Re-emergence of a genetic outlier strain of equine arteritis virus: Impact on phylogeny

Abstract

Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory and reproductive disease of equids, which is notifiable in some countries including the Great Britain (GB) and to the OIE. Herein, we present the case of a persistently infected stallion and the phylogenetic tracing of the virus strain isolated. Discussing EAV occurrence and phylogenetic analysis we review features, which may aid to harmonise and enhance the classification of EAV.

Keywords: Classification; Equine arteritis virus; Full genome sequencing; Phylogeny.

Fig. 1

EAV genome organisation (adapted from Snijder and Kikkert, 2013 and GenBank's genome section on EAV). The ORF1ab (blue) is expressed as a fusion protein, from the genomic RNA, despite the −1 programmed ribosomal frameshift required for ORF1b (light blue). The genes encoding the structural proteins (red) are translated from subgenomic RNAs. Polyprotein cleavage sites are depicted above ORF1ab. Blue arrowheads: sites cleaved by PLP domains of nsp1/nsp2; red arrowheads: sites cleaved by the nsp4. The graph displays the relative sizes and locations of the resulting proteins. Proteins expressed in frame to each other are displayed on the same axis. NSP: non-structural protein; GP: glycoprotein; M: membrane protein; E: envelope protein; N: nucleocapsid protein. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Phylogenetic comparison of EAV full length genome sequences. GB_Glos_2012 was compared against against all of the full genome sequences (n = 32; excluding molecular clones) available in GenBank. The arrows indicate the strains selected from each cluster for genomic comparison (Table 2) with GB_Glos_2012. The Maximum-likelihood phylogeny was constructed using the GTR +G+ I model. Sequences are listed by their accession numbers followed by strain and country of isolation. Percentage of a 1000 bootstrap replicates are cited at nodes for values ≥50%.

Fig. 3

Phylogenetic analysis of ORF5. Maximum-likelihood tree using GTR +G+ I model with 101 EAV sequences shown. Phylogenetic grouping as suggested by Stadejek et al. (1999), Mittelholzer et al. (2006) and Zhang et al. (2007) are labelled on the right hand side of the tree. Phylogenetic scheme suggested from this work is displayed on the left of the tree. Sequences are listed by their accession numbers followed by strain name, country of isolation and where available year of isolation. Percentage of a 1000 bootstrap replicates are cited at nodes for values ≥50%.