Distribution of HLA-A, -B, -C, -DRB1, -DQB1, -DPB1 allele frequencies in patients with COVID-19 bilateral pneumonia in Russians, living in the Chelyabinsk region (Russia)

Tatiana, A. Suslova; Mikhail, N. Vavilov; Svetlana, V. Belyaeva; Alexander, V. Evdokimov; Daria, S. Stashkevich; Alexander, Galkin; Ilya, A. Kofiadi

doi:10.1016/j.humimm.2022.04.009

Cited by 7 publications

(9 citation statements)

References 26 publications

(33 reference statements)

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“…Previously, the HLA-A*01:01 allele was considered a risk allele for infection and severe course of COVID-19 in the first wave ( Pisanti et al, 2020 ; Ishii, 2020 ; Shkurnikov et al, 2021 ; Naemi et al, 2021 ). At the same time, the protective role of this allele against the formation of severe bilateral pneumonia caused by COVID-19 was also reported ( Suslova et al, 2022 ).…”

Section: Discussionmentioning

confidence: 76%

HLA-A01:01* allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire

Shkurnikov

Nersisyan

Averinskaya

et al. 2023

PeerJ

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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 diminishing 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 immunoprevalent 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: 76%

HLA-A01:01* allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire

Shkurnikov

Nersisyan

Averinskaya

et al. 2023

PeerJ

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“…For example, HLA-DPA1*01:03 is associated with improved clinical outcomes of covid-19 [ 37 ], while HLA-DPA1*02:02 is associated with reduced antibody response after covid-19 vaccination [ 38 ]. HLA-DPB1*04:01 is associated with an increased risk of covid-19 double pneumonia [ 39 ], while HLA-DPB1*04:02 is associated with improved clinical outcomes of covid-19 [ 40 ]. HLA-DRB1*13:02 is associated with an increased risk of covid-19 symptoms, while HLA-DRB1*15:01 is associated with an enhanced T-cell response after covid-19 vaccination [ 41 ].…”

Section: Resultsmentioning

confidence: 99%

Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks

Li,

Han,

et al. 2023

BMC Genomics

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To explore the potential network markers and related signaling pathways of human B cells infected by COVID-19, we performed standardized integration and analysis of single-cell sequencing data to construct conditional cell-specific networks (CCSN) for each cell. Then the peripheral blood cells were clustered and annotated based on the conditional network degree matrix (CNDM) and gene expression matrix (GEM), respectively, and B cells were selected for further analysis. Besides, based on the CNDM of B cells, the hub genes and ‘dark’ genes (a gene has a significant difference between case and control samples not in a gene expression level but in a conditional network degree level) closely related to COVID-19 were revealed. Interestingly, some of the ‘dark’ genes and differential degree genes (DDGs) encoded key proteins in the JAK-STAT pathway, which had antiviral effects. The protein p21 encoded by the ‘dark’ gene CDKN1A was a key regulator for the COVID-19 infection-related signaling pathway. Elevated levels of proteins encoded by some DDGs were directly related to disease severity of patients with COVID-19. In short, the proteins encoded by ‘dark’ genes complement some missing links in COVID-19 and these signaling pathways played an important role in the growth and activation of B cells.

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“…Previously, the HLA-A*01:01 allele was considered a risk allele for infection and severe course of COVID-19 in the first wave (17,(36)(37)(38). At the same time, the protective role of this allele against the formation of Severe Bilateral Pneumonia caused by COVID-19 was also reported (39). We suggested that the decrease in the frequency of HLA-A*01:01 carriers among patients of the third wave could be associated with the characteristics of the previously formed T-cell responses.…”

Section: Discussionmentioning

confidence: 99%

“…Previously, the HLA-A*01:01 allele was considered a risk allele for infection and severe course of COVID-19 in the first wave (17,(35)(36)(37). At the same time, the protective role of this allele against the formation of Severe Bilateral Pneumonia caused by COVID-19 was also reported (38).…”

Section: Discussionmentioning

confidence: 99%

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.

show abstract

Distribution of HLA-A, -B, -C, -DRB1, -DQB1, -DPB1 allele frequencies in patients with COVID-19 bilateral pneumonia in Russians, living in the Chelyabinsk region (Russia)

Cited by 7 publications

References 26 publications

HLA-A01:01* allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire

HLA-A01:01* allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire

Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks

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

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Distribution of HLA-A, -B, -C, -DRB1, -DQB1, -DPB1 allele frequencies in patients with COVID-19 bilateral pneumonia in Russians, living in the Chelyabinsk region (Russia)

Cited by 7 publications

References 26 publications

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

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

Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks

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

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Product

Resources

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HLA-A01:01* allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire

HLA-A01:01* allele diminishing 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