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.