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Viruses
Special Issues
Virus Discovery, Classification and Characterization
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Virus Discovery, Classification and Characterization

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

Deadline for manuscript submissions: 30 September 2024 | Viewed by 3775

Special Issue Editors

Dr. Krisztián Bányai

E-Mail Website
Guest Editor
Veterinary Medical Research Institute, 1143 Budapest, Hungary
Interests: virus discovery; metagenomics; genomic epidemiology
Special Issues, Collections and Topics in MDPI journals
Dr. Enikő Fehér

E-Mail Website
Guest Editor
Veterinary Medical Research Institute, 1143 Budapest, Hungary
Interests: virus discovery; metagenomics; genomic epidemiology
Special Issues, Collections and Topics in MDPI journals
Dr. Eszter Kaszab

E-Mail Website
Guest Editor
Veterinary Medical Research Institute, 1143 Budapest, Hungary
Interests: virus discovery; metagenomics; bioinformatics

Special Issue Information

Dear Colleagues,

In recent years, viral metagenomics has become an important tool for experts working in the field of virus discovery, classification, and characterization. Improved sample preparation and amplification methods, together with rapidly evolving sequencing technologies and bioinformatics pipelines, have made virus metagenomics a powerful approach for new discoveries. Viral metagenomics can be used to determine viral diversity in the environment or in any microbial community, to reveal the potential viral etiology of disease from pathological/clinical specimens, and to characterize viruses of unknown origin isolated in cell cultures. Using this approach, numerous novel virus species have been described over the past decade from all domains of life. The new paradigm in virus taxonomy also takes into account new discoveries in viral metagenomics and is likely to facilitate the classification and further characterization of uncultured viral agents. 

The aims of this Special Issue include all aspects of virus discovery (including new methods, new viruses, and new host–virus relationships) where next-generation sequencing has been central to the process. The Guest Editors hope that the new Special Issue entitled ‘Virus Discovery, Classification and Characterization’ will be a useful collection of papers and a source of information that reflects the state of the art in virus metagenomics.

Dr. Krisztián Bányai
Dr. Enikő Fehér
Dr. Eszter Kaszab
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

  • metagenomics
  • next generation sequencing
  • virus discovery
  • molecular epidemiology
  • taxonomy
  • virus–host relationship

Published Papers (3 papers)

