ArticleiScience2021
The impact of viral mutations on recognition by SARS-CoV-2 specific T cells.
Open access · goldAbstract read
In one paragraph
Article in iScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
0numbers the graph read from it
0cells of the map it votes in
69citing papers in PubMed
5.2field-weighted citation impact, top 3% of its field
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
69 citing papers in PubMed, 89 citations in OpenAlex.
- A bireporter recombinant SARS-CoV-2 Omicron BA.5 forMicrobiology spectrum · 2026Article
- Cross-task interpretability through unified modeling reveals a universal shortcut bias in neoantigen prediction.Cell genomics · 2026Article
- MPXV H3L elicits broadly directed CD4 T cell responses in mpox patients and MVA vaccinees.Npj viruses · 2026Article
- Comprehensive longitudinal profiling identifies differential frequency, epitope specificity, and effector function of CD8EBioMedicine · 2026Article
- Position-5-driven reorientation of an immunodominant HLA-A*24:02 SARS-CoV-2 epitope drives universal T cell escape.JCI insight · 2026Article
- Extensive evolution and T cell escape by SARS-CoV-2 in a 2.5-year persistent infection of an immunocompromised host.iScience · 2026Article
- Genomic Characterization of SARS-CoV-2 NB.1.8.1 and PQ.2 from the Infants and Young Children with Gastrointestinal Symptoms.Infection and drug resistance · 2026Article
- SARS-CoV-2 variants: biology, pathogenicity, immunity and control.Nature reviews. Microbiology · 2026Review
- Long-persisting SARS-CoV-2 spike-specific CD4Nature communications · 2025Article
- SARS-CoV-2: The Interplay Between Evolution and Host Immunity.Annual review of immunology · 2025Review
- The Impact of Vaccination Frequency on COVID-19 Public Health Outcomes: A Model-Based Analysis.Vaccines · 2025Article
- Identification of patient demographic, clinical, and SARS-CoV-2 genomic factors associated with severe COVID-19 using supervised machine learning: a retrospective multicenter study.BMC infectious diseases · 2025Article
- Comprehensive Analysis of the Immune Response to SARS-CoV-2 Epitopes: Unveiling Potential Targets for Vaccine Development.Biology · 2025Article
- Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya.Virus evolution · 2025Article
- Review
- Comparison of different T cell assays for the retrospective determination of SARS-CoV-2 infection.The Journal of general virology · 2024Article
- Features of Highly Homologous T-Cell Receptor Repertoire in the Immune Response to Mutations in Immunogenic Epitopes.International journal of molecular sciences · 2024Article
- In-silico evaluation of the T-cell based immune response against SARS-CoV-2 omicron variants.Scientific reports · 2024Article
- Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2.eLife · 2024Article
- Conservation of HLA Spike Protein Epitopes Supports T Cell Cross-Protection in SARS-CoV-2 Vaccinated Individuals against the Potentially Zoonotic Coronavirus Khosta-2.International journal of molecular sciences · 2024Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
24 authors at 10 institutions in 5 countries.
Thushan I de SilvaThe Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
Guihai LiuChinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
Benjamin B LindseyThe Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
Danning DongChinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
Shona C MooreNIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK.
Nienyun Sharon HsuThe Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
Dhruv ShahThe Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
Dannielle WellingtonChinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
Alexander J MentzerNuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK.
Adrienn AngyalThe Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
Rebecca BrownThe Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
Matthew D ParkerSheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK.
Zixi YingChinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
Xuan YaoChinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
Lance TurtleNIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK.
Susanna DunachieCentre For Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LG, UK.
COVID-19 Genomics UK (COG-UK) Consortium
Mala K MainiDivision of Infection and Immunity, University College London, London WC1E 6BT, UK.
Graham OggChinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
Julian C KnightChinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
ISARIC4C Investigators
Yanchun PengChinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
Sarah L Rowland-JonesThe Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
Tao DongChinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
University of Oxford · GBUniversity of Sheffield · GBCentre for Human Genetics · GBChinese Academy of Medical Sciences & Peking Union Medical College · CNUniversity of Liverpool · GBCapital Medical University · CNCentre National de la Recherche Scientifique · FRMRC Unit the Gambia · GMUniversity College London · GBXinjiang Medical University · CN
Funding
Cancer Research UK 26603Medical Research Council G0600520Medical Research Council G1001046Medical Research Council MC_PC_19012Medical Research Council MC_PC_19025Medical Research Council MC_PC_19027Medical Research Council MC_PC_19059Medical Research Council MC_UP_A090_1006Medical Research Council MC_UU_00008/11Medical Research Council MR/L018942/1Medical Research Council MR/P011705/1Medical Research Council MR/P011705/2Medical Research Council MR/R015600/1Medical Research Council MR/S032304/1Medical Research Council MR/V001329/1Medical Research Council MR/V028448/1Wellcome Trust 204911/Z/16/ZWellcome Trust 204969/Z/16/Z
Abstract
We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY
Indexed as
Immune responseImmunologyMolecular biologyPhylogeneticsVirology
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Read underepoch 390
Registered trials
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.