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Viruses
Special Issues
Animal Virus Discovery and Genetic Diversity
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Animal Virus Discovery and Genetic Diversity

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

Deadline for manuscript submissions: 30 November 2024 | Viewed by 4627

Special Issue Editor

Dr. Ryan Troyer

E-Mail Website
Guest Editor
Department of Microbiology & Immunology, University of Western Ontario, London, ON, Canada
Interests: viral genetic diversity and evolution; virus discovery; zoonotic and emerging viruses; mucosal immunity and respiratory viruses; vaccines

Special Issue Information

Dear Colleagues,

Viruses are the most abundant and diverse biological entities on earth. Recent advances in metagenomic sequencing have ushered in a “golden age” of virus discovery, vastly expanding our understanding of the global virome. Yet the majority of investigations into animal virus diversity have focused on relatively few animal species and it is likely that the vast majority of viral diversity in animals remains uncharacterized. Viral genetic diversity exerts great practical importance by facilitating adaptation to new hosts and environments as well as the evasion of host immune responses and anti-viral therapeutics. Recently, the COVID-19 pandemic has also bluntly highlighted that certain viruses within the spectrum of animal virus diversity can have massive importance as zoonotic agents. For this Special Issue, we invite the submission of original research and review articles that investigate the importance of animal virus genetic diversity at all levels: in individual hosts, within populations, and within ecosystems. Also welcome are articles that identify and characterize novel animal viruses of potential importance.  

Dr. Ryan Troyer
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. 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

  • animal virus
  • evolution
  • genetic
  • diversity
  • richness
  • emerging viruses
  • virome
  • metagenomics
  • ecology
  • cross-species transmission
  • zoonotic

Published Papers (6 papers)

