Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.3
3.8
Journals
Viruses
Special Issues
Virus Bioinformatics 2024
share announcement

Virus Bioinformatics 2024

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

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 12645

Special Issue Editors

Prof. Dr. Manja Marz

E-Mail Website
Guest Editor
Bioinformatics and High-Throughput Analysis and European Virus Bioinformatics Center, Friedrich Schiller University Jena, Jena, Germany
Interests: high throughput sequencing analysis; bioinformatic analysis and system biology of viruses; comparative genomics; identification and annotation of non-coding RNAs; coevolution of proteins and RNAs; algorithmic bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Franziska Hufsky

E-Mail Website
Guest Editor
The European Virus Bioinformatics Center, Friedrich Schiller University Jena, Jena, Germany
Interests: computational metabolomics and mass spectrometry; algorithms in bioinformatics; virus bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is published alongside the International Virus Bioinformatics Meeting 2024 (https://evbc.uni-jena.de/events/vibiom2024/), taking place in Leuven, Belgium, on 28–30 May, 2024. ViBioM has become synonymous with scientific exchange and dialogue between different disciplines, and attracts some of the most influential scientists in virus bioinformatics.  

This Special Issue presents original research articles and review papers covering the recent advancements and our current understanding of the computational technological aspects of virology. Scientific results of interdisciplinary research are often difficult to publish in journals in either area. To facilitate publications in the field of virus bioinformatics, the European Virus Bioinformatics Center has been running this recurring Special Issue since 2019.

We encourage you to publish your work in this Special Issue and present it at ViBioM 2024. However, this is not an obligation for publication.

All papers should be submitted online at https://www.mdpi.com/journal/viruses. Please select the correct Special Issue when submitting your paper to Viruses.

Prof. Dr. Manja Marz
Dr. Franziska Hufsky
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

  • virus bioinformatics
  • software
  • viral metagenomics and ecology
  • virus–host interactions
  • viral diversity and evolution
  • virus identification

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

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

Related Special Issues

Published Papers (7 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Other

26 pages, 5920 KiB  
Article
Complete Genome Classification System of Rotavirus alphagastroenteritidis: An Updated Analysis
by Ricardo Gabriel Díaz Alarcón, Karina Salvatierra, Emiliano Gómez Quintero, Domingo Javier Liotta, Viviana Parreño and Samuel Orlando Miño
Viruses 2025, 17(2), 211; https://doi.org/10.3390/v17020211 - 31 Jan 2025
Viewed by 861
Abstract
Rotavirus alphagastroenteritidis is the major causative agent of acute gastroenteritis in both children under the age of 5 and young mammals and birds globally. RVAs are non-enveloped viruses with a genome comprising 11 double-stranded RNA segments. In 2008, the Rotavirus Classification Working Group [...] Read more.
Rotavirus alphagastroenteritidis is the major causative agent of acute gastroenteritis in both children under the age of 5 and young mammals and birds globally. RVAs are non-enveloped viruses with a genome comprising 11 double-stranded RNA segments. In 2008, the Rotavirus Classification Working Group pioneered a comprehensive and complete RVA genome classification system, establishing a specific threshold, which measures the genetic distances between homologous genes. The aim of this study was to perform an updated systematic analysis of the genetic variability across all RVA genes. Our investigation involved assessing the established cutoff values for each RVA genome segment and determining the need for any updates. To achieve this objective, multiple sequence alignments were constructed for all 11 genes and one for each genotype with discrepancies. Also, pairwise distances along with their cutoff values were evaluated. The analyses provided insights into the current relevance of cutoff values, which remain applicable for the majority of genotypes. In conclusion, this study fortifies the current classification system by highlighting its robustness and accurate genotyping of Rotavirus alphagastroenteritidis. Full article
(This article belongs to the Special Issue Virus Bioinformatics 2024)
►▼ Show Figures

