ArticleScientific reports2020
Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
65 citing papers in PubMed, 2 syntheses or guidelines pooled it, 100 citations in OpenAlex.
- Emerging role of artificial intelligence in therapeutics for COVID-19: a systematic review.Journal of biomolecular structure & dynamics · 2022Pooled it
- Landscape of epitopes targeted by T cells in 852 individuals recovered from COVID-19: Meta-analysis, immunoprevalence, and web platform.Cell reports. Medicine · 2021Pooled it
- SARS-CoV-2-specific CD8+ T cell responses in convalescent COVID-19 individuals.The Journal of clinical investigation · 2021Trial
- AI-driven epitope prediction: a system review, comparative analysis, and practical guide for vaccine development.NPJ vaccines · 2025Review
- Challenges and opportunities in mRNA vaccine development against bacteria.Nature microbiology · 2025Review
- Pan-Variant SARS-CoV-2 Vaccines Induce Protective Immunity by Targeting Conserved Epitopes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Biophysics of SARS-CoV-2 spike protein's receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights.Biophysical reviews · 2025Review
- Toward equitable major histocompatibility complex binding predictions.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Deep learning enhances the prediction of HLA class I-presented CD8Nature machine intelligence · 2025Article
- Epitope mapping using immunopeptidomics reveals novel immunodominant CD8 T cell epitopes of the AAV9 capsid.Frontiers in immunology · 2025Article
- T Cell Peptide Prediction, Immune Response, and Host-Pathogen Relationship in Vaccinated and Recovered from Mild COVID-19 Subjects.Biomolecules · 2024Article
- Mapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes.Nature communications · 2024Article
- Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy.Journal for immunotherapy of cancer · 2024Article
- GraphMHC: Neoantigen prediction model applying the graph neural network to molecular structure.PloS one · 2024Article
- Immunodominant conserved moieties on spike protein of SARS-CoV-2 renders virulence factor for the design of epitope-based peptide vaccines.Virusdisease · 2023Article
- Spheromers reveal robust T cell responses to the Pfizer/BioNTech vaccine and attenuated peripheral CD8Immunity · 2023Article
- The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions.Immunoinformatics (Amsterdam, Netherlands) · 2023Review
- New Short RNA Motifs Potentially Relevant in the SARS-CoV-2 Genome.Current genomics · 2023Article
- Impact of peptide:HLA complex stability for the identification of SARS-CoV-2-specific CD8Frontiers in immunology · 2023Article
- Lynch syndrome cancer vaccines: A roadmap for the development of precision immunoprevention strategies.Frontiers in oncology · 2023Review
5 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
7 authors at 3 institutions in 2 countries.
Funding
Abstract
The outbreak of SARS-CoV-2 (2019-nCoV) virus has highlighted the need for fast and efficacious vaccine development. Stimulation of a proper immune response that leads to protection is highly dependent on presentation of epitopes to circulating T-cells via the HLA complex. SARS-CoV-2 is a large RNA virus and testing of all of its overlapping peptides in vitro to deconvolute an immune response is not feasible. Therefore HLA-binding prediction tools are often used to narrow down the number of peptides to test. We tested NetMHC suite tools' predictions by using an in vitro peptide-MHC stability assay. We assessed 777 peptides that were predicted to be good binders across 11 MHC alleles in a complex-stability assay and tested a selection of 19 epitope-HLA-binding prediction tools against the assay. In this investigation of potential SARS-CoV-2 epitopes we found that current prediction tools vary in performance when assessing binding stability, and they are highly dependent on the MHC allele in question. Designing a COVID-19 vaccine where only a few epitope targets are included is therefore a very challenging task. Here, we present 174 SARS-CoV-2 epitopes with high prediction binding scores, validated to bind stably to 11 HLA alleles. Our findings may contribute to the design of an efficacious vaccine against COVID-19.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.