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Viruses
Special Issues
Animal Virus Discovery and Genetic Diversity: 2nd Edition
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Animal Virus Discovery and Genetic Diversity: 2nd Edition

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

Deadline for manuscript submissions: 30 June 2026 | Viewed by 5778

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 Issues, Collections and Topics in MDPI journals

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 250 words) can be sent to the Editorial Office for assessment.

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

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Related Special Issue

Published Papers (5 papers)

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Research

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13 pages, 1099 KB  
Article
Identification and Long-Term Detection of Hepacivirus bovis Genotype 1 and 2 on a Cattle Farm in Germany
by Nadine Hake, Christian von Holtum, Dirk Höper, Ard M. Nijhof, Klaas Dietze and Bernd Hoffmann
Viruses 2026, 18(1), 78; https://doi.org/10.3390/v18010078 - 6 Jan 2026
Viewed by 568
Abstract
In 2020, a dairy farm in northwest Germany reported several cows with severe respiratory disease, fever, and reduced milk production. Multiple direct and indirect diagnostic methods were used to identify the cause of the disease. However, the pathogens detected could not be correlated [...] Read more.
In 2020, a dairy farm in northwest Germany reported several cows with severe respiratory disease, fever, and reduced milk production. Multiple direct and indirect diagnostic methods were used to identify the cause of the disease. However, the pathogens detected could not be correlated with the severity of the clinical symptoms, so further diagnostic steps were taken. Blood and nasal swab samples were examined using next-generation sequencing (NGS) as part of a metagenomic analysis. For the first time in Germany, Hepacivirus bovis genotype 2 was detected. Real-time RT-PCR assays confirmed the presence of BovHepV genotypes 1 and 2 in the herd between 2020 and 2023. Analyses of complete and partial genome sequences demonstrated the presence of different virus variants in the herd over several years. In addition, the sequence data indicated that cattle can be reinfected with viruses belonging either to different BovHepV subtypes or to the same subtype. Although no direct link could be established between the detection of bovine hepaciviruses and the observed clinical symptoms, the PCR and sequence data obtained provide valuable insights into the epidemiology and pathogenesis of BovHepV infections. Full article
(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity: 2nd Edition)
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16 pages, 3734 KB  
Article
Virome Analysis of Small Mammals from the Brazilian Amazon
by Leonardo Henrique Almeida Hernández, Fábio Silva da Silva, Thito Yan Bezerra da Paz, Daniel Damous Dias, Bruno de Cássio Veloso de Barros, Bruno Tardelli Diniz Nunes, Lívia Medeiros Neves Casseb, Sandro Patroca da Silva, Pedro Fernando da Costa Vasconcelos and Ana Cecília Ribeiro Cruz
Viruses 2025, 17(9), 1251; https://doi.org/10.3390/v17091251 - 16 Sep 2025
Viewed by 1013
Abstract
The municipalities of Peixe-Boi and Santa Bárbara do Pará, both in the Pará State (eastern Amazon), have more than half of their territory deforested. Understanding the viral diversity in wildlife that inhabits the surroundings of human communities contributes to strengthening surveillance. Samples from [...] Read more.
The municipalities of Peixe-Boi and Santa Bárbara do Pará, both in the Pará State (eastern Amazon), have more than half of their territory deforested. Understanding the viral diversity in wildlife that inhabits the surroundings of human communities contributes to strengthening surveillance. Samples from eleven bats, seven opossums, and eight rodents from the two locations were screened by high-throughput sequencing for virome analysis. Viral reads were assigned into twenty viral families, from which the most abundant was Retroviridae. Host order, tissue type, and season showed a significant effect on viral composition. Five viral genomes of bat ERVs with intact genes were recovered, showing the need to understand their endogenous nature. In addition, a new Buritiense virus (Hantaviridae) strain was also obtained, supporting its circulation in Santa Bárbara do Pará and expanding its genomic information. Together, these findings reinforce the need for continuous surveillance in wild animals, especially in the Amazon region, to anticipate potential threats to public health. Full article
(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity: 2nd Edition)
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18 pages, 445 KB  
Article
Thirty-Five Years of IBV Evolution in Chile Reveals a Novel Lineage and Evidence of Vaccine-Driven Recombination
by Miguel Guzmán, Leandro Cádiz, Leonardo Sáenz, Héctor Hidalgo and Claudio Verdugo
Viruses 2025, 17(8), 1111; https://doi.org/10.3390/v17081111 - 13 Aug 2025
Cited by 2 | Viewed by 1390
Abstract
Infectious bronchitis virus (IBV) remains a major threat to poultry health worldwide due to frequent genetic changes mainly driven by recombination and limited cross-protection between genotypes. In this study, we analyzed IBV strains collected from clinical outbreaks in Chile between 1986 and 2021 [...] Read more.
