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Viruses
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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: closed (30 September 2024) | Viewed by 13499

Special Issue Editors

Dr. Krisztián Bányai

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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

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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

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Published Papers (7 papers)

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Research

21 pages, 3252 KiB  
Article
Identification and Characterization of Novel Serpentoviruses in Viperid and Elapid Snakes
by Steven B. Tillis, Sarah B. Chaney, Esther E. V. Crouch, Donal Boyer, Kevin Torregrosa, Avishai D. Shuter, Anibal Armendaris, April L. Childress, Denise McAloose, Jean A. Paré, Robert J. Ossiboff and Kenneth J. Conley
Viruses 2024, 16(9), 1477; https://doi.org/10.3390/v16091477 - 17 Sep 2024
Viewed by 1343
Abstract
Viruses in the subfamily Serpentovirinae (order Nidovirales, family Tobaniviridae) can cause significant morbidity and mortality in captive snakes, but documented infections have been limited to snakes of the Boidae, Colubridae, Homalopsidae, and Pythonidae families. Infections can either be [...] Read more.
Viruses in the subfamily Serpentovirinae (order Nidovirales, family Tobaniviridae) can cause significant morbidity and mortality in captive snakes, but documented infections have been limited to snakes of the Boidae, Colubridae, Homalopsidae, and Pythonidae families. Infections can either be subclinical or associated with oral and/or respiratory disease. Beginning in June 2019, a population of over 150 confiscated snakes was screened for serpentovirus as part of a quarantine disease investigation. Antemortem oropharyngeal swabs or lung tissue collected postmortem were screened for serpentovirus by PCR, and 92/165 (56.0%) of snakes tested were positive for serpentovirus. Serpentoviruses were detected in fourteen species of Viperidae native to Asia, Africa, and South America and a single species of Elapidae native to Australia. When present, clinical signs included thin body condition, abnormal behavior or breathing, stomatitis, and/or mortality. Postmortem findings included variably severe inflammation, necrosis, and/or epithelial proliferation throughout the respiratory and upper gastrointestinal tracts. Genetic characterization of the detected serpentoviruses identified four unique viral clades phylogenetically distinct from recognized serpentovirus genera. Pairwise uncorrected distance analysis supported the phylogenetic analysis and indicated that the viper serpentoviruses likely represent the first members of a novel genus in the subfamily Serpentovirinae. The reported findings represent the first documentation of serpentoviruses in venomous snakes (Viperidae and Elapidae), greatly expanding the susceptible host range for these viruses and highlighting the importance of serpentovirus screening in all captive snake populations. Full article
(This article belongs to the Special Issue Virus Discovery, Classification and Characterization)
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5 pages, 491 KiB  
Communication
SCANellome V2: Update of the Primate Anellovirus Reference Sequences Database
by Florian Laubscher, Laurent Kaiser and Samuel Cordey
Viruses 2024, 16(9), 1349; https://doi.org/10.3390/v16091349 - 23 Aug 2024
Viewed by 844
Abstract
Anelloviruses are ubiquitous in humans and represent a major component of the human virome. Its best-known representative is Torque teno virus (i.e., the Alphatorquevirus genus), which is considered a potential immunity biomarker. Recent metagenomic investigations revealed not only the extraordinary genomic diversity of [...] Read more.
Anelloviruses are ubiquitous in humans and represent a major component of the human virome. Its best-known representative is Torque teno virus (i.e., the Alphatorquevirus genus), which is considered a potential immunity biomarker. Recent metagenomic investigations revealed not only the extraordinary genomic diversity of anellovirus sequences, but also that co-detection of genera, genotypes, or species seems to be the rule in humans. SCANellome was developed to represent a user-friendly tool to analyze the primate (both human and non-human) anellovirus composition at the genus, species, and genotype level from metagenomics data based on an up-to-date database. This SCANellome update includes >900 additional reference sequences from GenBank. Using a clustering at 90% identity, the FASTA database was updated and generated 134 new representative sequences. Based on ORF1, the analysis of these new sequences indicates the presence of 206 potential new species, including four nonhuman primates, and adds four new non-human primate species which will be the subject of a proposal to the International Committee on Taxonomy of Viruses (ICTV). In addition, SCANellome V2 provides now the user with an interactive up-to-date phylogenetic analysis (of ORF1) to show the distribution among the 12 human and nonhuman primate genera of these new potential species. Finally, the Anelloviridae taxonomy was updated to rename species names in binomial format as required by the ICTV. Full article
(This article belongs to the Special Issue Virus Discovery, Classification and Characterization)
