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

Jin, Xiaoxiao; Liu, Xiaotao; Shen, Chuanlai

doi:10.1016/j.virusres.2022.199024

Cited by 12 publications

(6 citation statements)

References 100 publications

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“…Despite this, little is known about the impact of viral mutations on HLA presentation and epitope-specific T cell recognition. Here, we investigated the impact of viral mutations within a well described HLA-A*02:01-restricted epitope derived from the spike protein, S 976-984 (VLNDILSRL) ( Jin et al, 2023 ; Saini et al, 2021 ; Tarke et al, 2022 ). The S976 epitope is a 9mer peptide derived from the S2 subunit of the Spike protein, restricted to HLA-A*02:01 and able to stimulate T cells derived from individuals following SARS-CoV-2 infection ( Wagner et al, 2022 ; Mallajosyula et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

“…The critical function and hydrophobicity of the HR domains are reflected in their sequence conservation within coronaviruses ( Liu et al, 2004 ), and are an attractive target for anti-viral drug development ( Xia et al, 2019 ; Xia et al, 2020 ; Xia et al, 2020 ). It was previously reported that the Spike-derived peptide S976 (S 976-984 , VLNDILSRL) is immunogenic and restricted by the HLA-A*02:01 molecule ( Jin et al, 2023 ; Saini et al, 2021 ; Tarke et al, 2022 ). Despite being located within the HR1 domain, the S976 epitope was mutated in two SARS-CoV-2 variants of concern (VoCs) isolates, S982A in Alpha and L981F in Omicron BA.1 variants.…”

Section: Introductionmentioning

confidence: 99%

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The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific

Ahn,

Maddumage,

Grant

et al. 2024

Current Research in Structural Biology

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific

Ahn,

Maddumage,

Grant

et al. 2024

Current Research in Structural Biology

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“…Systemic analysis of the T cell epitopes in VOCs indicated that at least 30 mutations can increase the ability for viral variants to evade T cell responses, and there are 19 mutations in Omicron and its sublineages. Because almost all of these mutations present in the CD4 + and CD8 + T cell epitopes of PS that have been identified by functional experiments so far, 45 these mutations deserve special attention. Mutation D614G is first reported at the beginning of the COVID‐19 pandemic.…”

Section: Discussionmentioning

confidence: 99%

Landscape of T cell epitopes displays hot mutations of SARS‐CoV‐2 variant spikes evading cellular immunity

Gan,

Cao,

Zhang

et al. 2024

Journal of Medical Virology

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The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been accompanied by the emergence of viral mutations that pose a great challenge to existing vaccine strategies. It is not fully understood with regard to the role of mutations on the SARS‐CoV‐2 spike protein from emerging viral variants in T cell immunity. In the current study, recombinant eukaryotic plasmids were constructed as DNA vaccines to express the spike protein from multiple SARS‐CoV‐2 strains. These DNA vaccines were used to immunize BALB/c mice, and cross‐T cell responses to the spike protein from these viral strains were quantitated using interferon‐γ (IFN‐γ) Elispot. Peptides covering the full‐length spike protein from different viral strains were used to detect epitope‐specific IFN‐γ+ CD4+ and CD8+ T cell responses by fluorescence‐activated cell sorting. SARS‐CoV‐2 Delta and Omicron BA.1 strains were found to have broad T cell cross‐reactivity, followed by the Beta strain. The landscapes of T cell epitopes on the spike protein demonstrated that at least 30 mutations emerging from Alpha to Omicron BA.5 can mediate the escape of T cell immunity. Omicron and its sublineages have 19 out of these 30 mutations, most of which are new, and a few are inherited from ancient circulating variants of concerns. The cross‐T cell immunity between SARS‐CoV‐2 prototype strain and Omicron strains can be attributed to the T cell epitopes located in the N‐terminal domain (181–246 aa [amino acids], 271–318 aa) and C‐terminal domain (1171–1273 aa) of the spike protein. These findings provide in vivo evidence for optimizing vaccine manufacturing and immunization strategies for current or future viral variants.

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“…ORM1 and HP were also highlighted as altered depending on the severity of the patients by Shen et al in serum [ 33 ] and by Beimdiek J et al in plasma, respectively [ 34 ]. The modulation and the polymorphism of the human leukocyte antigen (HLA) play a key role in the immune response, and its variants could affect COVID-19 progression and severity [ 35 , 36 ]. Additionally, a gradual augment depending on the disease severity of the neutrophil degranulation has been revealed by a trans-omics study performed by Wu et al [ 37 ].…”

Section: Discussionmentioning

confidence: 99%

Plasma Proteomic Variables Related to COVID-19 Severity: An Untargeted nLC-MS/MS Investigation

Pagani

Chinello

Risca

et al. 2023

IJMS

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Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection leads to a wide range of clinical manifestations and determines the need for personalized and precision medicine. To better understand the biological determinants of this heterogeneity, we explored the plasma proteome of 43 COVID-19 patients with different outcomes by an untargeted liquid chromatography-mass spectrometry approach. The comparison between asymptomatic or pauci-symptomatic subjects (MILDs), and hospitalised patients in need of oxygen support therapy (SEVEREs) highlighted 29 proteins emerged as differentially expressed: 12 overexpressed in MILDs and 17 in SEVEREs. Moreover, a supervised analysis based on a decision-tree recognised three proteins (Fetuin-A, Ig lambda-2chain-C-region, Vitronectin) that are able to robustly discriminate between the two classes independently from the infection stage. In silico functional annotation of the 29 deregulated proteins pinpointed several functions possibly related to the severity; no pathway was associated exclusively to MILDs, while several only to SEVEREs, and some associated to both MILDs and SEVEREs; SARS-CoV-2 signalling pathway was significantly enriched by proteins up-expressed in SEVEREs (SAA1/2, CRP, HP, LRG1) and in MILDs (GSN, HRG). In conclusion, our analysis could provide key information for ‘proteomically’ defining possible upstream mechanisms and mediators triggering or limiting the domino effect of the immune-related response and characterizing severe exacerbations.

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

Cited by 12 publications

References 100 publications

The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific

The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific

Landscape of T cell epitopes displays hot mutations of SARS‐CoV‐2 variant spikes evading cellular immunity

Plasma Proteomic Variables Related to COVID-19 Severity: An Untargeted nLC-MS/MS Investigation

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