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Research

15 pages, 1865 KiB  
Article
A Novel Mastadenovirus from Nyctalus noctula which Represents a Distinct Evolutionary Branch of Viruses from Bats in Europe
by Anna S. Speranskaya, Alexander V. Dorokhin, Elena V. Korneenko, Ivan K. Chudinov, Andrei E. Samoilov and Sergei V. Kruskop
Viruses 2024, 16(8), 1207; https://doi.org/10.3390/v16081207 - 26 Jul 2024
Abstract
Bats are natural hosts of a wide variety of viruses, including adenoviruses. European bats are known to carry mastadenoviruses categorized as species B (widespread in European Vespertilionidae bats) and whose taxonomy has not been clarified. We examined fecal samples from Vespertilionidae bats (five [...] Read more.
Bats are natural hosts of a wide variety of viruses, including adenoviruses. European bats are known to carry mastadenoviruses categorized as species B (widespread in European Vespertilionidae bats) and whose taxonomy has not been clarified. We examined fecal samples from Vespertilionidae bats (five species) captured in central Russia and found that 2/12 (16%) were positive for mastadenoviruses. The partial genome of the mastadenovirus was assembled from Pipistrellus nathusii, representing the bat adenovirus species B. The complete genome (37,915 nt) of a novel mastadenovirus was assembled from Nyctalus noctula and named BatAdV/MOW15-Nn19/Quixote. Comparative studies showed significant divergence of the Quixote genome sequence from European bat mastadenoviruses, while the only known virus showing low similarity was the isolate WA3301 from an Australian bat, and together they formed a subclade that separated from other BatAdVs. Phylogenetic and comparative analysis of the protein-coding genes provided evidence that Quixote is related to a novel species within the genus Mastadenovirus, provisionally named “K” (as the next available letter for the species). Phylogenetic analyses revealed that some earlier viruses from Western European bats, for which only partial DNA polymerase genes are known, are most likely members of the tentatively named species “K”. Thus, at least two species of mastadenovirus are circulating in bats throughout Europe, from western to eastern areas. Full article
(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity)
13 pages, 1924 KiB  
Article
Prevalence and Sequence Analysis of Equine Rhinitis Viruses among Horses in Poland
by Karol Stasiak, Magdalena Dunowska and Jerzy Rola
Viruses 2024, 16(8), 1204; https://doi.org/10.3390/v16081204 - 26 Jul 2024
Abstract
Equine rhinitis A (ERAV) and B (ERBV) viruses are respiratory pathogens with worldwide distribution. The current study aimed to determine the frequency of infection of ERAV and ERBV among horses and foals at Polish national studs, and to determine genetic variability within the [...] Read more.
Equine rhinitis A (ERAV) and B (ERBV) viruses are respiratory pathogens with worldwide distribution. The current study aimed to determine the frequency of infection of ERAV and ERBV among horses and foals at Polish national studs, and to determine genetic variability within the viruses obtained. Virus-specific quantitative RT-PCR assays targeting a 5′ untranslated region were used to screen nasal swabs collected from 621 horses at 16 national horse studs from throughout Poland, including 553 healthy horses and 68 horses with respiratory disease. A partial DNA polymerase gene was amplified and sequenced from the qRT-PCR-positive samples. The obtained sequences were analysed using phylogeny and genetic network analysis. None of the nasal swabs were positive for ERAV, whereas ERBV was found in 11/621 (1.78%) samples collected from 10 healthy horses and one foal affected by respiratory disease. Partial DNA polymerase gene sequence variability was correlated with individual horses and studs from which samples were collected when only Polish sequences were analysed, but there was no correlation between country of origin and ERBV sequence when Polish and international sequences were included in the network. The report presents the first detection of ERBV in Poland. Full article
(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity)
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8 pages, 3006 KiB  
Communication
Bovine Rhinitis B Virus Variant as the Putative Cause of Bronchitis in Goat Kids
by Andrew Noel, Jianqiang Zhang, Huigang Shen, Anugrah Saxena, Jennifer Groeltz-Thrush, Ganwu Li and Michael C. Rahe
Viruses 2024, 16(7), 1023; https://doi.org/10.3390/v16071023 - 25 Jun 2024
Viewed by 633
Abstract
A diagnostic investigation into an outbreak of fatal respiratory disease among young goats in Iowa, USA revealed bronchitis lesions of unknown etiology and secondary bacterial bronchopneumonia. Hypothesis-free metagenomics identified a previously unreported picornavirus (USA/IA26017/2023), and further phylogenetic analysis classified USA/IA26017/2023 as an aphthovirus [...] Read more.
A diagnostic investigation into an outbreak of fatal respiratory disease among young goats in Iowa, USA revealed bronchitis lesions of unknown etiology and secondary bacterial bronchopneumonia. Hypothesis-free metagenomics identified a previously unreported picornavirus (USA/IA26017/2023), and further phylogenetic analysis classified USA/IA26017/2023 as an aphthovirus related to bovine rhinitis B virus. Viral nucleic acid was localized to lesions of bronchitis using in situ hybridization. This marks the first report of a picornavirus putatively causing respiratory disease in goats and highlights the potential for cross-species transmission of aphthoviruses. Full article
