Bioinformatics Research on Viruses

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Virology".

Deadline for manuscript submissions: closed (31 July 2025) | Viewed by 241

Special Issue Editors


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Guest Editor
Leibniz Institute on Aging—Fritz Lipmann Institute, Jena, Germany
Interests: aging

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Guest Editor
European Virus Bioinformatics Center, Friedrich Schiller University Jena, Jena, Germany
Interests: high throughput sequencing analysis; bioinformatic analysis; algorithmic bioinformatics; microbiome

Special Issue Information

Dear Colleagues,

The “Bioinformatics Research on Viruses” Special Issue highlights the transformative impact of computational biology on understanding viral complexity in the modern era. With viruses representing both a global health challenge and a biological enigma, this Special Issue seeks contributions that utilize bioinformatics to decode viral mechanisms, evolution, and interactions with hosts. Key areas of interest include the design of innovative algorithms for high-throughput viral genome analysis, the elucidation of viral–host co-evolutionary dynamics, and the prediction of viral behaviors under environmental and therapeutic pressures. This Special Issue also encourages submissions that explore the role of artificial intelligence and machine learning in virology, providing new avenues for surveillance, vaccine design, and antiviral drug development. By fostering an intersection of virology and computational sciences, this Special Issue aims to inspire cutting-edge discoveries and practical applications in viral research.

Prof. Dr. Manja Marz
Dr. Paula Istvan
Guest Editors

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Keywords

  • viral bioinformatics
  • genomic epidemiology
  • virus–host co-evolution
  • AI in virology
  • high-throughput sequencing
  • viral dynamics
  • therapeutic bioinformatics
  • computational virology tools
  • emerging viral threats
  • systems virology

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Published Papers (1 paper)

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Research

15 pages, 313 KB  
Article
Viral Quasispecies Inference from Single Observations—Mutagens as Accelerators of Quasispecies Evolution
by Josep Gregori, Miquel Salicrú, Marta Ibáñez-Lligoña, Sergi Colomer-Castell, Carolina Campos, Alvaro González-Camuesco and Josep Quer
Microorganisms 2025, 13(9), 2029; https://doi.org/10.3390/microorganisms13092029 (registering DOI) - 30 Aug 2025
Abstract
RNA virus populations exist as quasispecies-complex, dynamic clouds of closely related but genetically diverse variants generated by high mutation rates during replication. Assessing quasispecies structure and diversity is crucial for understanding viral evolution, adaptation, and response to antiviral treatments. However, comparing single quasispecies [...] Read more.
RNA virus populations exist as quasispecies-complex, dynamic clouds of closely related but genetically diverse variants generated by high mutation rates during replication. Assessing quasispecies structure and diversity is crucial for understanding viral evolution, adaptation, and response to antiviral treatments. However, comparing single quasispecies observations from individual biosamples, especially at different infection or treatment time points, presents statistical challenges. Traditional inferential tests are inapplicable due to the lack of replicate observations, and resampling-based approaches such as the bootstrap and jackknife are limited by biases and non-independence, particularly for diversity indices sensitive to rare haplotypes. In this study, we address these limitations by applying the delta method to derive analytical variances for a set of quasispecies structure indicators specifically designed to assess the quasispecies maturation state. We demonstrate the utility of this approach using high-depth next-generation sequencing data from hepatitis C virus (HCV) quasispecies evolving in vitro under various conditions, including free evolution and exposure to antiviral or mutagenic treatments. Our results reveal that with highly fit HCV quasispecies, sofosbuvir inhibits quasispecies genetic diversity, while mutagenic treatments accelerate maturation, compared to untreated controls. We emphasize the interpretation of results through absolute differences, log-fold changes, and standardized effect sizes, moving beyond mere statistical significance. This framework enables robust, quantitative comparisons of quasispecies diversity from single observations, providing valuable insights into viral adaptation and treatment response. The R code and session info with required libraries and versions is provided in the supplementary material. Full article
(This article belongs to the Special Issue Bioinformatics Research on Viruses)
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