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Molecular Evolution and Genetic Diversity in Viruses

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

Deadline for manuscript submissions: 20 May 2026 | Viewed by 722

Special Issue Editor


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Guest Editor
Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt, Germany
Interests: gastroepidemiology

Special Issue Information

Dear Colleagues,

Molecular evolution and genetic diversity are fundamental in understanding how viruses emerge, adapt, and persist. Viruses, RNA viruses in particular, evolve rapidly due to high mutation rates, recombination, and genome reassortment-key drivers of their genetic diversity and ability to evade immunity. The quasispecies nature of viral populations within hosts further enhances their adaptability and pathogenic potential. 

Advancements in sequencing technologies and bioinformatics have enabled real-time tracking of viral evolution, as seen during the SARS-CoV-2 pandemic. These tools are critical in identifying emerging variants, understanding viral transmission, monitoring the evolution of antiviral drug resistance, and guiding the development of antiviral therapies and vaccines. Viral phylogenetics and metagenomics continue to uncover the extensive genetic diversity of viruses across hosts and environments, deepening our understanding of viral evolution and supporting the early detection of epidemic strains. 

In light of the significant impact of viral evolution on disease dynamics, we invite submissions of original research, perspectives, and comprehensive reviews addressing the multifaceted aspects of viral molecular evolution and diversity. Topics of interest include, but not limited to: 

  • Mechanisms of viral mutation, recombination, and reassortment
  • Evolutionary genomics of RNA and DNA viruses
  • Quasispecies dynamics and intra-host evolution
  • Evolution of antiviral resistance
  • Viral phylogenetics and evolutionary modelling
  • Zoonotic transmission and viral emergence
  • Genomic surveillance of viral variants
  • Implications for vaccine and drug development

Dr. Jennifer H. Lun
Guest Editor

Manuscript Submission Information

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Keywords

  • viral mutation
  • recombination reassortment
  • viral genomics
  • quasispecies dynamics
  • antiviral resistance
  • viral phylogenetics
  • zoonotic transmission
  • genomic surveillance

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Published Papers (1 paper)

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Research

21 pages, 4036 KB  
Article
From Genome Diversity to Inferred Functional Constraints: An Integrated Evolutionary Analysis of Hepatitis B Virus Genotype F
by Ruy D. Chacón, Obert Marín-Sánchez, Jimmy Ango-Bedriñana and Homero Ango-Aguilar
Int. J. Mol. Sci. 2026, 27(5), 2284; https://doi.org/10.3390/ijms27052284 - 28 Feb 2026
Viewed by 470
Abstract
Hepatitis B virus (HBV) genotype F is one of the most genetically divergent and evolutionarily ancient HBV lineages and predominantly circulates in indigenous and admixed populations of the Americas. Here, we performed a comprehensive evolutionary and inferred functional characterization of the HBV genotype [...] Read more.
Hepatitis B virus (HBV) genotype F is one of the most genetically divergent and evolutionarily ancient HBV lineages and predominantly circulates in indigenous and admixed populations of the Americas. Here, we performed a comprehensive evolutionary and inferred functional characterization of the HBV genotype F via the largest curated dataset of complete genomes. Phylogenomic reconstruction, recombination screening, and phylogenetic network analyses were integrated with codon-based selective pressure inference, surface protein posttranslational modification profiling, mutational analysis of antigenic regions, and reverse transcriptase (RT) drug resistance assessment. The HBV-F subgenotype exhibited a well-resolved phylogenetic structure and limited intragenotypic recombination, while intergenotypic recombination contributed substantially to reticulate evolutionary signals. Selective pressure analyses revealed strong purifying selection in replication-associated domains of the polymerase, in contrast to episodic adaptive evolution in surface-exposed and regulatory proteins, particularly the X protein. N-glycosylation sites in large surface proteins are highly conserved. Some mutations in the major hydrophilic region (MHR) were significantly detected, whereas RT drug resistance mutations were rare and followed canonical lamivudine-associated pathways. Collectively, these findings highlight the balance between deep evolutionary conservation and localized adaptive flexibility in shaping the HBV genotype F and provide a genotype-specific framework for interpreting viral fitness, immune interactions, and antiviral resistance. Full article
(This article belongs to the Special Issue Molecular Evolution and Genetic Diversity in Viruses)
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