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Viruses
Special Issues
Bioinformatics and Computational Approaches in Viral Genomics and Evolution 2025
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Bioinformatics and Computational Approaches in Viral Genomics and Evolution 2025

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".

Deadline for manuscript submissions: 16 December 2025 | Viewed by 836

Special Issue Editors

Dr. Camila Malta Romano

E-Mail Website
Guest Editor
Laboratório de Virologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil
Interests: virus evolution; genomics and phylogenetics
Prof. Dr. Mariana Severo Ramundo

E-Mail Website
Guest Editor
1. Laboratory of Immunology, INCOR, Hospital das Clínicas HCFMUSP, Faculty of Medicine, University of São Paulo, São Paulo 05403-900, Brazil
2. Department of Internal Medicine, Discipline of Clinical Immunology and Allergy, Faculty of Medicine, University of São Paulo, São Paulo 01246-903, Brazil
Interests: bioinformatics; systems biology; artificial intelligence
Dr. Nilson Coimbra

E-Mail
Guest Editor
Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, SP, Brazil
Interests: bioinformatics; computational biology and evolution

Special Issue Information

Dear Colleagues,

We are pleased to invite submissions to a Special Issue of Viruses titled “Bioinformatics and Computational Approaches in Viral Genomics and Evolution 2025”.

The rapid evolution of viral pathogens and the urgency for surveillance of emergent and reemergent viruses highlight the critical need for advanced computational methods in understanding their behavior, transmission, and adaptation. The integration of bioinformatics tools and genomic data analysis is essential for monitoring viral evolution, predicting new threats, and developing targeted interventions.

This Special Issue seeks to highlight innovative computational techniques, including genome-wide analysis, pipelines for NGS-generated genome assembly, phylogenetic modeling, and machine learning approaches, to study viral evolution. We welcome original research, reviews, and short communications on topics such as:

  • Bioinformatics tools for viral genome analysis and surveillance;
  • Computational methods for studying viral evolution and mutation;
  • Integration of genomic data with clinical and epidemiological information;
  • Computational models for understanding viral–host interactions and pathogenicity;
  • Advances in computational epidemiology and viral surveillance networks.

We invite contributions that advance our understanding of viral genomics, providing insights that will assist in the global fight against infectious diseases. We look forward to your submissions.

Dr. Camila Malta Romano
Prof. Dr. Mariana Severo Ramundo
Dr. Nilson Coimbra
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

  • bioinformatics tools
  • genomic surveillance
  • viral evolution
  • computational genomics
  • host-pathogen interactions

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

27 pages, 10890 KiB  
Article
Integrating Sequence- and Structure-Based Similarity Metrics for the Demarcation of Multiple Viral Taxonomic Levels
by Igor C. dos Santos, Rebecca di Stephano de Souza, Igor Tolstoy, Liliane S. Oliveira and Arthur Gruber
Viruses 2025, 17(5), 642; https://doi.org/10.3390/v17050642 (registering DOI) - 29 Apr 2025
Abstract
Viruses exhibit significantly greater diversity than cellular organisms, posing a complex challenge to their taxonomic classification. While primary sequences may diverge considerably, protein functional domains can maintain conserved 3D structures throughout evolution. Consequently, structural homology of viral proteins can reveal deep taxonomic relationships, [...] Read more.
Viruses exhibit significantly greater diversity than cellular organisms, posing a complex challenge to their taxonomic classification. While primary sequences may diverge considerably, protein functional domains can maintain conserved 3D structures throughout evolution. Consequently, structural homology of viral proteins can reveal deep taxonomic relationships, overcoming limitations inherent in sequence-based methods. In this work, we introduce MPACT (Multimetric Pairwise Comparison Tool), an integrated tool that utilizes both sequence- and structure-based metrics. The program incorporates five metrics: sequence identity, similarity, maximum likelihood distance, TM-score, and 3Di-character similarity. MPACT generates heatmaps and distance trees to visualize viral relationships across multiple levels, enabling users to substantiate viral taxa demarcation. Taxa delineation can be achieved by specifying appropriate score cutoffs for each metric, facilitating the definition of viral groups, and storing their corresponding sequence data. By analyzing diverse viral datasets spanning various levels of divergence, we demonstrate MPACT’s capability to reveal viral relationships, even among distantly related taxa. This tool provides a comprehensive approach to assist viral classification, exceeding the current methods by integrating multiple metrics and uncovering deeper evolutionary connections. Full article
(This article belongs to the Special Issue Bioinformatics and Computational Approaches in Viral Genomics and Evolution 2025)
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11 pages, 1517 KiB  
Article
A Spatiotemporal Analysis of a High-Resolution Molecular Network Reveals Shifts of HIV-1 Transmission Hotspots in Guangzhou, China
by Huanchang Yan, Yifan Lu, Shunming Li, Hao Wu, Jingyang Hu, Yefei Luo, Qingmei Li, Lingxuan Lai, Weiping Huang, Jing Gu, Lijun Ma, Yuantao Hao, Zhigang Han, Xin-lin Chen and Yu Liu
Viruses 2025, 17(3), 384; https://doi.org/10.3390/v17030384 - 7 Mar 2025
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Abstract
Background: High-resolution and longitudinal HIV molecular surveillance can inform the evolving hotspots to tailor regionally focused control strategies. Methods: HIV-1 pol sequences of three predominant genotypes (CRF01_AE, CRF07_BC, and CRF55_01B) were collected for molecular network reconstruction from people living with HIV (PLWH) in [...] Read more.
Background: High-resolution and longitudinal HIV molecular surveillance can inform the evolving hotspots to tailor regionally focused control strategies. Methods: HIV-1 pol sequences of three predominant genotypes (CRF01_AE, CRF07_BC, and CRF55_01B) were collected for molecular network reconstruction from people living with HIV (PLWH) in Guangzhou (2018–2020). They were categorized by geographical residences into central, suburban, and outer suburban areas. Clustering rates, assortativity coefficients, and intensity matrices were employed to assess transmission dynamics, geographic mixing patterns, and intra- and inter-area transmission, respectively. Results: Of the 2469 PLWH, 55.5% resided in the central area. Clustering rates showed no significant differences across areas (44.5%, 40.6% vs. 45.7%; p = 0.184). However, the transmission hotspots for CRF01_AE and CRF55_01B shifted to the outer suburban area. PLWH tended to form links within their local area (assortativity coefficient = 0.227, p < 0.001), particularly for CRF01_AE (0.512, p < 0.001; intra-area intensity = 69.2%). The central area exhibited the highest but decreasing intra-area transmission (74.5% to 30.2%), while intra- and inter-area transmission involving the outer suburban area increased (23.1% to 38.2%). Conclusions: Despite most PLWH residing in the central area, the outer suburban area emerged as the hotspot, requiring interventions towards both intra- and inter-area transmission. Full article
(This article belongs to the Special Issue Bioinformatics and Computational Approaches in Viral Genomics and Evolution 2025)
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