Genomic analysis of a Canadian equine rhinitis A virus reveals low diversity among field isolates.
Abstract: Equine rhinitis A virus (ERAV) is an ubiquitous virus, routinely identified in equine respiratory infections; however, its role in disease and genetic features are not well defined due to a lack of genomic characterization of the recovered isolates. Therefore, we sequenced the full-length genome of a Canadian ERAV (ERAV/ON/05) and compared it with other ERAV sequences currently available in GenBank. The ERAV/ON/05 genome is 7,839 nucleotides (nts) in length with a variable 5'UTR and a more conserved 3'UTR. When ERAV/ON/05 was compared to other reported ERAV isolates, an insertion of 13 nt in the 5'UTR was identified. Further phylogenetic analysis demonstrated that ERAV/ON/05 is closely related to the ERAV/PERV isolate, which was isolated in 1962 in the United Kingdom. The polyprotein of ERAV/ON/05 had a 96 % nucleotide and amino acid sequence identity to reported ERAVs, and it appears that, despite the high error rate of RNA-dependent RNA polymerase, this isolate has retained high sequence identity to the strain first described by Plummer in 1962.
Publication Date: 2012-11-24 PubMed ID: 23180486DOI: 10.1007/s11262-012-0848-0Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The research investigates the genomic characterization of a equine rhinitis A virus (ERAV) from Canada, finding that it exhibits low diversity compared with other isolates and maintains high sequence identity to a strain first described in 1962 in the UK.
Introduction
- The study focuses on the Equine rhinitis A virus (ERAV), a common virus identified in equine (horse) respiratory infections. Despite its prevalence, knowledge of its genetic features and definitive role in causing disease remains limited, primarily due to a lack of comprehensive characterization of the recovered virus isolates.
Methodology
- Researchers sequenced the entire genome of a Canadian ERAV isolate known as ERAV/ON/05. Following this, they compared the genome with other available ERAV sequences housed in GenBank, an open-access, annotated collection of all publicly available nucleotide sequences and their protein translations.
Findings
- The genome of ERAV/ON/05 was found to be 7,839 nucleotides (nts) long, with a fluctuating 5’UTR (an untranslated region of mRNA directly upstream from the initiation codon) and a more consistent 3’UTR (untranslated region at the end of an mRNA molecule).
- In comparison with other ERAV isolates, researchers identified a unique insertion of 13 nts in the 5’UTR of ERAV/ON/05.
Phylogenetic Analysis
- Upon further phylogenetic analysis, which is used to infer evolutionary relationships, it was found that ERAV/ON/05 shares a close genetic relationship with the ERAV/PERV isolate. This particular isolate was captured in 1962 in the United Kingdom.
Observations
- The polyprotein of ERAV/ON/05 contained a notable 96% nucleotide and amino acid sequence identity with other ERAVs that have been reported. This indicates a high degree of genetic conservation in ERAV.
- Despite RNA-dependent RNA polymerase’s known high error rate, the ERAV/ON/05 isolate managed to retain considerable sequence identity to the strain that Plummer first described in 1962.
Conclusion
- The research concludes that there is low diversity among ERAV isolates, underlining the genetic stability of this virus over time and across geographical locations. This baseline understanding of ERAV’s genomic character offers valuable insights for future studies, particularly in understanding its pathogenic role and devising effective health interventions for equine respiratory infections caused by ERAV.
Cite This Article
APA
Diaz-Méndez A, Viel L, Shewen P, Nagy E.
(2012).
Genomic analysis of a Canadian equine rhinitis A virus reveals low diversity among field isolates.
Virus Genes, 46(2), 280-286.
https://doi.org/10.1007/s11262-012-0848-0 Publication
Researcher Affiliations
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada. adiaz@uoguelph.ca
MeSH Terms
- Animals
- Aphthovirus / classification
- Aphthovirus / genetics
- Aphthovirus / isolation & purification
- Base Sequence
- Genetic Variation
- Genomics
- Horse Diseases / virology
- Horses
- Molecular Sequence Data
- Phylogeny
- Picornaviridae Infections / veterinary
- Picornaviridae Infections / virology
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Citations
This article has been cited 1 times.- Peng T, Yang F, Yang F, Cao W, Zheng H, Zhu Z. Structural diversity and biological role of the 5' untranslated regions of picornavirus.. RNA Biol 2023 Jan;20(1):548-562.
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