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Microorganisms
Special Issues
Respiratory Viruses in the Age of Metagenomics
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Respiratory Viruses in the Age of Metagenomics

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Systems Microbiology".

Deadline for manuscript submissions: closed (31 March 2021) | Viewed by 12836

Special Issue Editor

Dr. Laurence Josset

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Guest Editor
1. University Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, F-69372 Lyon, France
2. Laboratoire de Virologie, IAI, CBN, Hospices Civils de Lyon, Lyon, France
3. Centre National de Reference Virus Influenzae, IAI, CBN, Hospices Civils de Lyon, Lyon, France
Interests: bioinformatics; influenza; molecular biology; virology; influenza A virus; virome; microbiome; respiratory tract infection; metagenomics

Special Issue Information

Dear Colleagues,

Respiratory viruses cause both common acute respiratory infections and severe complications, including pneumonia and exacerbation of chronic respiratory diseases. A large number of individuals are affected each year worldwide, with substantial medical and economic impact.

In recent years, clinical metagenomic next-generation sequencing (mNGS) has been shifting paradigms in microbiology by providing access to genomes of whole microbial communities in clinical samples. Combined with other omics approaches, mNGS allows one to take a holistic perspective of respiratory virus infection and presents new prospects in the field of respiratory viruses’ surveillance and biology, including improved diagnosis and surveillance and a better understanding of pathogenesis and options for treatment.

The aim of this Special Issue is to present advances in our understanding of respiratory viruses’ epidemiology, pathogenesis, and control, in the era metagenomics.

For this purpose, we welcome the submission of research articles, review articles, and short communications using mNGS to provide novel insights into the various aspects of respiratory virus infection: the diagnosis of new or divergent viruses, technical challenges and the interpretation issues of mNGS, epidemiology, within-host evolution of respiratory viruses, virus–host interactions (pathogenesis, host responses to infection, the role of the respiratory virome, interactions with the microbiome), clinical management, therapy, and prevention.

Dr. Laurence Josset
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. Microorganisms 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 2700 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

  • Respiratory viruses;
  • Metagenomics;
  • Microbiome;
  • Virome;
  • Next-generation sequencing;
  • Respiratory tract infection;
  • Influenza;
  • Respiratory syncytial virus;
  • Epidemiology;
  • Diagnosis;
  • Diversity;
  • Pathogenesis;
  • Treatment;
  • Prevention.

Published Papers (3 papers)