(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity)
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16 pages, 50497 KiB  
Article
Determination and Characterization of Novel Papillomavirus and Parvovirus Associated with Mass Mortality of Chinese Tongue Sole (Cynoglossus semilaevis) in China
by Shuxia Xue, Xinrui Liu, Yuru Liu, Chang Lu, Lei Jia, Yanguang Yu, Houfu Liu, Siyu Yang, Zhu Zeng, Hui Li, Jiatong Qin, Yuxuan Wang and Jinsheng Sun
Viruses 2024, 16(5), 705; https://doi.org/10.3390/v16050705 - 29 Apr 2024
Viewed by 718
Abstract
A massive mortality event concerning farmed Chinese tongue soles occurred in Tianjin, China, and the causative agent remains unknown. Here, a novel Cynoglossus semilaevis papillomavirus (CsPaV) and parvovirus (CsPV) were simultaneously isolated and identified from diseased fish via electron microscopy, virus isolation, genome [...] Read more.
A massive mortality event concerning farmed Chinese tongue soles occurred in Tianjin, China, and the causative agent remains unknown. Here, a novel Cynoglossus semilaevis papillomavirus (CsPaV) and parvovirus (CsPV) were simultaneously isolated and identified from diseased fish via electron microscopy, virus isolation, genome sequencing, experimental challenges, and fluorescence in situ hybridization (FISH). Electron microscopy showed large numbers of virus particles present in the tissues of diseased fish. Viruses that were isolated and propagated in flounder gill cells (FG) induced typical cytopathic effects (CPE). The cumulative mortality of fish given intraperitoneal injections reached 100% at 7 dpi. The complete genomes of CsPaV and CsPV comprised 5939 bp and 3663 bp, respectively, and the genomes shared no nucleotide sequence similarities with other viruses. Phylogenetic analysis based on the L1 and NS1 protein sequences revealed that CsPaV and CsPV were novel members of the Papillomaviridae and Parvoviridae families. The FISH results showed positive signals in the spleen tissues of infected fish, and both viruses could co-infect single cells. This study represents the first report where novel papillomavirus and parvovirus are identified in farmed marine cultured fish, and it provides a basis for further studies on the prevention and treatment of emerging viral diseases. Full article
(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity)
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17 pages, 6049 KiB  
Article
Two Lineages of Papillomaviruses Identified from Caracals (Caracal caracal) in South Africa
by Simona Kraberger, Laurel E. K. Serieys, Gabriella R. M. Leighton, Matthew D. De Koch, John S. Munday, Jacqueline M. Bishop and Arvind Varsani
Viruses 2024, 16(5), 701; https://doi.org/10.3390/v16050701 - 29 Apr 2024
Viewed by 848
Abstract
Papillomaviruses (PV) infect epithelial cells and can cause hyperplastic or neoplastic lesions. In felids, most described PVs are from domestic cats (Felis catus; n = 7 types), with one type identified in each of the five wild felid species studied to [...] Read more.
Papillomaviruses (PV) infect epithelial cells and can cause hyperplastic or neoplastic lesions. In felids, most described PVs are from domestic cats (Felis catus; n = 7 types), with one type identified in each of the five wild felid species studied to date (Panthera uncia, Puma concolor, Leopardus wiedii, Panthera leo persica and Lynx rufus). PVs from domestic cats are highly diverse and are currently classified into three genera (Lambdapapillomavirus, Dyothetapapillomavirus, and Taupapillomavirus), whereas those from wild felids, although diverse, are all classified into the Lambdapapillomavirus genus. In this study, we used a metagenomic approach to identify ten novel PV genomes from rectal swabs of five deceased caracals (Caracal caracal) living in the greater Cape Town area, South Africa. These are the first PVs to be described from caracals, and represent six new PV types, i.e., Caracal caracal papillomavirus (CcarPV) 1–6. These CcarPV fall into two phylogenetically distinct genera: Lambdapapillomavirus, and Treisetapapillomavirus. Two or more PV types were identified in a single individual for three of the five caracals, and four caracals shared at least one of the same PV types with another caracal. This study broadens our understanding of wild felid PVs and provides evidence that there may be several wild felid PV lineages. Full article
(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity)
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18 pages, 5398 KiB  
Article
Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups
by Runbo Luo, Aohan Guan, Bin Ma, Yuan Gao, Yuna Peng, Yanling He, Qianshuai Xu, Kexin Li, Yanan Zhong, Rui Luo, Ruibing Cao, Hui Jin, Yan Lin and Peng Shang
Viruses 2024, 16(4), 606; https://doi.org/10.3390/v16040606 - 14 Apr 2024
Viewed by 1312
Abstract
Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai–Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude [...] Read more.
Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai–Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions. Full article
(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity)
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