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Biomedicines
Special Issues
Emerging Issues in COVID and T Cells
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Emerging Issues in COVID and T Cells

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Immunology and Immunotherapy".

Deadline for manuscript submissions: closed (29 February 2024) | Viewed by 6116

Special Issue Editor

Dr. Emilia Jaskuła

E-Mail Website
Guest Editor
1. L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
2. Lower Silesian Oncology, Pulmonology, and Hematology Center, Wroclaw, Poland
Interests: viral infections immunity; risk factors affecting the outcome of patients post hematopoietic stem cell transplantation (virus infection, GvHD, relapses); HSCT; immunotherapy; hematology; TCR receptors; transplantation immunity; immunology of allogeneic cell transplantation

Special Issue Information

Dear Colleagues,

Natural or artificial immunization that provides lifelong immunity to antigens is particularly desirable for eradicating a pathogen from a population and for pandemic control. This immunization can only be achieved by certain infections and vaccines. In light of the COVID-19 pandemic, it is particularly relevant to know how long postvaccination and/or postinfectious immunity lasts, to identify its most prominent components, and to determine what factors influence it.

A substantial amount of information on COVID-19 immunity focuses on the antibody response. This is because it is relatively easy to measure the B-lymphocyte response. We have many standardized methods for measuring antibodies and neutralizing antibodies. As a result, we are now reasonably familiar with the dynamics of antibody appearance, class switching, and their decline. However, as variants such as Omicron evolve to avoid antibodies, the role of another part of the immune system, T cells, seems to become more prominent. Unlike antibodies, T lymphocytes attack infected cells, not directly at the virus. The activity of T cells is driven by the presentation of antigen, which is only a small fragment of the virus. It appears that mutations in subsequent COVID-19 variants do not affect the effective action of T cells to eliminate the infection. This explains why there are decreasing numbers of fatalities with each successive wave of the pandemic, even in regions with low vaccination rates.

We already know a great deal about the critical role of T cells in other viral infections, but their importance for battling SARS-CoV-2 remains unclear. In addition to the role of cytotoxic CD8+ lymphocytes directly involved in the elimination of infected cells, we must consider other subpopulations of T cells that are relevant in the development of an immune response after infection and vaccination and defense against infection including CD4+ lymphocytes; Tfh lymphocytes activating and supporting B lymphocytes for the production of antibodies; regulatory lymphocytes protecting against the excessive response of the immune system to the pathogen; γδ T cells, which possess receptors (TCRs) that can recognize stress signals from infected cells; and other T-cell subpopulations.

In this research topic, we would like to include recent scientific developments on the role of T cells in SARS-CoV-2 infection and immune response post vaccination.

We cordially invite authors to contribute original research articles or reviews focusing on, but not limited to, the following:

  • Functional characterization of SARS-CoV-2 T-cell response to infection and vaccination.
  • Phenotypic characteristic of T-cell subpopulations during SARS-CoV-2 infection and/or post-vaccination.
  • Mechanisms regulating infection/vaccine-induced T-cell longevity.
  • Characterization of immune memory induced by SARS-CoV-2 infections and vaccines.
  • Cross-talk between T cells and other immune system components in infection or vaccination.
  • Factors that influence T-cell responses (immunizing; immunosenescence; malignancy onset; or the influence of associated immunotherapies, drugs, or immunosuppression).
  • Role of TCRs and HLA in T-cell response to SARS-CoV-2 infection or vaccines.
  • Identify the factors mediating COVID-19 immune protection.
  • Vaccine response in immunocompromised patients.
  • COVID-19 complications.

Dr. Emilia Jaskuła
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • T cells
  • CD8
  • CD4
  • Tfh
  • Treg
  • gamma delta T cells
  • TCR
  • epitope recognition
  • T-cell response
  • SARS-CoV-2
  • COVID-19

Published Papers (3 papers)