Figure 1

12 pages, 1736 KiB  
Article
Evolutionary Insights from Association Rule Mining of Co-Occurring Mutations in Influenza Hemagglutinin and Neuraminidase
by Valentina Galeone, Carol Lee, Michael T. Monaghan, Denis C. Bauer and Laurence O. W. Wilson
Viruses 2024, 16(10), 1515; https://doi.org/10.3390/v16101515 - 25 Sep 2024
Viewed by 1482
Abstract
Seasonal influenza viruses continuously evolve via antigenic drift. This leads to recurring epidemics, globally significant mortality rates, and the need for annually updated vaccines. Co-occurring mutations in hemagglutinin (HA) and neuraminidase (NA) are suggested to have synergistic interactions where mutations can increase the [...] Read more.
Seasonal influenza viruses continuously evolve via antigenic drift. This leads to recurring epidemics, globally significant mortality rates, and the need for annually updated vaccines. Co-occurring mutations in hemagglutinin (HA) and neuraminidase (NA) are suggested to have synergistic interactions where mutations can increase the chances of immune escape and viral fitness. Association rule mining was used to identify temporal relationships of co-occurring HA–NA mutations of influenza virus A/H3N2 and its role in antigenic evolution. A total of 64 clusters were found. These included well-known mutations responsible for antigenic drift, as well as previously undiscovered groups. A majority (41/64) were associated with known antigenic sites, and 38/64 involved mutations across both HA and NA. The emergence and disappearance of N-glycosylation sites in the pattern of N-X-[S/T] were also identified, which are crucial post-translational processes to maintain protein stability and functional balance (e.g., emergence of NA:339ASP and disappearance of HA:187ASP). Our study offers an alternative approach to the existing mutual-information and phylogenetic methods used to identify co-occurring mutations, enabling faster processing of large amounts of data. Our approach can facilitate the prediction of critical mutations given their occurrence in a previous season, facilitating vaccine development for the next flu season and leading to better preparation for future pandemics. Full article
(This article belongs to the Special Issue Virus Bioinformatics 2024)
►▼ Show Figures

Figure 1

7 pages, 396 KiB  
Article
CIEVaD: A Lightweight Workflow Collection for the Rapid and On-Demand Deployment of End-to-End Testing for Genomic Variant Detection
by Thomas Krannich, Dimitri Ternovoj, Sofia Paraskevopoulou and Stephan Fuchs
Viruses 2024, 16(9), 1444; https://doi.org/10.3390/v16091444 - 11 Sep 2024
Viewed by 1110
Abstract
The identification of genomic variants has become a routine task in the age of genome sequencing. In particular, small genomic variants of a single or few nucleotides are routinely investigated for their impact on an organism’s phenotype. Hence, the precise and robust detection [...] Read more.
The identification of genomic variants has become a routine task in the age of genome sequencing. In particular, small genomic variants of a single or few nucleotides are routinely investigated for their impact on an organism’s phenotype. Hence, the precise and robust detection of the variants’ exact genomic locations and changes in nucleotide composition is vital in many biological applications. Although a plethora of methods exist for the many key steps of variant detection, thoroughly testing the detection process and evaluating its results is still a cumbersome procedure. In this work, we present a collection of easy-to-apply and highly modifiable workflows to facilitate the generation of synthetic test data, as well as to evaluate the accordance of a user-provided set of variants with the test data. The workflows are implemented in Nextflow and are open-source and freely available on Github under the GPL-3.0 license. Full article
(This article belongs to the Special Issue Virus Bioinformatics 2024)
►▼ Show Figures

Figure A1

19 pages, 8930 KiB  
Article
Aedes Mosquito Virome in Southwestern Cameroon: Lack of Core Virome, But a Very Rich and Diverse Virome in Ae. africanus Compared to Other Aedes Species
by Karelle Celes Mbigha Donfack, Lander De Coninck, Stephen Mbigha Ghogomu and Jelle Matthijnssens
Viruses 2024, 16(7), 1172; https://doi.org/10.3390/v16071172 - 21 Jul 2024
Viewed by 1818
Abstract
In Cameroon, Aedes mosquitoes transmit various arboviruses, posing significant health risks. We aimed to characterize the Aedes virome in southwestern Cameroon and identify potential core viruses which might be associated with vector competence. A total of 398 Aedes mosquitoes were collected from four [...] Read more.
In Cameroon, Aedes mosquitoes transmit various arboviruses, posing significant health risks. We aimed to characterize the Aedes virome in southwestern Cameroon and identify potential core viruses which might be associated with vector competence. A total of 398 Aedes mosquitoes were collected from four locations (Bafoussam, Buea, Edea, and Yaounde). Aedes albopictus dominated all sites except for Bafoussam, where Aedes africanus prevailed. Metagenomic analyses of the mosquitoes grouped per species into 54 pools revealed notable differences in the eukaryotic viromes between Ae. africanus and Ae. albopictus, with the former exhibiting greater richness and diversity. Thirty-seven eukaryotic virus species from 16 families were identified, including six novel viruses with near complete genome sequences. Seven viruses were further quantified in individual mosquitoes via qRT-PCR. Although none of them could be identified as core viruses, Guangzhou sobemo-like virus and Bafoussam mosquito solemovirus, were highly prevalent regionally in Ae. albopictus and Ae. africanus, respectively. This study highlights the diverse eukaryotic virome of Aedes species in southwestern Cameroon. Despite their shared genus, Aedes species exhibit limited viral sharing, with varying viral abundance and prevalence across locations. Ae. africanus, an understudied vector, harbors a rich and diverse virome, suggesting potential implications for arbovirus vector competence. Full article
(This article belongs to the Special Issue Virus Bioinformatics 2024)
►▼ Show Figures