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21 pages, 4517 KiB  
Article
Sylvatic Mosquito Viromes in the Cerrado Biome of Minas Gerais, Brazil: Discovery of New Viruses and Implications for Arbovirus Transmission
by Luis Janssen Maia, Arthur Batista Silva, Cirilo Henrique de Oliveira, Fabricio Souza Campos, Leonardo Assis da Silva, Filipe Vieira Santos de Abreu and Bergmann Morais Ribeiro
Viruses 2024, 16(8), 1276; https://doi.org/10.3390/v16081276 - 9 Aug 2024
Viewed by 2281
Abstract
Studies on animal virome have mainly concentrated on chordates and medically significant invertebrates, often overlooking sylvatic mosquitoes, constituting a major part of mosquito species diversity. Despite their potential role in arbovirus transmission, the viromes of sylvatic mosquitoes remain largely unexplored. These mosquitoes may [...] Read more.
Studies on animal virome have mainly concentrated on chordates and medically significant invertebrates, often overlooking sylvatic mosquitoes, constituting a major part of mosquito species diversity. Despite their potential role in arbovirus transmission, the viromes of sylvatic mosquitoes remain largely unexplored. These mosquitoes may also harbor insect-specific viruses (ISVs), affecting arboviral transmission dynamics. The Cerrado biome, known for rapid deforestation and its status as a biodiversity hotspot, offers an ideal setting for investigating mosquito viromes due to potential zoonotic spillover risks from land use changes. This study aimed to characterize the viromes of sylvatic mosquitoes collected from various locations within Minas Gerais state, Brazil. The total RNA was extracted from mosquito pools of Psorophora albipes, Sabethes albiprivus, Sa. chloropterus, Psorophora ferox, and Coquillettidia venezuelensis species, followed by high-throughput sequencing (HTS). Bioinformatic analysis included quality control, contig assembly, and viral detection. Sequencing data analysis revealed 11 near-complete viral genomes (new viruses are indicated with asterisks) across seven viral families and one unassigned genus. These included: Xinmoviridae (Ferox mosquito mononega-like virus* and Albipes mosquito Gordis-like virus*), Phasmaviridae (Sabethes albiprivus phasmavirus*), Lispiviridae (Pedras lispivirus variant MG), Iflaviridae (Sabethes albiprivus iflavivirus*), Virgaviridae (Buriti virga-like virus variant MG and Sabethes albiprivus virgavirus 1*), Flaviviridae (Psorophora ferox flavivirus*), Mesoniviridae (Alphamesonivirus cavallyense variant MG), and the genus Negevirus (Biggie virus variant MG virus and Coquillettidia venezuelensis negevirus*). Moreover, the presence of ISVs and potential novel arboviruses underscores the need for ongoing surveillance and control strategies to mitigate the risk of emerging infectious diseases. Full article
(This article belongs to the Special Issue Virus Discovery, Classification and Characterization)
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15 pages, 4012 KiB  
Article
Molecular Detection and Genetic Characterization of Two Dugbe Orthonairovirus Isolates Detected from Ticks in Southern Senegal
by Mignane Ndiaye, Aminata Badji, Idrissa Dieng, Anna S. Dolgova, Moufid Mhamadi, Anastasiia D. Kirichenko, Anna S. Gladkikh, Alioune Gaye, Ousmane Faye, Amadou Alpha Sall, Mawlouth Diallo, Vladimir G. Dedkov and Oumar Faye
Viruses 2024, 16(6), 964; https://doi.org/10.3390/v16060964 - 15 Jun 2024
Viewed by 1269
Abstract
Dugbe virus (DUGV) is a tick-borne arbovirus first isolated in Nigeria in 1964. It has been detected in many African countries using such diverse methods as serological tests, virus isolation, and molecular detection. In Senegal, reports of DUGV isolates mainly occurred in the [...] Read more.
Dugbe virus (DUGV) is a tick-borne arbovirus first isolated in Nigeria in 1964. It has been detected in many African countries using such diverse methods as serological tests, virus isolation, and molecular detection. In Senegal, reports of DUGV isolates mainly occurred in the 1970s and 1980s. Here, we report a contemporary detection of three novel DUGV isolates upon screening of a total of 2877 individual ticks regrouped into 844 pools. The three positive pools were identified as Amblyomma variegatum, the main known vector of DUGV, collected in the southern part of the country (Kolda region). Interestingly, phylogenetic analysis indicates that the newly sequenced isolates are globally related to the previously characterized isolates in West Africa, thus highlighting potentially endemic, unnoticed viral transmission. This study was also an opportunity to develop a rapid and affordable protocol for full-genome sequencing of DUGV using nanopore technology. The results suggest a relatively low mutation rate and relatively conservative evolution of DUGV isolates. Full article
(This article belongs to the Special Issue Virus Discovery, Classification and Characterization)
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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 - 6 Mar 2024
Viewed by 2126
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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15 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
Cited by 2 | Viewed by 2201
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 - 5 Nov 2023
Cited by 1 | Viewed by 2097
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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