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Viruses
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Metagenomics of Emerging Viruses
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Metagenomics of Emerging Viruses

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

Deadline for manuscript submissions: closed (15 August 2022) | Viewed by 6217

Special Issue Editors

Dr. Steven T. Pullan

E-Mail Website
Guest Editor
UK Health Security Agency, Research & Evaluation, Porton Down, Salisbury, UK
Interests: high-consequence pathogens; emerging pathogens; viral metagenomics
Dr. F. Xavier López-Labrador

E-Mail Website1 Website2
Guest Editor
Virology Laboratory, Genomics and Health Area, FISABIO - Center for Public Health Research, Generalitat Valenciana, Spain
Interests: human viruses; immunology; diagnostics; molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genome sequencing has long been established as a key tool in viral discovery and, in more recent years, has become one of the most important components of public health response activity for both local- and pandemic-scale outbreaks. Metagenomic approaches, used appropriately alongside more targeted methodologies, have been of major benefit in the advancement of this area in research, clinical, and public health settings.

This Special Issue invites reviews, opinion articles, or original research papers that explore any methodological developments in, or applications of, metagenomic sequencing methods to the discovery, surveillance, and characterization of emerging viruses and the outbreaks associated with them. Both laboratory and solely bioinformatic analysis-based papers are welcome. Surveillance studies of viruses present in environmental samples and potential animal reservoirs or insect vectors are within scope, as is the characterization of clinical outbreaks. Papers focussing on viral enrichment and host depletion methods to enhance metagenomic viral detection from primary samples will be highly regarded.

Dr. Steven T. Pullan
Dr. F. Xavier López-Labrador
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

  • metagenomic
  • emerging viruses
  • surveillance
  • host depletion
  • viral enrichment
  • sequencing
  • outbreaks

Published Papers (2 papers)

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Research

11 pages, 2368 KiB  
Article
Phage Diving: An Exploration of the Carcharhinid Shark Epidermal Virome
by Ryan D. Hesse, Michael Roach, Emma N. Kerr, Bhavya Papudeshi, Laís F. O. Lima, Asha Z. Goodman, Lisa Hoopes, Mark Scott, Lauren Meyer, Charlie Huveneers and Elizabeth A. Dinsdale
Viruses 2022, 14(9), 1969; https://doi.org/10.3390/v14091969 - 5 Sep 2022
Cited by 5 | Viewed by 2809
Abstract
The epidermal microbiome is a critical element of marine organismal immunity, but the epidermal virome of marine organisms remains largely unexplored. The epidermis of sharks represents a unique viromic ecosystem. Sharks secrete a thin layer of mucus which harbors a diverse microbiome, while [...] Read more.
The epidermal microbiome is a critical element of marine organismal immunity, but the epidermal virome of marine organisms remains largely unexplored. The epidermis of sharks represents a unique viromic ecosystem. Sharks secrete a thin layer of mucus which harbors a diverse microbiome, while their hydrodynamic dermal denticles simultaneously repel environmental microbes. Here, we sampled the virome from the epidermis of three shark species in the family Carcharhinidae: the genetically and morphologically similar Carcharhinus obscurus (n = 6) and Carcharhinus galapagensis (n = 10) and the outgroup Galeocerdo cuvier (n = 15). Virome taxonomy was characterized using shotgun metagenomics and compared with a suite of multivariate analyses. All three sharks retain species-specific but highly similar epidermal viromes dominated by uncharacterized bacteriophages which vary slightly in proportional abundance within and among shark species. Intraspecific variation was lower among C. galapagensis than among C. obscurus and G. cuvier. Using both the annotated and unannotated reads, we were able to determine that the Carcharhinus galapagensis viromes were more similar to that of G. cuvier than they were to that of C. obscurus, suggesting that behavioral niche may be a more prominent driver of virome than host phylogeny. Full article
(This article belongs to the Special Issue Metagenomics of Emerging Viruses)
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12 pages, 1909 KiB  
Article
Targeted Virome Sequencing Enhances Unbiased Detection and Genome Assembly of Known and Emerging Viruses—The Example of SARS-CoV-2
by Vasiliki Pogka, Gethsimani Papadopoulou, Vaia Valiakou, Dionyssios N. Sgouras, Andreas F. Mentis and Timokratis Karamitros
Viruses 2022, 14(6), 1272; https://doi.org/10.3390/v14061272 - 11 Jun 2022
Cited by 4 | Viewed by 2918
Abstract
Targeted virome enrichment and sequencing (VirCapSeq-VERT) utilizes a pool of oligos (baits) to enrich all known—up to 2015—vertebrate-infecting viruses, increasing their detection sensitivity. The hybridisation of the baits to the target sequences can be partial, thus enabling the detection and genomic reconstruction of [...] Read more.
Targeted virome enrichment and sequencing (VirCapSeq-VERT) utilizes a pool of oligos (baits) to enrich all known—up to 2015—vertebrate-infecting viruses, increasing their detection sensitivity. The hybridisation of the baits to the target sequences can be partial, thus enabling the detection and genomic reconstruction of novel pathogens with <40% genetic diversity compared to the strains used for the baits’ design. In this study, we deploy this method in multiplexed mixes of viral extracts, and we assess its performance in the unbiased detection of DNA and RNA viruses after cDNA synthesis. We further assess its efficiency in depleting various background genomic material. Finally, as a proof-of-concept, we explore the potential usage of the method for the characterization of unknown, emerging human viruses, such as SARS-CoV-2, which may not be included in the baits’ panel. We mixed positive samples of equimolar DNA/RNA viral extracts from SARS-CoV-2, coronavirus OC43, cytomegalovirus, influenza A virus H3N2, parvovirus B19, respiratory syncytial virus, adenovirus C and coxsackievirus A16. Targeted virome enrichment was performed on a dsDNA mix, followed by sequencing on the NextSeq500 (Illumina) and the portable MinION sequencer, to evaluate its usability as a point-of-care (PoC) application. Genome mapping assembly was performed using viral reference sequences. The untargeted libraries contained less than 1% of total reads mapped on most viral genomes, while RNA viruses remained undetected. In the targeted libraries, the percentage of viral-mapped reads were substantially increased, allowing full genome assembly in most cases. Targeted virome sequencing can enrich a broad range of viruses, potentially enabling the discovery of emerging viruses. Full article
(This article belongs to the Special Issue Metagenomics of Emerging Viruses)
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