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Viral Infection: Molecular Mechanisms and Vaccine Approaches

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Immunology".

Deadline for manuscript submissions: 28 February 2027 | Viewed by 364

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Guest Editor
Engineering School in Biomedical & Biotechnology, Euromed Faculty of Pharmacy, Euro-Mediterranean University of Fez, Eco-Campus UEMF, Route de Meknes (RN6, Rond-Point Bensouda), Fez 30070, Morocco
Interests: microbiology; recombinant DNA technology; protein engineering; virology; veterinary sciences; phagotherapy and antibiotherapy; vaccine development; tRNA modifications and related mitochondrial diseases

Special Issue Information

Dear Colleagues,

Viruses continue to represent one of the most significant medical challenges humanity faces in the 21st century, affecting human and animal health as well as agriculture, with major repercussions for socioeconomic stability. The COVID-19 pandemic is an illustrative example of the immense challenges posed by viral diseases. The continuous emergence and re-emergence of viral pathogens has underscored the urgent need to deepen our molecular understanding of viral infection and to invest resources and effort in accelerating the development of innovative antiviral strategies and new vaccines.

This Special Issue aims to gather original research articles and comprehensive reviews that address the molecular and mechanistic bases of viral infection and support the development of more effective and accessible vaccines. Accordingly, we invite submissions that elucidate the fundamental mechanisms governing virus–host interactions at the molecular, cellular and structural levels.

Furthermore, this Special Issue seeks to highlight the translation of molecular discoveries into the design of next-generation vaccines. Relevant topics include the molecular engineering of viral antigens and the development of platforms based on virus-like particles, recombinant proteins, mRNA and other innovative vaccine technologies.

Dr. Ismaïl Moukadiri
Guest Editor

Manuscript Submission Information

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Keywords

  • viral infection
  • molecular virology
  • molecular mechanisms
  • antigen engineering
  • next-generation vaccine design

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Published Papers (1 paper)

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Research

20 pages, 1826 KB  
Article
Cross-Virus RNA Language Models for Within-Family RNA–RNA Interaction Prediction in SARS-CoV-2 and Porcine Deltacoronavirus
by Xu Yang, Weiwei Shen, Yixue Li, Liucun Zhu and Tao Huang
Int. J. Mol. Sci. 2026, 27(17), 7565; https://doi.org/10.3390/ijms27177565 - 24 Aug 2026
Abstract
RNA large language models (RNA LLMs) show potential for predicting viral RNA–RNA interactions (RRIs), but their ability to transfer between viruses remains unclear. Here, we evaluated three nucleotide language models using vRIC-seq-derived RRI datasets from two members of the Coronaviridae family, SARS-CoV-2 and [...] Read more.
RNA large language models (RNA LLMs) show potential for predicting viral RNA–RNA interactions (RRIs), but their ability to transfer between viruses remains unclear. Here, we evaluated three nucleotide language models using vRIC-seq-derived RRI datasets from two members of the Coronaviridae family, SARS-CoV-2 and porcine deltacoronavirus (PDCoV). We compared within-virus five-fold cross-validation with bidirectional cross-virus testing. DNABERT achieved within-virus AUC values of 0.9595 for PDCoV and 0.9741 for SARS-CoV-2. Under cross-virus transfer, its AUC decreased to 0.8372 when trained on PDCoV and tested on SARS-CoV-2 and to 0.8116 in the reverse direction, with corresponding F1 scores of 0.7847 and 0.7617. RNAErnie retained similar but slightly lower cross-virus discrimination, whereas the Nucleotide Transformer approached random discrimination. These results provide a two-virus proof of concept that sequence-based models can retain partially shared discriminative signals across coronavirus genera. They do not establish functional, tropism-related, or receptor-dependent transferability, and broader evaluation across additional viruses and orthogonal structural validation will be required before application to emerging-virus screening. Full article
(This article belongs to the Special Issue Viral Infection: Molecular Mechanisms and Vaccine Approaches)
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