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Research

27 pages, 3455 KiB  
Article
Comparative Transcriptomic and Molecular Pathway Analyses of HL-CZ Human Pro-Monocytic Cells Expressing SARS-CoV-2 Spike S1, S2, NP, NSP15 and NSP16 Genes
by Anshika Sharma, Joe W. Ong, Mun Fai Loke, Eng Guan Chua, Joseph J. Lee, Hyung Won Choi, Yee Joo Tan, Sunil K. Lal and Vincent T. Chow
Microorganisms 2021, 9(6), 1193; https://doi.org/10.3390/microorganisms9061193 - 31 May 2021
Cited by 9 | Viewed by 3689
Abstract
The ongoing COVID-19 pandemic is a clear and present threat to global public health. Research into how the causative SARS-CoV-2 virus together with its individual constituent genes and proteins interact with target host cells can facilitate the development of improved strategies to manage [...] Read more.
The ongoing COVID-19 pandemic is a clear and present threat to global public health. Research into how the causative SARS-CoV-2 virus together with its individual constituent genes and proteins interact with target host cells can facilitate the development of improved strategies to manage the acute and long-term complications of COVID-19. In this study, to better understand the biological roles of critical SARS-CoV-2 proteins, we determined and compared the host transcriptomic responses of the HL-CZ human pro-monocytic cell line upon transfection with key viral genes encoding the spike S1 subunit, S2 subunit, nucleocapsid protein (NP), NSP15 (endoribonuclease), and NSP16 (2′-O-ribose-methyltransferase). RNA sequencing followed by gene set enrichment analysis and other bioinformatics tools revealed that host genes associated with topologically incorrect protein, virus receptor activity, heat shock protein binding, endoplasmic reticulum stress, antigen processing and presentation were up-regulated in the presence of viral spike S1 expression. With spike S2 expression, pro-monocytic genes associated with the interferon-gamma-mediated signaling pathway, regulation of phosphatidylinositol 3-kinase activity, adipocytokine signaling pathway, and insulin signaling pathway were down-regulated, whereas those associated with cytokine-mediated signaling were up-regulated. The expression of NSP15 induced the up-regulation of genes associated with neutrophil degranulation, neutrophil-mediated immunity, oxidative phosphorylation, prion disease, and pathways of neurodegeneration. The expression of NSP16 resulted in the down-regulation of genes associated with S-adenosylmethionine-dependent methyltransferase activity. The expression of NP down-regulated genes associated with positive regulation of neurogenesis, nervous system development, and heart development. Taken together, the complex transcriptomic alterations arising from these viral-host gene interactions offer useful insights into host genes and their pathways that potentially contribute to SARS-CoV-2 pathogenesis. Full article
(This article belongs to the Special Issue Respiratory Viruses in the Age of Metagenomics)
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17 pages, 3485 KiB  
Article
Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses
by Marina Sabatier, Antonin Bal, Grégory Destras, Hadrien Regue, Grégory Quéromès, Valérie Cheynet, Bruno Lina, Claire Bardel, Karen Brengel-Pesce, Vincent Navratil and Laurence Josset
Microorganisms 2020, 8(10), 1539; https://doi.org/10.3390/microorganisms8101539 - 06 Oct 2020
Cited by 11 | Viewed by 5591
Abstract
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods [...] Read more.
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization. Full article
(This article belongs to the Special Issue Respiratory Viruses in the Age of Metagenomics)
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24 pages, 3633 KiB  
Article
Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes
by Hebah A. Al Khatib, Muna A. Al Maslamani, Peter V. Coyle, I. Richard Thompson, Elmoubasher A. Farag, Asmaa A. Al Thani and Hadi M. Yassine
Microorganisms 2020, 8(1), 133; https://doi.org/10.3390/microorganisms8010133 - 17 Jan 2020
Cited by 3 | Viewed by 2847
Abstract
The diversity of RNA viruses dictates their evolution in a particular host, community or environment. Here, we reported within- and between-host pH1N1virus diversity at consensus and sub-consensus levels over a three-year period (2015–2017) and its implications on disease severity. A total of 90 [...] Read more.
The diversity of RNA viruses dictates their evolution in a particular host, community or environment. Here, we reported within- and between-host pH1N1virus diversity at consensus and sub-consensus levels over a three-year period (2015–2017) and its implications on disease severity. A total of 90 nasal samples positive for the pH1N1 virus were deep-sequenced and analyzed to detect low-frequency variants (LFVs) and haplotypes. Parallel evolution of LFVs was seen in the hemagglutinin (HA) gene across three scales: among patients (33%), across years (22%), and at global scale. Remarkably, investigating the emergence of LFVs at the consensus level demonstrated that within-host virus evolution recapitulates evolutionary dynamics seen at the global scale. Analysis of virus diversity at the HA haplotype level revealed the clustering of low-frequency haplotypes from early 2015 with dominant strains of 2016, indicating rapid haplotype evolution. Haplotype sharing was also noticed in all years, strongly suggesting haplotype transmission among patients infected during a specific influenza season. Finally, more than half of patients with severe symptoms harbored a larger number of haplotypes, mostly in patients under the age of five. Therefore, patient age, haplotype diversity, and the presence of certain LFVs should be considered when interpreting illness severity. In addition to its importance in understanding virus evolution, sub-consensus virus diversity together with whole genome sequencing is essential to explain variabilities in clinical outcomes that cannot be explained by either analysis alone. Full article
(This article belongs to the Special Issue Respiratory Viruses in the Age of Metagenomics)
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