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Scientific reports2023; 13(1); 3703; doi: 10.1038/s41598-023-30875-7

Discovery and comparative genomic analysis of a novel equine anellovirus, representing the first complete Mutorquevirus genome.

Abstract: The complete genome of a novel torque teno virus species (Torque teno equus virus 2 (TTEqV2) isolate Alberta/2018) was obtained by high-throughput sequencing (HTS) of nucleic acid extracted from the lung and liver tissue of a Quarter Horse gelding that died of nonsuppurative encephalitis in Alberta, Canada. The 2805 nucleotide circular genome is the first complete genome from the Mutorquevirus genus and has been approved as a new species by the International Committee on Taxonomy of Viruses. The genome contains several characteristic features of torque teno virus (TTV) genomes, including an ORF1 encoding a putative 631 aa capsid protein with an arginine-rich N-terminus, several rolling circle replication associated amino acid motifs, and a downstream polyadenylation signal. A smaller overlapping ORF2 encodes a protein with an amino acid motif (WXHXCXCXH) which, in general, is highly conserved in TTVs and anelloviruses. The UTR contains two GC-rich tracts, two highly conserved 15 nucleotide sequences, and what appears to be an atypical TATA-box sequence also observed in two other TTV genera. Codon usage analysis of TTEqV2 and 11 other selected anelloviruses from five host species revealed a bias toward adenine ending (A3) codons in the anelloviruses, while in contrast, A3 codons were observed at a low frequency in horse and the four other associated host species examined. Phylogenetic analysis of TTV ORF1 sequences available to date shows TTEqV2 clusters with the only other currently reported member of the Mutorquevirus genus, Torque teno equus virus 1 (TTEqV1, KR902501). Genome-wide pairwise alignment of TTEqV2 and TTEqV1 shows the absence of several highly conserved TTV features within the UTR of TTEqV1, suggesting it is incomplete and TTEqV2 is the first complete genome within the genus Mutorquevirus.
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Publication Date: 2023-03-06 PubMed ID: 36878942PubMed Central: PMC9988894DOI: 10.1038/s41598-023-30875-7Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research paper discusses the discovery and genome mapping of a new species of Torque teno virus found in a Quarter Horse gelding in Alberta, Canada. It presents the first fully detailed Mutorquevirus genome and reveals differences from standard Torque teno virus genomes in the viral and host preference for certain codons for protein synthesis.

Technical Detailing of the Discovered Virus

  • Scientists were able to extract the full genome of the Torque teno equus virus 2 (TTEqV2) from the lung and liver tissues of a Quarter Horse. The genome contains 2805 nucleotides.
  • It became the first complete genome from the Mutorquevirus genus, gaining approval as a new species by the International Committee on Taxonomy of Viruses.
  • The genome comprises of several characteristic features of a standard torque teno virus (TTV) genome that includes an ORF1 and ORF2, a protein with a specific amino acid pattern, and a downstream signal.

Distinguishing Features of the TTEqV2 Species

  • An in-depth codon usage analysis was performed detailing a strong preference for A3 codons (adenine-ending) in TTEqV2 and other selected Anelloviruses. This finding contrasts with the lower frequency of A3 codon usage seen in Horse and the four other host species examined.
  • When compared to Torque teno equus virus 1 (TTEqV1), TTEqV2 is found to be lacking some highly conserved TTV features in the untranslated region, suggesting the TTEqV2 genome is more complete.

Scientific Relevance and Conclusion

  • The discovery of the full TTEqV2 genome provides more insights into the genetic composition of the Mutorquevirus genus, and the codon usage patterns highlight a new area of viral-host interactions.
  • The anomalies found between the TTEqV1 and TTEqV2 genomes indicate possible gaps in earlier research or a divergence of species within the genus.
  • This research on the genetic makeup of TTEqV2 presents new ground for understanding, diagnosing, and potentially treating diseases caused by similar viruses.

Cite This Article

APA
Fisher M, Nebroski M, Davies J, Janzen E, Sullivan D, Lung O. (2023). Discovery and comparative genomic analysis of a novel equine anellovirus, representing the first complete Mutorquevirus genome. Sci Rep, 13(1), 3703. https://doi.org/10.1038/s41598-023-30875-7

Publication

Scientific reports
ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English
Volume: 13
Issue: 1
Pages: 3703
PII: 3703

Researcher Affiliations

Fisher, Mathew
  • National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada.
Nebroski, Michelle
  • National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada.
Davies, Jennifer
  • Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.
Janzen, Eugene
  • Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.
Sullivan, Daniel
  • National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada.
Lung, Oliver
  • National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada. oliver.lung@inspection.gc.ca.
  • Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada. oliver.lung@inspection.gc.ca.

MeSH Terms

  • Horses
  • Animals
  • Male
  • Anelloviridae
  • Phylogeny
  • Torque teno virus
  • Alberta
  • Genomics

Conflict of Interest Statement

The authors declare no competing interests.

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