Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2

Titov, Aleksei; Shaykhutdinova, Regina; Shcherbakova, Olga V.; Serdyuk, Yana; Sheetikov, Savely; Zornikova, Ksenia V.; Maleeva, Alexandra V.; Khmelevskaya, Alexandra; Dianov, Dmitry Vladimirovich; Shakirova, Naina T.; Malko, Dmitry B.; Shkurnikov, M. Yu.; Nersisyan, Stepan; Tonevitsky, Alexander G.; Хамаганова, Е Г; Ershov, Anton V; Osipova, E. Yu.; Nikolaev, Ruslan; Pershin, Dmitriy; Vedmedskia, Viktoria A.; Maschan, Mikhail; Ginanova, Victoria R; Efimov, Grigory A.

doi:10.1172/jci.insight.157699

Cited by 18 publications

(25 citation statements)

References 65 publications

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“…Furthermore, it was shown that the response of PBMCs of HLA-A*01:01 + convalescents to the epitopes derived from nonstructural proteins was higher than to the structural proteins. This was not observed for HLA-A*01:01convalescents (11). This further suggests high importance of ORF1ab-focused T-cell response for carriers of HLA-A*01:01.…”

Section: Discussionmentioning

confidence: 75%

“…Reads were analyzed using HLA-Expert Software (DNA-Technology LLC, Russia) and the IPD-IMGT/HLA database 3.41.0 (30). HLA-genotyping of convalescent donors was performed using the One Lambda ALLType kit (Thermo Fisher Scientific, USA), which uses multiplex PCR to amplify full HLA-A/B/C gene sequences, and from exon 2 to the 30 UTR of the HLA525 DRB1/3/4/5/DQB1 genes as described previously (11). Prepared libraries were run on Illumina MiSeq sequencer using a standard flow-cell with 2х150 paired-end sequencing.…”

Section: Design and Participantsmentioning

confidence: 99%

“…Full details of the T-cell expansion are provided in the manuscript (11). Briefly, PBMCs sampled form COVID-19 convalescents were expanded for 12 days with the pre-selected 94 SARS-CoV-2 peptides (final concentration of each = 10 μM).…”

Section: T-cell Expansionmentioning

confidence: 99%

“…Anti-IFN-γ ELISA Culture 96-well plates with cells, incubated with peptide pools or individual peptides were centrifuged for 3 minutes at 700g, and 100 μL of the medium was transferred to the ELISA plates and the detection of IFN-γ was performed (11). OD was measured at 450 nm on a MultiScan FC (Thermo Fisher Scientific) instrument (OD450).…”

Section: Cell Stimulation With Individual Peptidesmentioning

confidence: 99%

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HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8⁺ T-cell repertoire

Shkurnikov

Nersisyan

Averinskaya

et al. 2022

Preprint

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In mid-2021, the SARS-CoV-2 Delta variant caused the third wave of the COVID-19 pandemic in several countries worldwide. The pivotal studies were aimed at studying changes in the efficiency of neutralizing antibodies to the spike protein. However, much less attention was paid to the T-cell response and the presentation of virus peptides by MHC-I molecules. In this study, we compared the features of the HLA-I genotype in symptomatic patients with COVID-19 in the first and third waves of the pandemic. As a result, we could identify the vanishing of carriers of the HLA-A*01:01 allele in the third wave and demonstrate the unique properties of this allele. Thus, HLA-A*01:01-binding immunodominant epitopes are mostly derived from ORF1ab. A set of epitopes from ORF1ab was tested, and their high immunogenicity was confirmed. Moreover, analysis of the results of single-cell phenotyping of T-cells in recovered patients showed that the predominant phenotype in HLA-A*01:01 carriers is central memory T-cells. The predominance of T-lymphocytes of this phenotype may contribute to forming long-term T-cell immunity in carriers of this allele. Our results can be the basis for highly effective vaccines based on ORF1ab peptides.

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Section: Discussionmentioning

confidence: 75%

Section: Design and Participantsmentioning

confidence: 99%

Section: T-cell Expansionmentioning

confidence: 99%

Section: Cell Stimulation With Individual Peptidesmentioning

confidence: 99%

See 2 more Smart Citations

HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8⁺ T-cell repertoire

Shkurnikov

Nersisyan

Averinskaya

et al. 2022

Preprint

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“…Other peptides associated with immunogenic T-cell epitopes have been described in [106,109,110]. In particular, several dozens of epitopes that induced immune response after disease or vaccination in the majority of carriers of a particular allele variant of MHC have been revealed in the recent systematic study that evaluated a panel of peptides for their immunogenicity [111]. Similar peptide panel could be used for evaluating the T cell-mediated immune response in individuals after infection or vaccination and for estimating its duration.…”

Section: Peptide Vaccinesmentioning

confidence: 99%

Will Peptides Help to Stop COVID-19?

Krut’

Chuvpilo

Astrakhantseva

et al. 2022

Biochemistry Moscow

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Peptides are widely used for the diagnostics, prevention, and therapy of certain human diseases. How useful can they be for the disease caused by the SARS-CoV-2 coronavirus? In this review, we discuss the possibility of using synthetic and recombinant peptides and polypeptides for prevention of COVID-19 via blocking the interaction between the virus and its main receptor ACE2, as well as components of antiviral vaccines, in particular, against new emerging virus variants.

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A systemic review of T-cell epitopes defined from the proteome of SARS-CoV-2

2023

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Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2

Cited by 18 publications

References 65 publications

HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8⁺ T-cell repertoire

HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8⁺ T-cell repertoire

Will Peptides Help to Stop COVID-19?

A systemic review of T-cell epitopes defined from the proteome of SARS-CoV-2

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Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2

Cited by 18 publications

References 65 publications

HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire

HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire

Will Peptides Help to Stop COVID-19?

A systemic review of T-cell epitopes defined from the proteome of SARS-CoV-2

Contact Info

Product

Resources

About

HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8⁺ T-cell repertoire

HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8⁺ T-cell repertoire