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Viruses
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Viromics
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Viromics

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

Deadline for manuscript submissions: closed (1 November 2021) | Viewed by 16610

Special Issue Editors

Dr. Jennifer R. Brum

E-Mail Website
Guest Editor
Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, USA
Interests: microbial oceanography; viral ecology
Special Issues, Collections and Topics in MDPI journals
Dr. Simon Roux

E-Mail Website
Guest Editor
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA
Interests: viral diversity; virus evolution; viruses of microbes; metagenomics; bioinformatics

Special Issue Information

Dear Colleagues,

Over the last 15 years, advances in viral metagenomics have contributed to the fast growth of, and many paradigm-shifting discoveries in, several fields of virology, including viral ecology and viral evolution. What started in marine environments and human microbiomes has now expanded to cover virtually all habitats and sample types. With the continuous development of new experimental and computational methods, the range of research questions that can be addressed through viromics approaches is also progressively expanding beyond descriptive studies. For instance, viromics is now used to investigate eco-evolutionary drivers of environmental viral communities, assess potential impacts of viruses on microbial metabolism, and detect known and/or novel pathogens. For the second edition of the “Viromics” Special Issue, we welcome submissions that cover new approaches, significant advances, and applications in any area of viromics.

Dr. Jennifer R. Brum
Dr. Simon Roux
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
  • viromics
  • viral ecology
  • virus discovery
  • pathogen surveillance
  • computational approaches in viromics

Related Special Issue

Published Papers (5 papers)