Infectious bronchitis virus (IBV) remains a major threat to poultry health worldwide due to frequent genetic changes mainly driven by recombination and limited cross-protection between genotypes. In this study, we analyzed IBV strains collected from clinical outbreaks in Chile between 1986 and 2021 to assess the long-term impacts of live-attenuated vaccines (Massachusetts and 4/91) on viral evolution. Phylogenetic analysis of the S1 and N genes revealed four major lineages circulating in Chile—GI-1, GI-13, GI-16, and a novel monophyletic clade we propose as GI-31. The latter, identified in isolates from 1986 to 1988, is highly divergent (22–24%) from other known lineages, representing a previously unreported South American IBV variant. Despite widespread Mass vaccination, genetically distinct field strains circulated during the 1980s, facilitating potential recombination with GI-1 vaccine-derived strains, including evidence of shared ancestry with GI-11, an endemic lineage from Brazil. Non-recombinant GI-16, likely introduced from Asia, was detected in isolates from 2009. Notably, a recombinant strain emerged in 2015, four years after 4/91 vaccine introduction, indicating vaccine–field-strain genetic exchange. By 2017, isolates with >99% identity to the 4/91 strain were recovered, suggesting vaccine-derived variants. In 2021, GI-1 re-emerged, showing recombination signatures between GI-1 and GI-13 (4/91-derived) strains, likely reflecting suboptimal or inconsistent vaccination strategies. Selection analyses showed strong purifying selection across most of the S1 gene, with limited sites under positive selection in the receptor-binding domain. Phylodynamic reconstruction revealed time-structured evolution and multiple introduction events over 35 years, with lineage-specific tMRCA estimates. Collectively, these findings highlight the emergence of a novel lineage in South America and demonstrate that vaccine use, while mitigating disease, has significantly shaped the evolution of IBV in Chile. Our results underscore the importance of continuous genomic surveillance to inform vaccine strategies and limit recombinant emergence. Full article
(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity: 2nd Edition)
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14 pages, 1382 KB  
Article
Molecular Identification and Characterization of a Novel Gammaherpesvirus in Wild Rabbits
by Fábio A. Abade dos Santos, Ana Duarte, Inês C. Varandas, Silvia S. Barros, Ana M. Henriques, Teresa Fagulha and Margarida D. Duarte
Viruses 2025, 17(7), 967; https://doi.org/10.3390/v17070967 - 10 Jul 2025
Cited by 1 | Viewed by 1761
Abstract
To date, five herpesviruses have been identified in Leporidae (LeHV-1, LeHV-2, LeHV-3, LeHV-4, and LeHV-5). Two of these have been shown to infect the European rabbit (Oryctolagus cuniculus), causing either asymptomatic infection (LeHV-2, a gammaherpesvirus) or virulent disease (LeHV-4, an alphaherpesvirus). Unfortunately, apart [...] Read more.
To date, five herpesviruses have been identified in Leporidae (LeHV-1, LeHV-2, LeHV-3, LeHV-4, and LeHV-5). Two of these have been shown to infect the European rabbit (Oryctolagus cuniculus), causing either asymptomatic infection (LeHV-2, a gammaherpesvirus) or virulent disease (LeHV-4, an alphaherpesvirus). Unfortunately, apart from LeHV-4, for which complete genome sequences are available, molecular data on leporid herpesviruses are extremely limited, with no sequences available in public databases for LeHV-1 and LeHV-3, and only a few short sequences for LeHV-2 and LeHV-5. In this study, we investigated the presence of herpesviruses in biological samples from wild rabbits (n = 34) found dead in the field during 2024. A pan-herpesvirus nested PCR directed to the herpesviral DNA polymerase gene was used for screening. Positive samples (n = 14, 41.17%) were further investigated by sequencing analysis of a longer region of the DNA polymerase gene, as well as the glycoprotein B gene and the terminase gene. Blastn analysis of the amplicons revealed the highest similarity to gammaherpesvirus. Phylogenetic analyses based on glycoprotein B, DNA polymerase, and concatenated amino acid sequences consistently placed the newly identified LeHV-6 in close proximity to LeHV-5. Both viruses form a well-supported clade within the Gammaherpesvirinae, clustering with rodent-associated herpesviruses, such as Murine herpesvirus, MuHV-4, and A. sylvaticus rhadinovirus 1. Considering the species susceptibility and the nucleotide similarities with the five previously described leporid herpesviruses, we conclude that a new rabbit gammaherpesvirus has been identified, which we propose to name LeHV-6. Full article
(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity: 2nd Edition)
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9 pages, 866 KB  
Brief Report
Characterization of a Novel, Highly Divergent Paramyxovirus Discovered in a Bearded Seal of Subarctic Canada
by Vadym Zaluzhnyi, Joost T. P. Verhoeven, Garry B. Stenson, Andrew S. Lang, Suzanne C. Dufour and Marta Canuti
Viruses 2026, 18(2), 172; https://doi.org/10.3390/v18020172 - 28 Jan 2026
Viewed by 566
Abstract
Seals are keystone animals in the Arctic and a valuable resource for Indigenous communities, but their virome is poorly understood. Through a preliminary investigation of the virome of seven North Atlantic bearded seals (Erignathus barbatus) from northwest Newfoundland, Canada, we discovered [...] Read more.
Seals are keystone animals in the Arctic and a valuable resource for Indigenous communities, but their virome is poorly understood. Through a preliminary investigation of the virome of seven North Atlantic bearded seals (Erignathus barbatus) from northwest Newfoundland, Canada, we discovered a new member of the Paramyxoviridae, a family including important animal pathogens. The complete coding genome sequence (15,898 nt) of the novel paramyxovirus, which we named bearded seal-associated paramyxovirus 1 (BSAPV-1), encoded five core paramyxoviral proteins—nucleoprotein, matrix, fusion, hemagglutinin-neuraminidase, and polymerase—and three proteins with no identifiable homologues that may represent the phosphoprotein, a small hydrophobic protein, and a transmembrane protein. Phylogenetic analysis, including BSAPV-1 and all 153 currently known paramyxoviral species, positioned the novel virus in a long-branched clade with Wenzhou Pacific spadenose shark paramyxovirus (Skoliovirinae, Scoliodonvirus scoliodontis), its closest relative (pairwise identity of the L protein: 30.1%). According to ICTV criteria, BSAPV-1 is likely the first member of a novel paramyxoviral subfamily. As the virus was found in combined tracheal/fecal swabs of a single animal, we could not conclude whether this is a seal virus or a virus associated with seal food. This study expands our knowledge about marine paramyxoviruses, and future studies should investigate BSAPV-1 ecology, spread, and host spectrum. Full article
(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity: 2nd Edition)
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