Submit to Viruses Review for Viruses Propose a Special Issue

Journal Browser

► Journal Browser

Applications of Next-Generation Sequencing in Virus Discovery

Special Issue Editors
Special Issue Information
Keywords
Published Papers

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

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 40902

Share This Special Issue

Special Issue Editors

Dr. Leyi Wang

E-Mail Website
Guest Editor

1. Department of Veterinary Clinical Medicine, University of Illinois Urbana Champaign (UIUC), Champaign, IL 61820, USA
2. 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
Special Issues, Collections and Topics in MDPI journals

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 Issues, Collections and Topics in MDPI journals

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

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

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

Published Papers (12 papers)

Download All Papers

Research

Jump to: Review, Other

10 pages, 1968 KiB

Open AccessArticle

Divergent Rhabdovirus Discovered in a Patient with New-Onset Nodding Syndrome

by Arthur W. D. Edridge, Gasim Abd-Elfarag, Martin Deijs, Maarten F. Jebbink, Michael Boele van Hensbroek and Lia van der Hoek

Viruses 2022, 14(2), 210; https://0-doi-org.brum.beds.ac.uk/10.3390/v14020210 - 21 Jan 2022

Cited by 7 | Viewed by 2765

Abstract

A divergent rhabdovirus was discovered in the bloodstream of a 15-year-old girl with Nodding syndrome from Mundri West County in South Sudan. Nodding syndrome is a progressive degenerative neuropathy of unknown cause affecting thousands of individuals in Sub-Saharan Africa. The index case was previously healthy until she developed head-nodding seizures four months prior to presentation. Virus discovery by VIDISCA-NGS on the patient’s plasma detected multiple sequence reads belonging to a divergent rhabdovirus. The viral load was 3.85 × 10³ copies/mL in the patient’s plasma and undetectable in her cerebrospinal fluid. Further genome walking allowed for the characterization of full coding sequences of all the viral proteins (N, P, M, U1, U2, G, U3, and L). We tentatively named the virus “Mundri virus” (MUNV) and classified it as a novel virus species based on the high divergence from other known viruses (all proteins had less than 43% amino acid identity). Phylogenetic analysis revealed that MUNV forms a monophyletic clade with several human-infecting tibroviruses prevalent in Central Africa. A bioinformatic machine-learning algorithm predicted MUNV to be an arbovirus (bagged prediction strength (BPS) of 0.9) transmitted by midges (BPS 0.4) with an artiodactyl host reservoir (BPS 0.9). An association between MUNV infection and Nodding syndrome was evaluated in a case–control study of 72 patients with Nodding syndrome (including the index case) matched to 65 healthy households and 48 community controls. No subject, besides the index case, was positive for MUNV RNA in their plasma. A serological assay detecting MUNV anti-nucleocapsid found, respectively, in 28%, 22%, and 16% of cases, household controls and community controls to be seropositive with no significant differences between cases and either control group. This suggests that MUNV commonly infects children in South Sudan yet may not be causally associated with Nodding syndrome. Full article

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)

► Show Figures

Figure 1

21 pages, 1821 KiB

Open AccessArticle

Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome

by Alba Folgueiras-González, Robin van den Braak, Martin Deijs, Wikke Kuller, Steven Sietsma, Valentijn Thuring, Lia van der Hoek and Ad de Groof

Viruses 2021, 13(12), 2538; https://0-doi-org.brum.beds.ac.uk/10.3390/v13122538 - 17 Dec 2021

Cited by 4 | Viewed by 2788

Abstract

A commercial pig farm with no history of porcine circovirus 2 (PCV2) or porcine reproductive and respiratory syndrome virus (PRRSV) repeatedly reported a significant reduction in body weight gain and wasting symptoms in approximately 20–30% of the pigs in the period between three and six weeks after weaning. As standard clinical interventions failed to tackle symptomatology, viral metagenomics were used to describe and monitor the enteric virome at birth, 3 weeks, 4 weeks, 6 weeks, and 9 weeks of age. The latter four sampling points were 7 days, 3 weeks, and 6 weeks post weaning, respectively. Fourteen distinct enteric viruses were identified within the herd, which all have previously been linked to enteric diseases. Here we show that wasting is associated with alterations in the enteric virome of the pigs, characterized by: (1) the presence of enterovirus G at 3 weeks of age, followed by a higher prevalence of the virus in wasting pigs at 6 weeks after weaning; (2) rotaviruses at 3 weeks of age; and (3) porcine sapovirus one week after weaning. However, the data do not provide a causal link between specific viral infections and the postweaning clinical problems on the farm. Together, our results offer evidence that disturbances in the enteric virome at the preweaning stage and early after weaning have a determining role in the development of intestinal barrier dysfunctions and nutrient uptake in the postweaning growth phase. Moreover, we show that the enteric viral load sharply increases in the week after weaning in both healthy and wasting pigs. This study is also the first to report the dynamics and co-infection of porcine rotavirus species and porcine astrovirus genetic lineages during the first 9 weeks of the life of domestic pigs. Full article

