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Microorganisms
Special Issues
Viral Metagenomic Analysis in Animals
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Viral Metagenomic Analysis in Animals

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

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 17234

Special Issue Editors

Prof. Dr. Cornel Fraefel

E-Mail Website
Guest Editor
Institute of Virology, University of Zurich, 8057 Zurich, Switzerland
Interests: herpes viruses; parvo viruses; virus-virus and virus-host interactions; zoonoses; molecular virology; virome analyses
Dr. Jakub Kubacki

E-Mail Website
Co-Guest Editor
Institute of Virology, University of Zurich, 8057 Zurich, Switzerland
Interests: emerging infectious diseases; metagenomic analysis; Next Generation Sequencing; virus discovery; diseases vectors and reservoirs

Special Issue Information

Dear Colleagues,

At an estimated number of 1031 particles, viruses are the most abundant biological entities on Earth. It is assumed that several hundred thousand different viruses exist, but the vast majority of them are yet to be discovered and characterized. The development of next-generation sequencing and bioinformatics pipelines has recently supported the unbiased hypothesis-free detection of viruses and understanding of entire viral communities. However, while the viromes of various samples, species, and diseases have been investigated, the effect of the virome composition on health and disease remains largely elusive.

This Special Issue of Microorganisms aims to present viral metagenomic approaches to characterize viral communities in companion animals, livestock and wildlife, as well as bioinformatics pipelines for viral population analyses.

As Guest Editors of this Special Issue, “Viral Metagenomic Analysis in Animals”, we invite you to submit research articles, review articles, and short communications related to these topics.

Prof. Dr. Cornel Fraefel
Guest Editor
Dr. Jakub Kubacki
Co-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

  • virome
  • viral metagenomic
  • viral community
  • next generation sequencing
  • emerging viruses
  • reservoir
  • livestock
  • wildlife

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Published Papers (4 papers)

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Research

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10 pages, 960 KiB  
Article
An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology
by Hon S. Ip, Sarah Uhm, Mary Lea Killian and Mia K. Torchetti
Microorganisms 2023, 11(2), 529; https://doi.org/10.3390/microorganisms11020529 - 19 Feb 2023
Cited by 8 | Viewed by 4993
Abstract
As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian [...] Read more.
As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken. Full article
(This article belongs to the Special Issue Viral Metagenomic Analysis in Animals)
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23 pages, 5966 KiB  
Article
Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck’s Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family
by Alina Matsvay, Marina Dyachkova, Anna Sai, Valentina Burskaia, Ilya Artyushin and German Shipulin
Microorganisms 2022, 10(8), 1540; https://doi.org/10.3390/microorganisms10081540 - 29 Jul 2022
Cited by 4 | Viewed by 2547
Abstract
Caliciviridae is a family of viral pathogens that naturally infects vertebrates, including humans, and causes a range of highly contagious infectious diseases. Caliciviruses are not well studied because of the lack of a universal approach to their cultivation; however, the development of molecular [...] Read more.
Caliciviridae is a family of viral pathogens that naturally infects vertebrates, including humans, and causes a range of highly contagious infectious diseases. Caliciviruses are not well studied because of the lack of a universal approach to their cultivation; however, the development of molecular genetics and bioinformatics methods can shed light on their genetic architecture and evolutionary relationships. Here, we present and characterize the complete genome sequence of calicivirus isolated from a sandpiper—Temminck’s stint (Calidris temminckii), preliminarily named Temminck’s stint calicivirus (TsCV). Its genome is a linear, non-segmented, single-stranded (+sense) RNA with genome organization typical of avian caliciviruses. Comparative studies have shown significant divergence of the nucleotide sequence of the TsCV genome, as well as the amino acid sequence of the major capsid protein from all publicly available genomic and protein sequences, with the highest genome sequence similarity to unclassified Ruddy turnstone calicivirus A (43.68%) and the lowest pairwise divergence of the major capsid protein with unclassified goose calicivirus (57.44%). Phylogenetic analysis, as well as a comparative analysis of the homologous proteins, showed evidence of another separate genus within the Caliciviridae family—previously proposed, but not yet accepted by International Committee on Taxonomy of Viruses (ICTV)—the Sanovirus genus, which combines seven previously unclassified genomic sequences of avian caliciviruses, including the newly discovered TsCV, which we propose to consider as a separate species. Full article
(This article belongs to the Special Issue Viral Metagenomic Analysis in Animals)
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17 pages, 13160 KiB  
Article
Differential Viral Genome Diversity of Healthy and RSS-Affected Broiler Flocks
by Jakub Kubacki, Weihong Qi and Cornel Fraefel
Microorganisms 2022, 10(6), 1092; https://doi.org/10.3390/microorganisms10061092 - 25 May 2022
Cited by 11 | Viewed by 2533
Abstract
The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. [...] Read more.
The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. To determine the difference in the virome of healthy and diseased broilers, samples from 11 healthy and 17 affected broiler flocks were collected at two time points and analyzed by Next-Generation Sequencing. Virus genomes of Parvoviridae, Astroviridae, Picornaviridae, Caliciviridae, Reoviridae, Adenoviridae, Coronaviridae, and Smacoviridae were identified at various days of poultry production. De novo sequence analysis revealed 288 full or partial avian virus genomes, of which 97 belonged to the novel genus Chaphamaparvovirus. This study expands the knowledge of the diversity of enteric viruses in healthy and RSS-affected broiler flocks and questions the association of some viruses with the diseases. Full article
(This article belongs to the Special Issue Viral Metagenomic Analysis in Animals)
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Review

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19 pages, 2133 KiB  
Review
Phylogenetic Diversity of Animal Oral and Gastrointestinal Viromes Useful in Surveillance of Zoonoses
by Anthony Michael Esposito, Michelle Marie Esposito and Albert Ptashnik
Microorganisms 2022, 10(9), 1815; https://doi.org/10.3390/microorganisms10091815 - 10 Sep 2022
Cited by 7 | Viewed by 5163
Abstract
Great emphasis has been placed on bacterial microbiomes in human and animal systems. In recent years, advances in metagenomics have allowed for the detection and characterization of more and more native viral particles also residing in these organisms. The digestive tracts of animals [...] Read more.
Great emphasis has been placed on bacterial microbiomes in human and animal systems. In recent years, advances in metagenomics have allowed for the detection and characterization of more and more native viral particles also residing in these organisms. The digestive tracts of animals and humans—from the oral cavity, to the gut, to fecal excretions—have become one such area of interest. Next-generation sequencing and bioinformatic analyses have uncovered vast phylogenetic virome diversity in companion animals, such as dogs and cats, as well as farm animals and wildlife such as bats. Zoonotic and arthropod-borne illnesses remain major causes of worldwide outbreaks, as demonstrated by the devastating COVID-19 pandemic. This highlights the increasing need to identify and study animal viromes to prevent such disastrous cross-species transmission outbreaks in the coming years. Novel viruses have been uncovered in the viromes of multiple organisms, including birds, bats, cats, and dogs. Although the exact consequences for public health have not yet become clear, many analyses have revealed viromes dominated by RNA viruses, which can be the most problematic to human health, as these genomes are known for their high mutation rates and immune system evasion capabilities. Furthermore, in the wake of worldwide disruption from the COVID-19 pandemic, it is evident that proper surveillance of viral biodiversity is crucial. For instance, gut viral metagenomic analysis in dogs has shown close relationships between the highly abundant canine coronavirus and human coronavirus strains 229E and NL63. Future studies and vigilance could potentially save many lives. Full article
(This article belongs to the Special Issue Viral Metagenomic Analysis in Animals)
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