Figure 1

19 pages, 4389 KiB  
Article
Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories
by Talya Conradie, Jose A. Caparros-Martin, Siobhon Egan, Anthony Kicic, Sulev Koks, Stephen M. Stick and Patricia Agudelo-Romero
Viruses 2024, 16(6), 953; https://doi.org/10.3390/v16060953 - 13 Jun 2024
Cited by 2 | Viewed by 2022
Abstract
Background: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases’ pathogenesis. Nevertheless, our understanding of respiratory microbiota [...] Read more.
Background: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases’ pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited. Methods: Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization. Results: Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed. Conclusion: By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology. Full article
(This article belongs to the Special Issue Virus Bioinformatics 2024)
►▼ Show Figures

Figure 1

19 pages, 2653 KiB  
Article
Respiratory Syncytial Virus Vaccine Design Using Structure-Based Machine-Learning Models
by Thomas C. McCarty and Iosif I. Vaisman
Viruses 2024, 16(6), 821; https://doi.org/10.3390/v16060821 - 22 May 2024
Cited by 1 | Viewed by 1999
Abstract
When designing live-attenuated respiratory syncytial virus (RSV) vaccine candidates, attenuating mutations can be developed through biologic selection or reverse-genetic manipulation and may include point mutations, codon and gene deletions, and genome rearrangements. Attenuation typically involves the reduction in virus replication, due to direct [...] Read more.
When designing live-attenuated respiratory syncytial virus (RSV) vaccine candidates, attenuating mutations can be developed through biologic selection or reverse-genetic manipulation and may include point mutations, codon and gene deletions, and genome rearrangements. Attenuation typically involves the reduction in virus replication, due to direct effects on viral structural and replicative machinery or viral factors that antagonize host defense or cause disease. However, attenuation must balance reduced replication and immunogenic antigen expression. In the present study, we explored a new approach in order to discover attenuating mutations. Specifically, we used protein structure modeling and computational methods to identify amino acid substitutions in the RSV nonstructural protein 1 (NS1) predicted to cause various levels of structural perturbation. Twelve different mutations predicted to alter the NS1 protein structure were introduced into infectious virus and analyzed in cell culture for effects on viral mRNA and protein expression, interferon and cytokine expression, and caspase activation. We found the use of structure-based machine learning to predict amino acid substitutions that reduce the thermodynamic stability of NS1 resulted in various levels of loss of NS1 function, exemplified by effects including reduced multi-cycle viral replication in cells competent for type I interferon, reduced expression of viral mRNAs and proteins, and increased interferon and apoptosis responses. Full article
(This article belongs to the Special Issue Virus Bioinformatics 2024)
►▼ Show Figures

Figure 1

Other

Jump to: Research

11 pages, 1054 KiB  
Technical Note
IAVCP (Influenza A Virus Consensus and Phylogeny): Automatic Identification of the Genomic Sequence of the Influenza A Virus from High-Throughput Sequencing Data
by Anastasiia Iu. Paremskaia, Pavel Yu. Volchkov and Andrei A. Deviatkin
Viruses 2024, 16(6), 873; https://doi.org/10.3390/v16060873 - 29 May 2024
Viewed by 1412
Abstract
Recently, high-throughput sequencing of influenza A viruses has become a routine test. It should be noted that the extremely high diversity of the influenza A virus complicates the task of determining the sequences of all eight genome segments. For a fast and accurate [...] Read more.
Recently, high-throughput sequencing of influenza A viruses has become a routine test. It should be noted that the extremely high diversity of the influenza A virus complicates the task of determining the sequences of all eight genome segments. For a fast and accurate analysis, it is necessary to select the most suitable reference for each segment. At the same time, there is no standardized method in the field of decoding sequencing results that allows the user to update the sequence databases to which the reads obtained by virus sequencing are compared. The IAVCP (influenza A virus consensus and phylogeny) was developed with the goal of automatically analyzing high-throughput sequencing data of influenza A viruses. Its goals include the extraction of a consensus genome directly from paired raw reads. In addition, the pipeline enables the identification of potential reassortment events in the evolutionary history of the virus of interest by analyzing the topological structure of phylogenetic trees that are automatically reconstructed. Full article
(This article belongs to the Special Issue Virus Bioinformatics 2024)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-7
Back to TopTop