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)

► Show Figures

Figure 1

23 pages, 3004 KiB

Open AccessArticle

Emergence of a Distinct Picobirnavirus Genotype Circulating in Patients Hospitalized with Acute Respiratory Illness

by Michael G. Berg, Kenn Forberg, Lester J. Perez, Ka-Cheung Luk, Todd V. Meyer and Gavin A. Cloherty

Viruses 2021, 13(12), 2534; https://0-doi-org.brum.beds.ac.uk/10.3390/v13122534 - 17 Dec 2021

Cited by 5 | Viewed by 4131

Abstract

Picobirnaviruses (PBV) are found in a wide range of hosts and typically associated with gastrointestinal infections in immunocompromised individuals. Here, a divergent PBV genome was assembled from a patient hospitalized for acute respiratory illness (ARI) in Colombia. The RdRp protein branched with sequences previously reported in patients with ARI from Cambodia and China. Sputa from hospitalized individuals (n = 130) were screened by RT-qPCR which enabled detection and subsequent metagenomic characterization of 25 additional PBV infections circulating in Colombia and the US. Phylogenetic analysis of RdRp highlighted the emergence of two dominant lineages linked to the index case and Asian strains, which together clustered as a distinct genotype. Bayesian inference further established capsid and RdRp sequences as both significantly associated with ARI. Various respiratory-tropic pathogens were detected in PBV+ patients, yet no specific bacteria was common among them and four individuals lacked co-infections, suggesting PBV may not be a prokaryotic virus nor exclusively opportunistic, respectively. Competing models for the origin and transmission of this PBV genotype are presented that attempt to reconcile vectoring by a bacterial host with human pathogenicity. A high prevalence in patients with ARI, an ability to reassort, and demonstrated global spread indicate PBV warrant greater public health concern. Full article

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)

► Show Figures

Figure 1

12 pages, 2698 KiB

Open AccessArticle

Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis

by Endrya do Socorro Fôro Ramos, Geovani de Oliveira Ribeiro, Fabiola Villanova, Flávio Augusto de Padua Milagres, Rafael Brustulin, Emerson Luiz Lima Araújo, Ramendra Pati Pandey, V. Samuel Raj, Xutao Deng, Eric Delwart, Adriana Luchs, Antonio Charlys da Costa and Élcio Leal

Viruses 2021, 13(12), 2365; https://0-doi-org.brum.beds.ac.uk/10.3390/v13122365 - 25 Nov 2021

Cited by 6 | Viewed by 2587

Abstract

Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples. Full article

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)

► Show Figures

Figure 1

21 pages, 4314 KiB

Open AccessArticle

Virome Analysis of Signal Crayfish (Pacifastacus leniusculus) along Its Invasion Range Reveals Diverse and Divergent RNA Viruses

by Katarina Bačnik, Denis Kutnjak, Silvija Černi, Ana Bielen and Sandra Hudina

Viruses 2021, 13(11), 2259; https://0-doi-org.brum.beds.ac.uk/10.3390/v13112259 - 11 Nov 2021

Cited by 5 | Viewed by 2300

Abstract

Crayfish are a keystone species of freshwater ecosystems and a successful invasive species. However, their pathogens, including viruses, remain understudied. The aim of this study was to analyze the virome of the invasive signal crayfish (Pacifastacus leniusculus) and to elucidate the potential differences in viral composition and abundance along its invasion range in the Korana River, Croatia. By the high-throughput sequencing of ribosomal RNA, depleted total RNA isolated from the crayfish hepatopancreas, and subsequent sequence data analysis, we identified novel and divergent RNA viruses, including signal crayfish-associated reo-like, hepe-like, toti-like, and picorna-like viruses, phylogenetically related to viruses previously associated with crustacean hosts. The patterns of reads abundance and calculated nucleotide diversities of the detected viral sequences varied along the invasion range. This could indicate the possible influence of different factors and processes on signal crayfish virome composition: e.g., the differences in signal crayfish population density, the non-random dispersal of host individuals from the core to the invasion fronts, and the transfer of viruses from the native co-occurring and phylogenetically related crayfish species. The study reveals a high, previously undiscovered diversity of divergent RNA viruses associated with signal crayfish, and sets foundations for understanding the potential risk of virus transmissions as a result of this invader’s dispersal. Full article