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Research

14 pages, 2961 KiB  
Article
Informative Regions In Viral Genomes
by Jaime Leonardo Moreno-Gallego and Alejandro Reyes
Viruses 2021, 13(6), 1164; https://doi.org/10.3390/v13061164 - 18 Jun 2021
Cited by 7 | Viewed by 3573
Abstract
Viruses, far from being just parasites affecting hosts’ fitness, are major players in any microbial ecosystem. In spite of their broad abundance, viruses, in particular bacteriophages, remain largely unknown since only about 20% of sequences obtained from viral community DNA surveys could be [...] Read more.
Viruses, far from being just parasites affecting hosts’ fitness, are major players in any microbial ecosystem. In spite of their broad abundance, viruses, in particular bacteriophages, remain largely unknown since only about 20% of sequences obtained from viral community DNA surveys could be annotated by comparison with public databases. In order to shed some light into this genetic dark matter we expanded the search of orthologous groups as potential markers to viral taxonomy from bacteriophages and included eukaryotic viruses, establishing a set of 31,150 ViPhOGs (Eukaryotic Viruses and Phages Orthologous Groups). To do this, we examine the non-redundant viral diversity stored in public databases, predict proteins in genomes lacking such information, and used all annotated and predicted proteins to identify potential protein domains. The clustering of domains and unannotated regions into orthologous groups was done using cogSoft. Finally, we employed a random forest implementation to classify genomes into their taxonomy and found that the presence or absence of ViPhOGs is significantly associated with their taxonomy. Furthermore, we established a set of 1457 ViPhOGs that given their importance for the classification could be considered as markers or signatures for the different taxonomic groups defined by the ICTV at the order, family, and genus levels. Full article
(This article belongs to the Special Issue Viromics)
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6 pages, 468 KiB  
Communication
Discriminating between JCPyV and BKPyV in Urinary Virome Data Sets
by Rita Mormando, Alan J. Wolfe and Catherine Putonti
Viruses 2021, 13(6), 1041; https://doi.org/10.3390/v13061041 - 31 May 2021
Viewed by 1978
Abstract
Polyomaviruses are abundant in the human body. The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are common viruses in the human urinary tract. Prior studies have estimated that JCPyV infects between 20 and 80% of adults and that BKPyV infects between 65 [...] Read more.
Polyomaviruses are abundant in the human body. The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are common viruses in the human urinary tract. Prior studies have estimated that JCPyV infects between 20 and 80% of adults and that BKPyV infects between 65 and 90% of individuals by age 10. However, these two viruses encode for the same six genes and share 75% nucleotide sequence identity across their genomes. While prior urinary virome studies have repeatedly reported the presence of JCPyV, we were interested in seeing how JCPyV prevalence compares to BKPyV. We retrieved all publicly available shotgun metagenomic sequencing reads from urinary microbiome and virome studies (n = 165). While one third of the data sets produced hits to JCPyV, upon further investigation were we able to determine that the majority of these were in fact BKPyV. This distinction was made by specifically mining for JCPyV and BKPyV and considering uniform coverage across the genome. This approach provides confidence in taxon calls, even between closely related viruses with significant sequence similarity. Full article
(This article belongs to the Special Issue Viromics)
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21 pages, 2998 KiB  
Article
Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay
by Katrine Wacenius Skov Alanin, Laura Milena Forero Junco, Jacob Bruun Jørgensen, Tue Kjærgaard Nielsen, Morten Arendt Rasmussen, Witold Kot and Lars Hestbjerg Hansen
Viruses 2021, 13(6), 959; https://doi.org/10.3390/v13060959 - 21 May 2021
Cited by 5 | Viewed by 3478
Abstract
Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the [...] Read more.
Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community’s shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome–host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum twofold change above zero in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone. Full article
(This article belongs to the Special Issue Viromics)
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12 pages, 1827 KiB  
Article
Identification of Epidemiological Traits by Analysis of SARS−CoV−2 Sequences
by Bohu Pan, Zuowei Ji, Sugunadevi Sakkiah, Wenjing Guo, Jie Liu, Tucker A. Patterson and Huixiao Hong
Viruses 2021, 13(5), 764; https://doi.org/10.3390/v13050764 - 27 Apr 2021
Cited by 5 | Viewed by 2799
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS−CoV−2) has caused the ongoing global COVID-19 pandemic that began in late December 2019. The rapid spread of SARS−CoV−2 is primarily due to person-to-person transmission. To understand the epidemiological traits of SARS−CoV−2 transmission, we conducted phylogenetic analysis [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS−CoV−2) has caused the ongoing global COVID-19 pandemic that began in late December 2019. The rapid spread of SARS−CoV−2 is primarily due to person-to-person transmission. To understand the epidemiological traits of SARS−CoV−2 transmission, we conducted phylogenetic analysis on genome sequences from >54K SARS−CoV−2 cases obtained from two public databases. Hierarchical clustering analysis on geographic patterns in the resulting phylogenetic trees revealed a co-expansion tendency of the virus among neighboring countries with diverse sources and transmission routes for SARS−CoV−2. Pairwise sequence similarity analysis demonstrated that SARS−CoV−2 is transmitted locally and evolves during transmission. However, no significant differences were seen among SARS−CoV−2 genomes grouped by host age or sex. Here, our identified epidemiological traits provide information to better prevent transmission of SARS−CoV−2 and to facilitate the development of effective vaccines and therapeutics against the virus. Full article
(This article belongs to the Special Issue Viromics)
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21 pages, 2563 KiB  
Article
Identification and Distribution of Novel Cressdnaviruses and Circular Molecules in Four Penguin Species in South Georgia and the Antarctic Peninsula
by Hila Levy, Rafaela S. Fontenele, Ciara Harding, Crystal Suazo, Simona Kraberger, Kara Schmidlin, Anni Djurhuus, Caitlin E. Black, Tom Hart, Adrian L. Smith and Arvind Varsani
Viruses 2020, 12(9), 1029; https://doi.org/10.3390/v12091029 - 16 Sep 2020
Cited by 10 | Viewed by 3814
Abstract
There is growing interest in uncovering the viral diversity present in wild animal species. The remote Antarctic region is home to a wealth of uncovered microbial diversity, some of which is associated with its megafauna, including penguin species, the dominant avian biota. Penguins [...] Read more.
There is growing interest in uncovering the viral diversity present in wild animal species. The remote Antarctic region is home to a wealth of uncovered microbial diversity, some of which is associated with its megafauna, including penguin species, the dominant avian biota. Penguins interface with a number of other biota in their roles as marine mesopredators and several species overlap in their ranges and habitats. To characterize the circular single-stranded viruses related to those in the phylum Cressdnaviricota from these environmental sentinel species, cloacal swabs (n = 95) were obtained from King Penguins in South Georgia, and congeneric Adélie Penguins, Chinstrap Penguins, and Gentoo Penguins across the South Shetland Islands and Antarctic Peninsula. Using a combination of high-throughput sequencing, abutting primers-based PCR recovery of circular genomic elements, cloning, and Sanger sequencing, we detected 97 novel sequences comprising 40 ssDNA viral genomes and 57 viral-like circular molecules from 45 individual penguins. We present their detection patterns, with Chinstrap Penguins harboring the highest number of new sequences. The novel Antarctic viruses identified appear to be host-specific, while one circular molecule was shared between sympatric Chinstrap and Gentoo Penguins. We also report viral genotype sharing between three adult-chick pairs, one in each Pygoscelid species. Sequence similarity network approaches coupled with Maximum likelihood phylogenies of the clusters indicate the 40 novel viral genomes do not fall within any known viral families and likely fall within the recently established phylum Cressdnaviricota based on their replication-associated protein sequences. Similarly, 83 capsid protein sequences encoded by the viruses or viral-like circular molecules identified in this study do not cluster with any of those encoded by classified viral groups. Further research is warranted to expand knowledge of the Antarctic virome and would help elucidate the importance of viral-like molecules in vertebrate host evolution. Full article
(This article belongs to the Special Issue Viromics)
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