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Research

27 pages, 21308 KiB  
Article
Xanthomonas Phage PBR31: Classifying the Unclassifiable
by Rashit I. Tarakanov, Peter V. Evseev, Ha T. N. Vo, Konstantin S. Troshin, Daria I. Gutnik, Aleksandr N. Ignatov, Stepan V. Toshchakov, Konstantin A. Miroshnikov, Ibrahim H. Jafarov and Fevzi S.-U. Dzhalilov
Viruses 2024, 16(3), 406; https://doi.org/10.3390/v16030406 - 06 Mar 2024
Viewed by 899
Abstract
The ability of bacteriophages to destroy bacteria has made them the subject of extensive research. Interest in bacteriophages has recently increased due to the spread of drug-resistant bacteria, although genomic research has not kept pace with the growth of genomic data. Genomic analysis [...] Read more.
The ability of bacteriophages to destroy bacteria has made them the subject of extensive research. Interest in bacteriophages has recently increased due to the spread of drug-resistant bacteria, although genomic research has not kept pace with the growth of genomic data. Genomic analysis and, especially, the taxonomic description of bacteriophages are often difficult due to the peculiarities of the evolution of bacteriophages, which often includes the horizontal transfer of genes and genomic modules. The latter is particularly pronounced for temperate bacteriophages, which are capable of integration into the bacterial chromosome. Xanthomonas phage PBR31 is a temperate bacteriophage, which has been neither described nor classified previously, that infects the plant pathogen Xanthomonas campestris pv. campestris. Genomic analysis, including phylogenetic studies, indicated the separation of phage PBR31 from known classified bacteriophages, as well as its distant relationship with other temperate bacteriophages, including the Lederbervirus group. Bioinformatic analysis of proteins revealed distinctive features of PBR31, including the presence of a protein similar to the small subunit of D-family DNA polymerase and advanced lysis machinery. Taxonomic analysis showed the possibility of assigning phage PBR31 to a new taxon, although the complete taxonomic description of Xanthomonas phage PBR31 and other related bacteriophages is complicated by the complex evolutionary history of the formation of its genome. The general biological features of the PBR31 phage were analysed for the first time. Due to its presumably temperate lifestyle, there is doubt as to whether the PBR31 phage is appropriate for phage control purposes. Bioinformatics analysis, however, revealed the presence of cell wall-degrading enzymes that can be utilised for the treatment of bacterial infections. Full article
(This article belongs to the Special Issue Virus Discovery, Classification and Characterization)
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16 pages, 17935 KiB  
Article
Unveiling CRESS DNA Virus Diversity in Oysters by Virome
by Peng Zhu, Chang Liu, Guang-Feng Liu, Hong Liu, Ke-Ming Xie, Hong-Sai Zhang, Xin Xu, Jian Xiao and Jing-Zhe Jiang
Viruses 2024, 16(2), 228; https://doi.org/10.3390/v16020228 - 31 Jan 2024
Viewed by 1029
Abstract
Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent, concerns are mounting about diseases that can harm both cultivated and wild oysters. Unfortunately, there is a lack of [...] Read more.
Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent, concerns are mounting about diseases that can harm both cultivated and wild oysters. Unfortunately, there is a lack of research on the viruses and other factors that can cause illness in shellfish. This means that it is harder to find ways to prevent these diseases and protect the oysters. This is part of a previously started project, the Dataset of Oyster Virome, in which we further study 30 almost complete genomes of oyster-associated CRESS DNA viruses. The replication-associated proteins and capsid proteins found in CRESS DNA viruses display varying evolutionary rates and frequently undergo recombination. Additionally, some CRESS DNA viruses have the capability for cross-species transmission. A plethora of unclassified CRESS DNA viruses are detectable in transcriptome libraries, exhibiting higher levels of transcriptional activity than those found in metagenome libraries. The study significantly enhances our understanding of the diversity of oyster-associated CRESS DNA viruses, emphasizing the widespread presence of CRESS DNA viruses in the natural environment and the substantial portion of CRESS DNA viruses that remain unidentified. This study’s findings provide a basis for further research on the biological and ecological roles of viruses in oysters and their environment. Full article
(This article belongs to the Special Issue Virus Discovery, Classification and Characterization)
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17 pages, 10930 KiB  
Article
Analysis of Pseudomonas aeruginosa Isolates from Patients with Cystic Fibrosis Revealed Novel Groups of Filamentous Bacteriophages
by Peter Evseev, Julia Bocharova, Dmitriy Shagin and Igor Chebotar
Viruses 2023, 15(11), 2215; https://doi.org/10.3390/v15112215 - 05 Nov 2023
Viewed by 1197
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can cause infections in humans, especially in hospital patients with compromised host defence mechanisms, including patients with cystic fibrosis. Filamentous bacteriophages represent a group of single-stranded DNA viruses infecting different bacteria, including P. aeruginosa and other [...] Read more.
Pseudomonas aeruginosa is an opportunistic pathogen that can cause infections in humans, especially in hospital patients with compromised host defence mechanisms, including patients with cystic fibrosis. Filamentous bacteriophages represent a group of single-stranded DNA viruses infecting different bacteria, including P. aeruginosa and other human and animal pathogens; many of them can replicate when integrated into the bacterial chromosome. Filamentous bacteriophages can contribute to the virulence of P. aeruginosa and influence the course of the disease. There are just a few isolated and officially classified filamentous bacteriophages infecting P. aeruginosa, but genomic studies indicated the frequent occurrence of integrated prophages in many P. aeruginosa genomes. An analysis of sequenced genomes of P. aeruginosa isolated from upper respiratory tract (throat and nasal swabs) and sputum specimens collected from Russian patients with cystic fibrosis indicated a higher diversity of filamentous bacteriophages than first thought. A detailed analysis of predicted bacterial proteins revealed prophage regions representing the filamentous phages known to be quite distantly related to known phages. Genomic comparisons and phylogenetic studies enabled the proposal of several new taxonomic groups of filamentous bacteriophages. Full article
(This article belongs to the Special Issue Virus Discovery, Classification and Characterization)
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