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)

► Show Figures

Figure 1

16 pages, 3440 KiB

Open AccessArticle

Discovery and Genetic Characterization of Novel Paramyxoviruses Related to the Genus Henipavirus in Crocidura Species in the Republic of Korea

by Seung-Ho Lee, Kijin Kim, Jongwoo Kim, Jin Sun No, Kyungmin Park, Shailesh Budhathoki, Seung Ho Lee, Jingyeong Lee, Seung Hye Cho, Seungchan Cho, Geum-Young Lee, Jusun Hwang, Heung-Chul Kim, Terry A. Klein, Chang-Sub Uhm, Won-Keun Kim and Jin-Won Song

Viruses 2021, 13(10), 2020; https://0-doi-org.brum.beds.ac.uk/10.3390/v13102020 - 07 Oct 2021

Cited by 21 | Viewed by 4779

Abstract

Paramyxoviruses, negative-sense single-stranded RNA viruses, pose a critical threat to human public health. Currently, 78 species, 17 genera, and 4 subfamilies of paramyxoviruses are harbored by multiple natural reservoirs, including rodents, bats, birds, reptiles, and fish. Henipaviruses are critical zoonotic pathogens that cause severe acute respiratory distress and neurological diseases in humans. Using reverse transcription-polymerase chain reaction, 115 Crocidura species individuals were examined for the prevalence of paramyxovirus infections. Paramyxovirus RNA was observed in 26 (22.6%) shrews collected at five trapping sites, Republic of Korea. Herein, we report two genetically distinct novel paramyxoviruses (genus: Henipavirus): Gamak virus (GAKV) and Daeryong virus (DARV) isolated from C. lasiura and C. shantungensis, respectively. Two GAKVs and one DARV were nearly completely sequenced using next-generation sequencing. GAKV and DARV contain six genes (3′-N-P-M-F-G-L-5′) with genome sizes of 18,460 nucleotides and 19,471 nucleotides, respectively. The phylogenetic inference demonstrated that GAKV and DARV form independent genetic lineages of Henipavirus in Crocidura species. GAKV-infected human lung epithelial cells elicited the induction of type I/III interferons, interferon-stimulated genes, and proinflammatory cytokines. In conclusion, this study contributes further understandings of the molecular prevalence, genetic characteristics and diversity, and zoonotic potential of novel paramyxoviruses in shrews. Full article

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)

► Show Figures

Figure 1

11 pages, 3811 KiB

Open AccessArticle

Next-Generation Sequencing Reveals Four Novel Viruses Associated with Calf Diarrhea

by Qi Wu, Jizong Li, Wei Wang, Jinzhu Zhou, Dandan Wang, Baochao Fan, Xuehan Zhang, Dongbo Sun, Ga Gong, Sizhu Suolang and Bin Li

Viruses 2021, 13(10), 1907; https://0-doi-org.brum.beds.ac.uk/10.3390/v13101907 - 23 Sep 2021

Cited by 11 | Viewed by 2517

Abstract

Calf diarrhea is one of the common diseases involved in the process of calf feeding. In this study, a sample of calf diarrhea that tested positive for bovine coronavirus and bovine astrovirus was subjected to high-throughput sequencing. The reassembly revealed the complete genomes of bovine norovirus, bovine astrovirus, bovine kobuvirus, and the S gene of bovine coronavirus. Phylogenetic analysis showed that the ORF2 region of bovine astrovirus had the lowest similarity with other strains and gathered in the Mamastrovirus unclassified genogroup, suggesting a new serotype/genotype could appear. Compared with the most closely related strain, there are six amino acid mutation sites in the S gene of bovine coronavirus, most of which are located in the S1 subunit region. The bovine norovirus identified in our study was BNoV-GIII 2, based on the VP1 sequences. The bovine kobuvirus is distributed in the Aichi virus B genus; the P1 gene shows as highly variable, while the 3D gene is highly conserved. These findings enriched our knowledge of the viruses in the role of calf diarrhea, and help to develop an effective strategy for disease prevention and control. Full article

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)

► Show Figures

Figure 1

21 pages, 2950 KiB

Open AccessArticle

Exploring the Cause of Diarrhoea and Poor Growth in 8–11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing

by Tarka Raj Bhatta, Anthony Chamings and Soren Alexandersen

Viruses 2021, 13(8), 1608; https://0-doi-org.brum.beds.ac.uk/10.3390/v13081608 - 13 Aug 2021

