Special Issue "Applications of Next-Generation Sequencing in Virus Discovery"

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

Deadline for manuscript submissions: 30 November 2021.

Special Issue Editors

Dr. Leyi Wang
E-Mail Website
Guest Editor
Department of Veterinary Clinical Medicine, University of Illinois Urbana Champaign (UIUC), Champaign, IL 61820, USA;
Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois Urbana Champaign (UIUC), Champaign, IL 61820, USA
Interests: animal viruses; coronavirus; picornavirus, influenza; diagnosis; new virus discovery; vaccine development
Dr. Ganwu Li
E-Mail Website
Guest Editor
Vet Diagnostic & Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA 50011, USA
Interests: New virus discovery; emerging and re-emerging infectious diseases; genomic epidemiology; molecular pathogenesis

Special Issue Information

Dear Colleagues,

In 2005, the emergence of next-generation sequencing (NGS) technology is mainly due to disadvantages of conventional Sanger sequencing method, including low throughput, labor intensive, time consuming, and high cost. Since then, NGS has tremendously transformed the biomedical field and advanced diagnostic-related investigations to the next level. There are three categories of applications including DNA sequencing, RNA sequencing, and protein sequencing. DNA sequencing consists of metagenomics sequencing, targeted genome sequencing, and whole genome sequencing; RNA sequencing has small RNA profiling and transcriptome sequencing; and protein sequencing includes ribosome profiling, CHIP-Seq, and DNA methelation sequencing. In the clinical microbiology field, NGS is commonly used.

Today, in addition to its routine application by public health officials for case investigations of food-borne bacteria, NGS has been frequently used to identify emerging and reemerging viral pathogens causing infectious diseases in human and animals. There are several viruses identified using NGS, including influenza D virus, porcine circovrius 3, porcine pegivirus, sparrow deltacoronavirus, and porcine nordavirus. NGS has also been successfully applied to the identification of viral variants, including PRRSV recombinants evolved from the wild type, and vaccine strains and PEDV variant with large deletion in the spike gene. In addition, viral gene sequencing is often used to study molecular epidemiology and/or the genetic relatedness of different viral strains. Compared to single and/or several gene(s) sequencing, whole genome sequencing of viruses is able to provide more comprehensive evidence reflecting viral evolution and differentiating viral strains.

In this issue, we would like to cover the applications of NGS for the discovery of new and reemerging viruses, the identification of new viral variants, and also for the better characterization of existing viruses.

Dr. Leyi Wang
Dr. Ganwu Li
Guest Editors

Manuscript Submission Information

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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 2200 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

  • Next-generation sequencing
  • Virus discovery
  • Emerging virus
  • Remerging virus
  • human virus
  • animal virus

Published Papers (3 papers)

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Research

Article
Exploring the Cause of Diarrhoea and Poor Growth in 8–11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing
Viruses 2021, 13(8), 1608; https://doi.org/10.3390/v13081608 - 13 Aug 2021
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Abstract
Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses [...] Read more.
Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth. Full article
(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)
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Article
Whole-Genome Sequence Analysis of Pseudorabies Virus Clinical Isolates from Pigs in China between 2012 and 2017 in China
Viruses 2021, 13(7), 1322; https://doi.org/10.3390/v13071322 - 08 Jul 2021
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Abstract
Pseudorabies virus (PRV) is an economically significant swine infectious agent. A PRV outbreak took place in China in 2011 with novel virulent variants. Although the association of viral genomic variability with pathogenicity is not fully confirmed, the knowledge concerning PRV genomic diversity and [...] Read more.
Pseudorabies virus (PRV) is an economically significant swine infectious agent. A PRV outbreak took place in China in 2011 with novel virulent variants. Although the association of viral genomic variability with pathogenicity is not fully confirmed, the knowledge concerning PRV genomic diversity and evolution is still limited. Here, we sequenced 54 genomes of novel PRV variants isolated in China from 2012 to 2017. Phylogenetic analysis revealed that China strains and US/Europe strains were classified into two separate genotypes. PRV strains isolated from 2012 to 2017 in China are highly related to each other and genetically close to classic China strains such as Ea, Fa, and SC. RDP analysis revealed 23 recombination events within novel PRV variants, indicating that recombination contributes significantly to the viral evolution. The selection pressure analysis indicated that most ORFs were under evolutionary constraint, and 19 amino acid residue sites in 15 ORFs were identified under positive selection. Additionally, 37 unique mutations were identified in 19 ORFs, which distinguish the novel variants from classic strains. Overall, our study suggested that novel PRV variants might evolve from classical PRV strains through point mutation and recombination mechanisms. Full article
(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)
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Communication
Variable Populations of Grapevine Virus T Are Present in Vineyards of Hungary
Viruses 2021, 13(6), 1119; https://doi.org/10.3390/v13061119 - 10 Jun 2021
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Abstract
Grapevine virus T (GVT) is a recently described foveavirus, which was identified from a transcriptome of a Teroldego grapevine cultivar in 2017. Recently, we surveyed vineyards and rootstock plantations in Hungary using small RNA (sRNA) high-throughput sequencing (HTS), at a time when GVT [...] Read more.
Grapevine virus T (GVT) is a recently described foveavirus, which was identified from a transcriptome of a Teroldego grapevine cultivar in 2017. Recently, we surveyed vineyards and rootstock plantations in Hungary using small RNA (sRNA) high-throughput sequencing (HTS), at a time when GVT had not yet been described. A re-analysis of our sRNA HTS datasets and a survey of grapevines by RT-PCR revealed the presence of GVT in most of the vineyards tested, while at rootstock fields its presence was very rare. The presence and high variability of the virus in the country was confirmed by sequence analysis of strains originating from different vineyards. In this study, we demonstrate the presence of GVT in Hungary and show its high diversity, suggesting that GVT presence may not seriously affect grapevine health and that it could have been present in European vineyards for a long time as a latent infection. Full article
(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)
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