Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib80","first-page":"147","article-title":"SARS-CoV-2 viral load and shedding kinetics","volume":"21","author":"Puhach","year":"2022","journal-title":"Nat Rev Microbiol"},{"key":"10.1016\/j.ebiom.2026.106310_bib81","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.adk1599","article-title":"SARS-CoV-2 viral clearance and evolution varies by type and severity of immunodeficiency","volume":"16","author":"Li","year":"2024","journal-title":"Sci Transl Med"},{"key":"10.1016\/j.ebiom.2026.106310_bib82","doi-asserted-by":"crossref","first-page":"1607","DOI":"10.1038\/s41590-024-01914-w","article-title":"Distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia","volume":"25","author":"Markov","year":"2024","journal-title":"Nat Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib83","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1010152","article-title":"Quantification of T-cell dynamics during latent cytomegalovirus infection in humans","volume":"17","author":"Van den Berg","year":"2021","journal-title":"PLoS Pathog"},{"key":"10.1016\/j.ebiom.2026.106310_bib84","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.coviro.2021.08.009","article-title":"Immunodominance complexity: lessons yet to be learned from dominant T cell responses to SARS-COV-2","volume":"50","author":"Wellington","year":"2021","journal-title":"Curr Opin Virol"},{"key":"10.1016\/j.ebiom.2026.106310_bib85","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1038\/s41586-021-03841-4","article-title":"Rapid and stable mobilization of CD8+ T cells by SARS-CoV-2 mRNA vaccine","volume":"597","author":"Oberhardt","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.ebiom.2026.106310_bib86","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1038\/s41586-020-2814-7","article-title":"COVID-19 vaccine BNT162b1 elicits human antibody and TH1 T cell responses","volume":"586","author":"Sahin","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.ebiom.2026.106310_bib87","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1016\/j.immuni.2021.04.006","article-title":"CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses","volume":"54","author":"Lineburg","year":"2021","journal-title":"Immunity"},{"key":"10.1016\/j.ebiom.2026.106310_bib88","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1038\/s41586-021-04186-8","article-title":"Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2","volume":"601","author":"Swadling","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.ebiom.2026.106310_bib89","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1038\/s41590-022-01184-4","article-title":"SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8+ T cells","volume":"23","author":"Minervina","year":"2022","journal-title":"Nat Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib90","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1038\/s41586-021-04232-5","article-title":"A COVID-19 peptide vaccine for the induction of SARS-CoV-2 T cell immunity","volume":"601","author":"Heitmann","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.ebiom.2026.106310_bib91","doi-asserted-by":"crossref","DOI":"10.1172\/jci.insight.146242","article-title":"Comorbid illnesses are associated with altered adaptive immune responses to SARS-CoV-2","volume":"6","author":"Yu","year":"2021","journal-title":"JCI Insight"},{"key":"10.1016\/j.ebiom.2026.106310_bib92","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1016\/j.jaci.2022.05.019","article-title":"Preexisting comorbidities shape the immune response associated with severe COVID-19","volume":"150","author":"Kreutmair","year":"2022","journal-title":"J Allergy Clin Immunol"},{"key":"10.1016\/j.ebiom.2026.106310_bib93","doi-asserted-by":"crossref","DOI":"10.1016\/j.immuno.2022.100009","article-title":"Recent advances in T-cell receptor repertoire analysis: bridging the gap with multimodal single-cell RNA sequencing","volume":"5","author":"Valkiers","year":"2022","journal-title":"ImmunoInformatics"}],"container-title":["eBioMedicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352396426001921?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352396426001921?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T23:26:22Z","timestamp":1783121182000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2352396426001921"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6]]},"references-count":92,"alternative-id":["S2352396426001921"],"URL":"https:\/\/doi.org\/10.1016\/j.ebiom.2026.106310","relation":{},"ISSN":["2352-3964"],"issn-type":[{"value":"2352-3964","type":"print"}],"subject":[],"published":{"date-parts":[[2026,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Comprehensive longitudinal profiling identifies differential frequency, epitope specificity, and effector function of CD8+ T-cells across COVID-19 disease severities","name":"articletitle","label":"Article Title"},{"value":"eBioMedicine","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ebiom.2026.106310","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"106310"}}