Skip to main content

ORIGINAL RESEARCH article

Front. Cell. Infect. Microbiol.
Sec. Microbial Vaccines
Volume 15 - 2025 | doi: 10.3389/fcimb.2025.1509226
This article is part of the Research Topic Vaccine and Infectious Disease Informatics View all 4 articles

Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebase

Provisionally accepted
Anthony Huffman Anthony Huffman 1Mehul Gautam Mehul Gautam 1Arya Gandhi Arya Gandhi 1Priscilla Du Priscilla Du 1Lauren Austin Lauren Austin 1Kallan Roan Kallan Roan 1Jie Zheng Jie Zheng 1Yongqun Oliver He Yongqun Oliver He 2*
  • 1 University of Michigan, Ann Arbor, Michigan, United States
  • 2 Unit for Lab Animal Medicine, Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States

The final, formatted version of the article will be published soon.

    Viral vaccines have been proven significant in protecting us against viral diseases such as COVID-19. To better understand and design viral vaccines, we systematically collected, manually annotated, and analyzed 2,847 viral vaccines against 95 viral species (including 74 RNA viral species and 20 DNA viral species), and stored the information of the vaccines, vaccine components (such as 542 vaccine antigens), vaccine formulations, and their induced host responses in the VIOLIN vaccine database. Enriched patterns were identified from our systematical analysis of the viral vaccines and vaccine antigens. A taxonomical analysis found various DNA and RNA viruses covered by the viral vaccines. These vaccines target different viral life cycle stages (e.g., viral entry, assembly, exit, and immune evasion) as identified in top ranked human and animal vaccines as well as HPV vaccines. The vaccine antigen proteins also show up in different virion locations in viruses such as HRSV vaccines. Both structural and non-structural viral proteins have been used for viral vaccine development. Protective vaccine antigens have a high probability of having the protegenicity score of >85% based on the Vaxign-ML calculation. While predicted adhesins still have significantly higher chances of being protective antigens, only 21.42% of protective viral vaccine antigens were predicted to be adhesins. Furthermore, our Gene Ontology (GO) enrichment analysis using a customized Fisher's exact test identified many enriched patterns such as viral entry into the host cell, DNA/RNA/ATP/ion binding, and suppression of host type 1 interferon-mediated signaling pathway. The viral vaccines and their associated entities and relations are also ontologically modeled and represented in the Vaccine Ontology (VO). A VIOLIN web interface was developed to support user friendly queries of viral vaccines.

    Keywords: virus, ontology, Gene Enrichment, reverse vaccinology, Antigens, adhesin, VIOLIN vaccine knowledgebase, Vaxign-ML

    Received: 10 Oct 2024; Accepted: 07 Jan 2025.

    Copyright: © 2025 Huffman, Gautam, Gandhi, Du, Austin, Roan, Zheng and He. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Yongqun Oliver He, Unit for Lab Animal Medicine, Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, 48109, MI, United States

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.