Viral Genomics: Elucidating Virology in a Metagenomic World

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

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 16119

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The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
Interests: virus evolution; virus ecology
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
Interests: viral metagenomics; coinfections; evolution; cross-species spillover of viruses
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Lawrence Livermore National Laboratory, Livermore, CA, USA
Interests: metagenomics; viromics; stable isotope probing; environmental sciences; biogeochemsitry

Special Issue Information

Dear Colleagues,

Viruses are one of the most prolific entities on earth, yet it has only been with the advent of modern molecular technologies and tools that we have begun to unearth the true breadth of viral diversity present. Recent advancements in high throughput methodology and sequencing have enabled characterization of viruses across each nucleic acid type and in many of their forms, such as proviruses, virions, and extracellular nucleic acid. These advancements have identified novel viruses and obtained full genomes leading to a new paradigm, where viral genomes are used to investigate viral diversity, molecular dynamics, evolution, and ecology, greatly expanding the known virosphere. To buttress these efforts, other technologies, such as stable isotope probing and bioorthogonal noncanonical amino acid tagging, can be used to provide increased resolution on viruses, revealing their activity and replication efficiency. This special issue aims to cover recent developments in understanding viral genetic diversity, evolution, and ecology using ‘omic approaches to analyze viral genomes.

Assoc. Prof. Arvind Varsani
Dr. Simona J. Kraberger
Dr. Gareth Trubl
Guest Editors

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Keywords

  • RNA virus
  • DNA virus
  • meta-omics
  • genome organisation
  • viral genetics
  • molecular evolution
  • viral ecology

Published Papers (4 papers)

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Research

12 pages, 1075 KiB  
Article
First Detection of Bat Astroviruses (BtAstVs) among Bats in Poland: The Genetic BtAstVs Diversity Reveals Multiple Co-Infection of Bats with Different Strains
by Anna Orłowska, Marcin Smreczak, Patrycja Potyrało, Arkadiusz Bomba, Paweł Trębas and Jerzy Rola
Viruses 2021, 13(2), 158; https://doi.org/10.3390/v13020158 - 22 Jan 2021
Cited by 5 | Viewed by 2222
Abstract
Background: Astroviruses (AstVs) are common pathogens of a wide range of animal hosts, including mammals and avians, causing gastrointestinal diseases, mainly gastroenteritis and diarrhea. They prompt a significant health problem in newborns and young children and economic losses in the poultry sector and [...] Read more.
Background: Astroviruses (AstVs) are common pathogens of a wide range of animal hosts, including mammals and avians, causing gastrointestinal diseases, mainly gastroenteritis and diarrhea. They prompt a significant health problem in newborns and young children and economic losses in the poultry sector and mink farms. Recent studies revealed a growing number of bat species carrying astroviruses with a noticeable prevalence and diversity. Here, we demonstrate the first detection of bat astroviruses (BtAstVs) circulating in the population of insectivorous bats in the territory of Poland. Results: Genetically diverse BtAstVs (n = 18) were found with a varying degree of bat species specificity in five out of 15 bat species in Poland previously recognized as BtAstV hosts. Astroviral RNA was found in 12 out of 98 (12.2%, 95% CI 7.1–20.2) bat intestines, six bat kidneys (6.1%, 95% CI 2.8–12.7) and two bat livers (2.0%, 95% CI 0.4–7.1). Deep sequencing of the astroviral RNA-dependent RNA polymerase (RdRp) region revealed co-infections in five single bat individuals with highly distinct astrovirus strains. Conclusions: The detection of highly distinct bat astroviruses in Polish bats favors virus recombination and the generation of novel divergent AstVs and creates a potential risk of virus transmission to domestic animals and humans in the country. These findings provide a new insight into molecular epidemiology, prevalence of astroviruses in European bat populations and the risk of interspecies transmission to other animals including humans. Full article
(This article belongs to the Special Issue Viral Genomics: Elucidating Virology in a Metagenomic World)
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14 pages, 1342 KiB  
Article
Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples
by Leonard Schuele, Hayley Cassidy, Erley Lizarazo, Katrin Strutzberg-Minder, Sabine Schuetze, Sandra Loebert, Claudia Lambrecht, Juergen Harlizius, Alex W. Friedrich, Silke Peter, Hubert G. M. Niesters, John W. A. Rossen and Natacha Couto
Viruses 2020, 12(12), 1358; https://doi.org/10.3390/v12121358 - 27 Nov 2020
Cited by 12 | Viewed by 5364
Abstract
Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed [...] Read more.
Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative. Full article
(This article belongs to the Special Issue Viral Genomics: Elucidating Virology in a Metagenomic World)
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9 pages, 355 KiB  
Article
Novel Circoviruses Detected in Feces of Sonoran Felids
by Natalie Payne, Simona Kraberger, Rafaela S Fontenele, Kara Schmidlin, Melissa H Bergeman, Ivonne Cassaigne, Melanie Culver, Arvind Varsani and Koenraad Van Doorslaer
Viruses 2020, 12(9), 1027; https://doi.org/10.3390/v12091027 - 15 Sep 2020
Cited by 13 | Viewed by 3226
Abstract
Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small [...] Read more.
Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small felid populations with lower genetic diversity are likely to be most threatened with extinction by emerging diseases, as with other selective pressures, due to having less adaptive potential. We used a metagenomic approach to identify novel circoviruses, which may have a negative impact on the population viability, from confirmed bobcat (Lynx rufus) and puma (Puma concolor) scats collected in Sonora, Mexico. Given some circoviruses are known to cause disease in their hosts, such as porcine and avian circoviruses, we took a non-invasive approach using scat to identify circoviruses in free-roaming bobcats and puma. Three circovirus genomes were determined, and, based on the current species demarcation, they represent two novel species. Phylogenetic analyses reveal that one circovirus species is more closely related to rodent associated circoviruses and the other to bat associated circoviruses, sharing highest genome-wide pairwise identity of approximately 70% and 63%, respectively. At this time, it is unknown whether these scat-derived circoviruses infect felids, their prey, or another organism that might have had contact with the scat in the environment. Further studies should be conducted to elucidate the host of these viruses and assess health impacts in felids. Full article
(This article belongs to the Special Issue Viral Genomics: Elucidating Virology in a Metagenomic World)
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10 pages, 1467 KiB  
Communication
High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics
by Silvia I. Sardi, Rejane H. Carvalho, Luis G. C. Pacheco, João P. P. d. Almeida, Emilia M. M. d. A. Belitardo, Carina S. Pinheiro, Gúbio S. Campos and Eric R. G. R. Aguiar
Viruses 2020, 12(7), 782; https://doi.org/10.3390/v12070782 - 21 Jul 2020
Cited by 4 | Viewed by 4444
Abstract
Arboviruses, including the Zika virus, have recently emerged as one of the most important threats to human health. The use of metagenomics-based approaches has already proven valuable to aid surveillance of arboviral infections, and the ability to reconstruct complete viral genomes from [...] Read more.
Arboviruses, including the Zika virus, have recently emerged as one of the most important threats to human health. The use of metagenomics-based approaches has already proven valuable to aid surveillance of arboviral infections, and the ability to reconstruct complete viral genomes from metatranscriptomics data is key to the development of new control strategies for these diseases. Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5′-UTR and 3′-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification. Full article
(This article belongs to the Special Issue Viral Genomics: Elucidating Virology in a Metagenomic World)
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