Identification and whole-genome characterization of a novel equine papillomavirus.
Abstract: Papillomaviruses (PVs) are small, non-enveloped viruses with double-stranded circular DNA genomes that infect a wide range of hosts, including mammals, birds, reptiles, and fish. While human papillomaviruses are extensively studied, recent advancements in high-throughput sequencing techniques have increased the detection and genetic characterization of PVs from various animal species. Here, we describe the identification and whole-genome characterization of a divergent equine papillomavirus (EcPV) detected through a viral metagenomic investigation of a horse in Denmark exhibiting neurological signs. Using Nanopore sequencing and Sanger sequencing, we assembled a complete viral genome of 7767 nucleotides. Phylogenetic analysis, based on concatenated E1, E2, L2, and L1 gene sequences, showed that the identified virus clustered within the same clade as EcPV3 (genus Dyoiotapapillomavirus) and EcPV6 (genus Dyorhopapillomavirus) but was situated on a distinct separate branch. Comparative genome analysis revealed approximately 52% nucleotide sequence similarity to EcPV3 and EcPV6, which share 66% similarity with each other. The L1 gene, commonly used for papillomavirus classification, exhibited a sequence identity to EcPV3 (58.4%) and EcPV6 (60.0%). The other viral genes displayed a 39-62% identity to the respective genes from EcPV3 and 6 further supporting the divergence of this newly identified PV. The combination of the phylogenetic analysis and the genetic divergence suggests that this newly identified papillomavirus may constitute a novel species or genus within the Papillomaviridae family. Our findings expand the known diversity of equine papillomaviruses and contribute valuable insights into their evolutionary relationships.
© 2025. The Author(s).
Publication Date: 2025-10-23 PubMed ID: 41128801PubMed Central: PMC12678564DOI: 10.1007/s11262-025-02190-yGoogle Scholar: Lookup
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- Journal Article
Summary
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Overview
- Researchers identified and fully sequenced the genome of a new equine papillomavirus found in a horse showing neurological symptoms in Denmark.
- This virus is genetically distinct from previously known equine papillomaviruses, suggesting it represents a new species or genus.
Background on Papillomaviruses
- PVs are small viruses with double-stranded circular DNA genomes that infect a wide range of vertebrate hosts including mammals, birds, reptiles, and fish.
- Human papillomaviruses have been extensively studied, but papillomaviruses in other animals, like horses, are less well characterized.
- Advances in sequencing technologies have enabled detection and detailed genetic characterization of PVs from diverse animal species.
Research Goal and Methods
- The researchers aimed to detect and genetically characterize papillomaviruses in a horse showing neurological signs, using viral metagenomics.
- They applied two sequencing techniques:
- Nanopore sequencing – a high-throughput method enabling long-read DNA sequencing.
- Sanger sequencing – a traditional approach used to confirm and complete genome assembly.
- Using these methods, they assembled the complete genome of the new virus, totaling 7,767 nucleotides in length.
Genetic and Phylogenetic Analysis
- The researchers conducted phylogenetic analysis using combined sequences from four viral genes: E1, E2, L2, and L1, commonly used markers for papillomavirus classification.
- The new virus grouped with two previously known equine papillomaviruses:
- EcPV3 (genus Dyoiotapapillomavirus)
- EcPV6 (genus Dyorhopapillomavirus)
- Despite clustering in the same clade, the novel virus formed a distinct branch, indicating it is genetically divergent from EcPV3 and EcPV6.
- Comparative genome similarity metrics showed:
- Approximately 52% overall nucleotide similarity to EcPV3 and EcPV6, while these two share 66% similarity with each other.
- L1 gene, crucial for papillomavirus classification, had only 58.4% identity with EcPV3 and 60.0% with EcPV6.
- Other viral genes exhibited 39–62% identity compared to corresponding genes in EcPV3 and EcPV6, reinforcing the idea of significant divergence.
Interpretations and Implications
- The combined phylogenetic relationships and genetic divergence suggest the new virus may belong to a previously unrecognized species or even a new genus within the Papillomaviridae family.
- This discovery expands the known genetic diversity of equine papillomaviruses, an important step in understanding viral evolution and host-virus interactions in horses.
- Identification of a papillomavirus in a horse with neurological symptoms might prompt further investigations into the clinical relevance and pathogenic potential of this virus, although causality is not established in this study.
Summary
- In summary, the study successfully discovered and genetically characterized a novel equine papillomavirus that is distinct from currently known equine PVs.
- This work highlights the utility of advanced sequencing technologies in identifying novel viruses and contributes valuable data towards the taxonomy and evolutionary history of papillomaviruses in horses.
Cite This Article
APA
Blomström AL, Hansen S, Riihimäki M.
(2025).
Identification and whole-genome characterization of a novel equine papillomavirus.
Virus Genes, 61(6), 747-751.
https://doi.org/10.1007/s11262-025-02190-y Publication
Researcher Affiliations
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden. anne-lie.blomstrom@slu.se.
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
MeSH Terms
- Animals
- Horses / virology
- Genome, Viral
- Phylogeny
- Papillomavirus Infections / virology
- Papillomavirus Infections / veterinary
- Horse Diseases / virology
- Papillomaviridae / genetics
- Papillomaviridae / classification
- Papillomaviridae / isolation & purification
- Whole Genome Sequencing
- Denmark
Grant Funding
- H-20-47-555 / The Swedish-Norwegian Foundation for Equine Research
Conflict of Interest Statement
Declarations. Conflict of interest: The authors declare no competing interests. Ethical approval: Ethical approval for the procedures was obtained from the University of Copenhagen, LATH Ethical committee (permit no. 2022-009) before any samples were collected.
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