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Research

9 pages, 277 KiB  
Article
Antiphospholipid Antibodies Occurrence in Acute SARS-CoV-2 Infection without Overt Thrombosis
by Alina Dima, Daniela Nicoleta Popescu, Ruxandra Moroti, Elisabeta Stoica, Georgiana State, Florentina Negoi, Ioana Adriana Berza and Magda Parvu
Biomedicines 2023, 11(5), 1241; https://doi.org/10.3390/biomedicines11051241 - 22 Apr 2023
Cited by 2 | Viewed by 1794
Abstract
We sought to determine the prevalence of antiphospholipid antibodies (aPLs) and their correlation with COVID-19 severity (in terms of clinical and laboratory parameters) in patients without thrombotic events during the early phase of infection. This was a cross-sectional study with the inclusion of [...] Read more.
We sought to determine the prevalence of antiphospholipid antibodies (aPLs) and their correlation with COVID-19 severity (in terms of clinical and laboratory parameters) in patients without thrombotic events during the early phase of infection. This was a cross-sectional study with the inclusion of hospitalized COVID-19 patients from a single department during the COVID-19 pandemic (April 2020–May 2021). Previous known immune disease or thrombophilia along with long-term anticoagulation and patients with overt arterial or venous thrombosis during SARS-CoV-2 infection were excluded. In all cases, data on four criteria for aPL were collected, namely lupus anticoagulant (LA), IgM and IgG anticardiolipin antibodies (aCL), as well as IgG anti-β2 glycoprotein I antibodies (aβ2GPI). One hundred and seventy-nine COVID-19 patients were included, with a mean age of 59.6 (14.5) years and a sex ratio of 0.8 male: female. LA was positive in 41.9%, while it was strongly positive in 4.5%; aCL IgM was found in 9.5%, aCL IgG in 4.5%, and aβ2GPI IgG in 1.7% of the sera tested. Clinical correlation: LA was more frequently expressed in severe COVID-19 cases than in moderate or mild cases (p = 0.027). Laboratory correlation: In univariate analysis, LA levels were correlated with D-dimer (p = 0.016), aPTT (p = 0.001), ferritin (p = 0.012), C-reactive protein (CRP) (p = 0.027), lymphocyte (p = 0.040), and platelet (p < 0.001) counts. However, in the multivariate analysis, only the CRP levels correlated with LA positivity: OR (95% CI) 1.008 (1.001–1.016), p = 0.042. LA was the most common aPL identified in the acute phase of COVID-19 and was correlated with infection severity in patients without overt thrombosis. Full article
(This article belongs to the Special Issue Emerging Issues in COVID and T Cells)
22 pages, 7639 KiB  
Article
High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2
by Rajendra Bhadane and Outi M. H. Salo-Ahen
Biomedicines 2022, 10(11), 2779; https://doi.org/10.3390/biomedicines10112779 - 01 Nov 2022
Cited by 2 | Viewed by 2227
Abstract
The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. Since the initial outbreak, the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus. Among all the variants, omicron is currently classified [...] Read more.
The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. Since the initial outbreak, the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus. Among all the variants, omicron is currently classified as a variant of concern (VOC) by the World Health Organization, as the previously circulating variants have been replaced by it. In this work, we have focused on the mutations observed in omicron sub lineages BA.1, BA.2, BA.4 and BA.5, particularly at the receptor-binding domain (RBD) of the spike protein that is responsible for the interactions with the host ACE2 receptor and binding of antibodies. Studying such mutations is particularly important for understanding the viral infectivity, spread of the disease and for tracking the escape routes of this virus from antibodies. Molecular dynamics (MD) based alchemical free energy calculations have been shown to be very accurate in predicting the free energy change, due to a mutation that could have a deleterious or a stabilizing effect on either the protein itself or its binding affinity to another protein. Here, we investigated the significance of five spike RBD mutations on the stability of the spike protein binding to ACE2 by free energy calculations using high throughput MD simulations. For comparison, we also used conventional MD simulations combined with a Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) based approach, and compared our results with the available experimental data. Overall, the alchemical free energy calculations performed far better than the MM-GBSA approach in predicting the individual impact of the mutations. When considering the experimental variation, the alchemical free energy method was able to produce a relatively accurate prediction for N501Y, the mutant that has previously been reported to increase the binding affinity to hACE2. On the other hand, the other individual mutations seem not to have a significant effect on the spike RBD binding affinity towards hACE2. Full article
(This article belongs to the Special Issue Emerging Issues in COVID and T Cells)
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14 pages, 944 KiB  
Article
Prediction of Conserved HLA Class I and Class II Epitopes from SARS-CoV-2 Licensed Vaccines Supports T-Cell Cross-Protection against SARS-CoV-1
by Daniel López
Biomedicines 2022, 10(7), 1622; https://doi.org/10.3390/biomedicines10071622 - 07 Jul 2022
Cited by 4 | Viewed by 1434
Abstract
Heterologous immunity-inducing vaccines against different pathogens are necessary to deal with new pandemics. In this study, the possible impact of COVID-19 licensed formulations in the cytotoxic and the helper cellular immune responses against SARS-CoV-1 is analyzed for the 567 and 41 most abundant [...] Read more.
Heterologous immunity-inducing vaccines against different pathogens are necessary to deal with new pandemics. In this study, the possible impact of COVID-19 licensed formulations in the cytotoxic and the helper cellular immune responses against SARS-CoV-1 is analyzed for the 567 and 41 most abundant HLA class I and II alleles, respectively. Computational prediction showed that most of these 608 alleles, which cover >90% of the human population, contain enough conserved T-cell epitopes among SARS-CoV-1 and SARS-CoV-2 spike proteins. In addition, the vast majority of these predicted peptides were defined as epitopes recognized by CD4+ or CD8+ T lymphocytes, showing a very high correlation between the bioinformatics prediction and the experimental assays. These data suggest that both cytotoxic and helper cellular immune protection elicited by the currently licensed COVID-19 vaccines should be effective against SARS-CoV-1 infection. Lastly, this study has potential implications for public health against current and future pandemics, given that the SARS-CoV-1 vaccines in pipeline since the early 20th century could generate similarly cross-protection against COVID-19. Full article
(This article belongs to the Special Issue Emerging Issues in COVID and T Cells)
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