{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T07:33:09Z","timestamp":1787643189951,"version":"build-2736575974"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,8,16]],"date-time":"2021-08-16T00:00:00Z","timestamp":1629072000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Laboratory of Molecular Physiology at HSE University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Rapidly appearing SARS-CoV-2 mutations can affect T cell epitopes, which can help the virus to evade either CD8 or CD4 T-cell responses. We developed T-cell COVID-19 Atlas (T-CoV, https:\/\/t-cov.hse.ru) \u2013 the comprehensive web portal, which allows one to analyze how SARS-CoV-2 mutations alter the presentation of viral peptides by HLA molecules. The data are presented for common virus variants and the most frequent HLA class I and class II alleles. Binding affinities of HLA molecules and viral peptides were assessed with accurate in silico methods. The obtained results highlight the importance of taking HLA alleles diversity into account: mutation-mediated alterations in HLA-peptide interactions were highly dependent on HLA alleles. For example, we found that the essential number of peptides tightly bound to HLA-B*07:02 in the reference Wuhan variant ceased to be tight binders for the Indian (Delta) and the UK (Alpha) variants. In summary, we believe that T-CoV will help researchers and clinicians to predict the susceptibility of individuals with different HLA genotypes to infection with variants of SARS-CoV-2 and\/or forecast its severity.<\/jats:p>","DOI":"10.1093\/nar\/gkab701","type":"journal-article","created":{"date-parts":[[2021,7,29]],"date-time":"2021-07-29T15:08:37Z","timestamp":1627571317000},"page":"D883-D887","source":"Crossref","is-referenced-by-count":44,"title":["T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8830-4679","authenticated-orcid":false,"given":"Stepan","family":"Nersisyan","sequence":"first","affiliation":[{"name":"Faculty of Biology and Biotechnology, HSE University, Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anton","family":"Zhiyanov","sequence":"additional","affiliation":[{"name":"Faculty of Biology and Biotechnology, HSE University, Moscow, Russia"},{"name":"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxim","family":"Shkurnikov","sequence":"additional","affiliation":[{"name":"Faculty of Biology and Biotechnology, HSE University, Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Tonevitsky","sequence":"additional","affiliation":[{"name":"Faculty of Biology and Biotechnology, HSE University, Moscow, Russia"},{"name":"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,8,16]]},"reference":[{"key":"2022010507413751100_B1","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1056\/NEJM200009073431006","article-title":"The HLA system","volume":"343","author":"Klein","year":"2000","journal-title":"N. Engl. J. Med."},{"key":"2022010507413751100_B2","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1038\/nri3152","article-title":"Expanding roles for CD4+ T cells in immunity to viruses","volume":"12","author":"Swain","year":"2012","journal-title":"Nat. Rev. Immunol."},{"key":"2022010507413751100_B3","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1164\/rccm.202005-1701LE","article-title":"COVID-19 severity correlates with weaker t-cell immunity, hypercytokinemia, and lung epithelium injury","volume":"202","author":"Wang","year":"2020","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"2022010507413751100_B4","doi-asserted-by":"crossref","first-page":"641900","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":"2022010507413751100_B5","doi-asserted-by":"crossref","first-page":"108572","DOI":"10.1016\/j.clim.2020.108572","article-title":"Possible role of HLA class-I genotype in SARS-CoV-2 infection and progression: A pilot study in a cohort of Covid-19 Spanish patients","volume":"219","author":"Iturrieta-Zuazo","year":"2020","journal-title":"Clin. Immunol."},{"key":"2022010507413751100_B6","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":"2022010507413751100_B7","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1016\/j.cell.2020.05.015","article-title":"Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals","volume":"181","author":"Grifoni","year":"2020","journal-title":"Cell"},{"key":"2022010507413751100_B8","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":"2022010507413751100_B9","doi-asserted-by":"crossref","first-page":"eabf4063","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":"2022010507413751100_B10","doi-asserted-by":"crossref","first-page":"eabg6461","DOI":"10.1126\/sciimmunol.abg6461","article-title":"SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 + T cell responses","volume":"6","author":"Agerer","year":"2021","journal-title":"Sci. Immunol."},{"key":"2022010507413751100_B11","doi-asserted-by":"crossref","first-page":"1418","DOI":"10.1126\/science.abh1282","article-title":"Prior SARS-CoV-2 infection rescues B and T cell responses to variants after first vaccine dose","volume":"372","author":"Reynolds","year":"2021","journal-title":"Science"},{"key":"2022010507413751100_B12","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":"2022010507413751100_B13","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.addr.2021.01.007","article-title":"In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives","volume":"171","author":"Sohail","year":"2021","journal-title":"Adv. Drug Deliv. Rev."},{"key":"2022010507413751100_B14","doi-asserted-by":"crossref","first-page":"78","DOI":"10.3389\/fphar.2020.00078","article-title":"Genetic diversity of HLA class I and class II alleles in thai populations: contribution to genotype-guided therapeutics","volume":"11","author":"Satapornpong","year":"2020","journal-title":"Front. Pharmacol."},{"key":"2022010507413751100_B15","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1002\/gch2.1018","article-title":"Data, disease and diplomacy: GISAID\u2019s innovative contribution to global health","volume":"1","author":"Elbe","year":"2017","journal-title":"Glob. Challenges"},{"key":"2022010507413751100_B16","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2022010507413751100_B17","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1111\/tan.13811","article-title":"Common, intermediate and well-documented HLA alleles in world populations: CIWD version 3.0.0","volume":"95","author":"Hurley","year":"2020","journal-title":"HLA"},{"key":"2022010507413751100_B18","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/j.humimm.2008.05.001","article-title":"Balancing selection and heterogeneity across the classical human leukocyte antigen loci: A meta-analytic review of 497 population studies","volume":"69","author":"Solberg","year":"2008","journal-title":"Hum. Immunol."},{"key":"2022010507413751100_B19","doi-asserted-by":"crossref","first-page":"56","DOI":"10.25080\/Majora-92bf1922-00a","article-title":"Data structures for statistical computing in python","volume-title":"Proceedings of the 9th Python in Science Conference","author":"McKinney","year":"2010"},{"key":"2022010507413751100_B20","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/s41586-020-2649-2","article-title":"Array programming with NumPy","volume":"585","author":"Harris","year":"2020","journal-title":"Nature"},{"key":"2022010507413751100_B21","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat. Methods"},{"key":"2022010507413751100_B22","doi-asserted-by":"crossref","first-page":"3021","DOI":"10.21105\/joss.03021","article-title":"seaborn: statistical data visualization","volume":"6","author":"Waskom","year":"2021","journal-title":"J. Open Source Softw."},{"key":"2022010507413751100_B23","first-page":"D783","article-title":"Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools","volume":"48","author":"Gonzalez-Galarza","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022010507413751100_B24","doi-asserted-by":"crossref","first-page":"104525","DOI":"10.1016\/j.meegid.2020.104525","article-title":"Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene","volume":"85","author":"Pereira","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"2022010507413751100_B25","doi-asserted-by":"crossref","first-page":"3962","DOI":"10.1016\/j.cell.2021.05.046","article-title":"Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs","volume":"184","author":"Weingarten-Gabbay","year":"2021","journal-title":"Cell"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D883\/42058585\/gkab701.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D883\/42058585\/gkab701.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,5]],"date-time":"2022-01-05T03:23:12Z","timestamp":1641352992000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D883\/6348188"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,16]]},"references-count":25,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2021,8,16]]},"published-print":{"date-parts":[[2022,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab701","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.07.06.451227","asserted-by":"object"}]},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,7]]},"published":{"date-parts":[[2021,8,16]]}}}