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Viruses
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Efficacy, Safety, and Immunogenicity of Vaccines against Viruses: From Network...
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Efficacy, Safety, and Immunogenicity of Vaccines against Viruses: From Network Medicine to Clinical Experimentation 2nd Edition

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viral Immunology, Vaccines, and Antivirals".

Deadline for manuscript submissions: 30 November 2024 | Viewed by 6910

Special Issue Editors

Dr. Pietro Hiram Guzzi

E-Mail Website
Guest Editor
Department of Surgical and Medical Sciences, University of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
Interests: computational biology; data science; bioinformatics; COVID-19
Special Issues, Collections and Topics in MDPI journals
Dr. Jayanta Kumar Das

E-Mail Website
Guest Editor
Biomedical Research Center, National Institute on Aging, National Institutes of Health, Bethesda, MD 21224, USA
Interests: computational bioinformatics; applied data science; machine learning
Special Issues, Collections and Topics in MDPI journals
Dr. Marianna Milano

E-Mail Website
Guest Editor
Department of Experimental and Clinical Medicine, University of Catanzaro, 88100 Catanzaro, Italy
Interests: bioinformatics; network analysis; biological data analysis; COVID-19
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Despite the availability of effective vaccines against many diseases (e.g., COVID-19, Influenza, Varicella Virus, HPV), there is a need to study both novel and the existing vaccines and create prioritization campaigns to maintain vaccine-induced protection against variant strains and breakthrough infections.

Bioinformatics and network medicine help the research community to investigate the efficacy, safety and immunogenicity of vaccines and the mutual relationships among them.

An increasing body of evidence confirms that the synergistic integration of network medicine and clinical experimentation may improve the quality of existing vaccines as well as the development of novel ones. This Special Issue aims to foster discussion on following topics:

  • Development of novel vaccines;
  • Study of the immunogenicity of existing vaccines;
  • Age- and sex-based differences;
  • Introduction of novel prioritisation methods.

Dr. Pietro Hiram Guzzi
Dr. Jayanta Kumar Das
Dr. Marianna Milano
Guest Editors

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. Viruses 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

  • vaccines
  • vaccine security
  • computational bioinformatics
  • network analysis
  • data science

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Published Papers (4 papers)

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Research

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16 pages, 3992 KiB  
Article
Non-HIV Vaccine-Induced Immune Responses as Potential Baseline Immunogenicity Predictors of ALVAC-HIV and AIDSVAX B/E-Induced Immune Responses
by Ying Huang, Shomoita Alam, Erica Andersen-Nissen, Lindsay N. Carpp, One B. Dintwe, Britta S. Flach, Nicole Grunenberg, Fatima Laher, Stephen C. De Rosa, Guido Ferrari, Craig Innes, Linda-Gail Bekker, James G. Kublin, M. Juliana McElrath, Georgia D. Tomaras, Glenda E. Gray and Peter B. Gilbert
Viruses 2024, 16(9), 1365; https://doi.org/10.3390/v16091365 - 27 Aug 2024
Viewed by 1182
Abstract
Identifying correlations between immune responses elicited via HIV and non-HIV vaccines could aid the search for correlates of HIV protection and increase statistical power in HIV vaccine-efficacy trial designs. An exploratory objective of the HVTN 097 phase 1b trial was to assess whether [...] Read more.
Identifying correlations between immune responses elicited via HIV and non-HIV vaccines could aid the search for correlates of HIV protection and increase statistical power in HIV vaccine-efficacy trial designs. An exploratory objective of the HVTN 097 phase 1b trial was to assess whether immune responses [focusing on those supported as correlates of risk (CoR) of HIV acquisition] induced via the RV144 pox-prime HIV vaccine regimen correlated with those induced via tetanus toxoid (TT) and/or hepatitis B virus (HBV) vaccines. We measured TT-specific and HBV-specific IgG-binding antibody responses and TT-specific and HBV-specific CD4+ T-cell responses at multiple time points in HVTN 097 participants, and we assessed their correlations at peak time points with HIV vaccine (ALVAC-HIV and AIDSVAX B/E)-induced responses. Four correlations were significant [false discovery rate-adjusted p-value (FDR) ≤ 0.2]. Three of these four were with IgG-binding antibody responses to TT measured one month after TT receipt, with the strongest and most significant correlation [rho = 0.368 (95% CI: 0.096, 0.588; p = 0.008; FDR = 0.137)] being with IgG-binding antibody responses to MN gp120 gDneg (B protein boost) measured two weeks after the second ALVAC-HIV and AIDSVAX B/E boost. The fourth significant correlation [(rho = 0.361; 95% CI: 0.049, 0.609; p = 0.021; FDR = 0.137)] was between CD4+ T-cell responses to a hepatitis B surface antigen peptide pool, measured 2 weeks after the third HBV vaccination, and IgG-binding antibody responses to gp70BCaseAV1V2 (B V1V2 immune correlate), measured two weeks after the second ALVAC-HIV and AIDSVAX B/E boost. These moderate correlations imply that either vaccine, TT or HBV, could potentially provide a moderately useful immunogenicity predictor for the ALVAC-HIV and AIDSVAX B/E HIV vaccine regimen. Full article
(This article belongs to the Special Issue Efficacy, Safety, and Immunogenicity of Vaccines against Viruses: From Network Medicine to Clinical Experimentation 2nd Edition)
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17 pages, 4140 KiB  
Article
Designing a Conserved Immunogenic Peptide Construct from the Nucleocapsid Protein of Puumala orthohantavirus
by Ayushi Sehgal, Diksha Sharma, Neha Kaushal, Yogita Gupta, Ekaterina Martynova, Emmanuel Kabwe, Sara Chandy, Albert Rizvanov, Svetlana Khaiboullina and Manoj Baranwal
Viruses 2024, 16(7), 1030; https://doi.org/10.3390/v16071030 - 26 Jun 2024
Viewed by 1222
Abstract
Puumala orthohantavirus (PUUV) is an emerging zoonotic virus endemic to Europe and Russia that causes nephropathia epidemica, a mild form of hemorrhagic fever with renal syndrome (HFRS). There are limited options for treatment and diagnosis of orthohantavirus infection, making the search for potential [...] Read more.
Puumala orthohantavirus (PUUV) is an emerging zoonotic virus endemic to Europe and Russia that causes nephropathia epidemica, a mild form of hemorrhagic fever with renal syndrome (HFRS). There are limited options for treatment and diagnosis of orthohantavirus infection, making the search for potential immunogenic candidates crucial. In the present work, various bioinformatics tools were employed to design conserved immunogenic peptides containing multiple epitopes of PUUV nucleocapsid protein. Eleven conserved peptides (90% conservancy) of the PUUV nucleocapsid protein were identified. Three conserved peptides containing multiple T and B cell epitopes were selected using a consensus epitope prediction algorithm. Molecular docking using the HPEP dock server demonstrated strong binding interactions between the epitopes and HLA molecules (ten alleles for each class I and II HLA). Moreover, an analysis of population coverage using the IEDB database revealed that the identified peptides have over 90% average population coverage across six continents. Molecular docking and simulation analysis reveal a stable interaction with peptide constructs of chosen immunogenic peptides and Toll-like receptor-4. These computational analyses demonstrate selected peptides’ immunogenic potential, which needs to be validated in different experimental systems. Full article
(This article belongs to the Special Issue Efficacy, Safety, and Immunogenicity of Vaccines against Viruses: From Network Medicine to Clinical Experimentation 2nd Edition)
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Review

