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Genes
Special Issues
Application of Next-Generation Sequencing in Clinical Virology
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Application of Next-Generation Sequencing in Clinical Virology

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Viral Genomics".

Deadline for manuscript submissions: closed (15 May 2023) | Viewed by 2811

Special Issue Editor

Prof. Dr. Jiguo Chen

E-Mail Website
Guest Editor
Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
Interests: virus-host cell interaction; emerging viral pathogens; clinical virology; next-generation sequencing (NGS); in vitro diagnostics (IVD)

Special Issue Information

Dear Colleagues,

Next-generation sequencing (NGS) is a new technology that can be used for broad detection of infectious pathogens and is rapidly becoming an essential platform in clinical laboratories. NGS provides an effective, unbiased way to identify known as well as emerging vial pathogens without prior knowledge of pathogens. Since the COVID-19 pandemic, NGS has rapidly become an important tool for SARS-CoV-2 genomic surveillance to detect novel variants and monitor trends in circulating variants, such as the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P1), Delta (B.1.617.2) and Omicron (B.1.1.529) variants. NGS continues to provide public health officials, vaccine and drug developers, and researchers with critical information in prevention, intervention, and therapeutics. Given the huge impact of NGS in clinical virology, a Special Issue of the journal Genes is being issued to explore various applications of next-generation sequencing in clinical virology. Authors are encouraged to submit original manuscripts describing utilization of NGS in clinical virology. Also encouraged are research papers describing new sequencing methodologies or instruments, and reviews or comparison studies of various NGS methods, as well as manuscripts dealing with bioinformatic methods of analysis.

Prof. Dr. Jiguo Chen
Guest Editor

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. Genes 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

  • clinical virology
  • next-generation sequencing (NGS)
  • emerging viral pathogens
  • in vitro diagnostics (IVD)
  • detection of viral infection
  • SARS-CoV-2
  • virus variants
  • bioinformatics

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Published Papers (1 paper)

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Research

13 pages, 2453 KiB  
Article
The Two-Faced Role of crAssphage Subfamilies in Obesity and Metabolic Syndrome: Between Good and Evil
by Melany Cervantes-Echeverría, Luigui Gallardo-Becerra, Fernanda Cornejo-Granados and Adrian Ochoa-Leyva
Genes 2023, 14(1), 139; https://doi.org/10.3390/genes14010139 - 4 Jan 2023
Cited by 9 | Viewed by 2372
Abstract
Viral metagenomic studies of the human gut microbiota have unraveled the differences in phage populations between health and disease, stimulating interest in phages’ role on bacterial ecosystem regulation. CrAssphage is a common and abundant family in the gut virome across human populations. Therefore, [...] Read more.
Viral metagenomic studies of the human gut microbiota have unraveled the differences in phage populations between health and disease, stimulating interest in phages’ role on bacterial ecosystem regulation. CrAssphage is a common and abundant family in the gut virome across human populations. Therefore, we explored its role in obesity (O) and obesity with metabolic syndrome (OMS) in a children’s cohort. We found a significantly decreased prevalence, diversity, and richness of the crAssphage Alpha subfamily in OMS mainly driven by a decrease in the Alpha_1 and Alpha_4 genera. On the contrary, there was a significant increase in the Beta subfamily in OMS, mainly driven by an increase in Beta_6. Additionally, an overabundance of the Delta_8 genus was observed in OMS. Notably, a decreased abundance of crAssphages was significantly correlated with the overabundance of Bacilli in the same group. The Bacilli class is a robust taxonomical biomarker of O and was also significantly abundant in our OMS cohort. Our results suggest that a loss of stability in the Alpha subfamily of crAssphages is associated with O and OMS. Contrary, an overabundance of the Delta subfamily was found in OMS. Our study advises the importance of considering the dual role (good and evil) of crAssphage subfamilies and their participation in conditions such as O, where we suggest that Alpha loss and Delta gain are associated with obese individuals. Full article
(This article belongs to the Special Issue Application of Next-Generation Sequencing in Clinical Virology)
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