ArticlePeerJ2022
Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules.
Article in PeerJ, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 30 citations in OpenAlex.
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- Monitoring SARS-CoV-2 variants in wastewater during periods of low clinical case surveillance in Ethiopia.mSphere · 2025Article
- An Italian Single-Center Genomic Surveillance Study: Two-Year Analysis of SARS-CoV-2 Spike Protein Mutations.International journal of molecular sciences · 2025Article
- Population-level toggling of T cell immune escape at human leukocyte antigen anchor residues in SARS-CoV-2 Spike proteins, in an ethnically diverse population region.PLoS computational biology · 2025Article
- Characterization of binding affinity changes of SARS-CoV-2 omicron variant peptides to population-specific HLA.Journal of biomedical science · 2025Article
- Genetic characterization of the respiratory tract viruses in Jilin, Northeast China, 2023.Frontiers in public health · 2025Article
- T Cell Peptide Prediction, Immune Response, and Host-Pathogen Relationship in Vaccinated and Recovered from Mild COVID-19 Subjects.Biomolecules · 2024Article
- Narrative Review Explaining the Role ofInfectious disease reports · 2024Review
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- Immunocompetent Mice As a Model for Preclinical Studies of mRNA Vaccine Immunogenicity.Doklady. Biochemistry and biophysics · 2023Article
- Epstein-Barr virus-acquired immunodeficiency in myalgic encephalomyelitis-Is it present in long COVID?Journal of translational medicine · 2023Review
- HLA Variation and SARS-CoV-2 Specific Antibody Response.Viruses · 2023Review
- MHC Class II Presentation in Autoimmunity.Cells · 2023Review
- Evaluating the effect of SARS-CoV-2 spike mutations with a linear doubly robust learner.Frontiers in cellular and infection microbiology · 2023Article
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- A systems approach evaluating the impact of SARS-CoV-2 variant of concern mutations on CD8+ T cell responses.Immunotherapy advances · 2023Article
- Relationship of Covid-19 Severity with SARS-CoV-2 NS8 Protein Mutations Depending on Virus Strain.Doklady. Biochemistry and biophysics · 2022Article
- Differences in Presentation of SARS-CoV-2 Omicron Strain Variant BA.1-BA.5 Peptides by HLA Molecules.Doklady. Biochemistry and biophysics · 2022Article
- On the peptide binding affinity changes in population-specific HLA repertoires to the SARS-CoV-2 variants Delta and Omicron.Journal of autoimmunity · 2022Article
- Molecular aspects of Omicron, vaccine development, and recombinant strain XE: A review.Journal of medical virology · 2022Review
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide both because of the Omicron BA.1 mutations (N211 deletion, L212I substitution and EPE 212-214 insertion) and the Omicron BA.2 mutations (V213G substitution). The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it.
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