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11 pages, 250 KiB  
Review
Evaluation of Vaccine Immunogenicity—Correlates to Real-World Protection: Influenza
by Csaba Laszlofy, Gyorgy Fazekas, Zoltan Barath and Zoltan Vajo
Viruses 2024, 16(3), 441; https://doi.org/10.3390/v16030441 - 12 Mar 2024
Cited by 1 | Viewed by 1872
Abstract
Recent events highlighted that, despite decades of studying vaccine immunogenicity and efforts toward finding correlates of protection, evaluating real-world vaccine efficacy as well as establishing meaningful licensing criteria still represents a significant challenge. In this paper, we review all aspects of influenza vaccine [...] Read more.
Recent events highlighted that, despite decades of studying vaccine immunogenicity and efforts toward finding correlates of protection, evaluating real-world vaccine efficacy as well as establishing meaningful licensing criteria still represents a significant challenge. In this paper, we review all aspects of influenza vaccine immunogenicity, including animal and human challenge studies, humoral and cellular immunity parameters, and their potential correlation with real-life protection from disease. Full article
(This article belongs to the Special Issue Efficacy, Safety, and Immunogenicity of Vaccines against Viruses: From Network Medicine to Clinical Experimentation 2nd Edition)

Other

Jump to: Research, Review

10 pages, 1924 KiB  
Brief Report
Cross-Reactivity Assessment of Vaccine-Derived SARS-CoV-2 T Cell Responses against BA.2.86 and JN.1
by Muhammad Saqib Sohail, Syed Faraz Ahmed, Ahmed Abdul Quadeer and Matthew R. McKay
Viruses 2024, 16(3), 473; https://doi.org/10.3390/v16030473 - 20 Mar 2024
Cited by 4 | Viewed by 2100
Abstract
The SARS-CoV-2 Omicron sub-variants BA.2.86 and JN.1 contain multiple mutations in the spike protein that were not present in previous variants of concern and Omicron sub-variants. Preliminary research suggests that these variants reduce the neutralizing capability of antibodies induced by vaccines, which is [...] Read more.
The SARS-CoV-2 Omicron sub-variants BA.2.86 and JN.1 contain multiple mutations in the spike protein that were not present in previous variants of concern and Omicron sub-variants. Preliminary research suggests that these variants reduce the neutralizing capability of antibodies induced by vaccines, which is particularly significant for JN.1. This raises concern as many widely deployed COVID-19 vaccines are based on the spike protein of the ancestral Wuhan strain of SARS-CoV-2. While T cell responses have been shown to be robust against previous SARS-CoV-2 variants, less is known about the impact of mutations in BA.2.86 and JN.1 on T cell responses. We evaluate the effect of mutations specific to BA.2.86 and JN.1 on experimentally determined T cell epitopes derived from the spike protein of the ancestral Wuhan strain and the spike protein of the XBB.1.5 strain that has been recommended as a booster vaccine. Our data suggest that BA.2.86 and JN.1 affect numerous T cell epitopes in spike compared to previous variants; however, the widespread loss of T cell recognition against these variants is unlikely. Full article
(This article belongs to the Special Issue Efficacy, Safety, and Immunogenicity of Vaccines against Viruses: From Network Medicine to Clinical Experimentation 2nd Edition)
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