Cited by 6 | Viewed by 3173

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 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)

► Show Figures

Figure 1

19 pages, 3322 KiB

Open AccessArticle

Whole-Genome Sequence Analysis of Pseudorabies Virus Clinical Isolates from Pigs in China between 2012 and 2017 in China

by Ruiming Hu, Leyi Wang, Qingyun Liu, Lin Hua, Xi Huang, Yue Zhang, Jie Fan, Hongjian Chen, Wenbo Song, Wan Liang, Nengshui Ding, Zuohua Li, Zhen Ding, Xibiao Tang, Zhong Peng and Bin Wu

Viruses 2021, 13(7), 1322; https://0-doi-org.brum.beds.ac.uk/10.3390/v13071322 - 08 Jul 2021

Cited by 10 | Viewed by 4888

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 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)

► Show Figures

Figure 1

7 pages, 2982 KiB

Open AccessCommunication

Variable Populations of Grapevine Virus T Are Present in Vineyards of Hungary

by Emese Demian, Aliz Holczbauer, Zsuzsanna Nagyne Galbacs, Nikoletta Jaksa-Czotter, Mihaly Turcsan, Robert Olah and Eva Varallyay

Viruses 2021, 13(6), 1119; https://0-doi-org.brum.beds.ac.uk/10.3390/v13061119 - 10 Jun 2021

Cited by 4 | Viewed by 2560

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 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)

► Show Figures

Graphical abstract

Review

Jump to: Research, Other

23 pages, 2186 KiB

Open AccessReview

Next-Generation Sequencing for Confronting Virus Pandemics

by Josep Quer, Sergi Colomer-Castell, Carolina Campos, Cristina Andrés, Maria Piñana, Maria Francesca Cortese, Alejandra González-Sánchez, Damir Garcia-Cehic, Marta Ibáñez, Tomàs Pumarola, Francisco Rodríguez-Frías, Andrés Antón and David Tabernero

Viruses 2022, 14(3), 600; https://0-doi-org.brum.beds.ac.uk/10.3390/v14030600 - 14 Mar 2022

Cited by 21 | Viewed by 4393

Abstract

Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission. Full article

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)

► Show Figures

Figure 1

Other

Jump to: Research, Review

8 pages, 309 KiB

Open AccessBrief Report

Metagenomic Analysis Reveals High Abundance of Torque Teno Mini Virus in the Respiratory Tract of Children with Acute Respiratory Illness

by Antonin Bal, Gregory Destras, Marina Sabatier, Maxime Pichon, Hadrien Regue, Guy Oriol, Yves Gillet, Bruno Lina, Karen Brengel-Pesce, Laurence Josset and Florence Morfin

Viruses 2022, 14(5), 955; https://0-doi-org.brum.beds.ac.uk/10.3390/v14050955 - 03 May 2022

Cited by 5 | Viewed by 1845

Abstract

Human Anelloviridae is a highly prevalent viral family, including three main genera—Alphatorquevirus (Torque teno virus, TTV), Betatorquevirus (Torque teno mini virus, TTMV), and Gammatorquevirus (Torque teno midi virus, TTMDV). To date, the characterization of Anelloviridae in the respiratory tract of children with acute respiratory infection (ARI) has been poorly reported and mainly focused on TTV. We performed a metagenomic analysis of eight respiratory samples collected from children with an ARI of unknown etiology (eight samples tested negative with a multiplex PCR assay, out of the 39 samples initially selected based on negative routine diagnostic testing). A total of 19 pediatric respiratory samples that tested positive for respiratory syncytial virus (RSV, n = 13) or influenza virus (n = 6) were also sequenced. Anelloviridae reads were detected in 16/27 samples, including 6/8 negative samples, 7/13 RSV samples and 3/6 influenza samples. For samples with a detection of at least one Anelloviridae genus, TTMV represented 87.1 (66.1–99.2)% of Anelloviridae reads, while TTV and TTMDV represented 0.8 (0.0–9.6)% and 0.7 (0.0–7.1)%, respectively (p < 0.001). Our findings highlight a high prevalence of TTMV in respiratory samples of children with an ARI of unknown etiology, as well as in samples with an RSV or influenza infection. Larger studies are needed to explore the role of TTMV in childhood respiratory diseases. Full article

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Applications of Next-Generation Sequencing in Virus Discovery

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Published Papers (12 papers)

Research

Review

Other

Further Information

Guidelines

MDPI Initiatives

Follow MDPI