Phylogenetic analysis of open reading frame 5 of field isolates of equine arteritis virus and identification of conserved and nonconserved regions in the GL envelope glycoprotein

Abstract

The variation and phylogenetic relationship of open reading frame 5 (ORF5) of 3 different laboratory strains of the original prototype Bucyrus strain of equine arteritis virus (EAV), the modified live virus vaccine (ARVAC, Fort Dodge Laboratories), and 18 field isolates of EAV from North America and Europe were determined by comparison of their gene sequences. The viruses differed from the published sequence by between 3 (99.6% homology) and 94 (87.8%) nucleotides and by between 3 (98.8%) and 24 (90.6%) amino acids. The field isolates differed from each other by between 2 (99.7%) and 110 (85.7%) nucleotides and by between 1 (99.6%) and 26 (89.8%) amino acids. Comparison of the nucleotide sequences of these viruses indicates that although they are very closely related, the ORF5 of each virus is distinct. The ORF5 of EAV encodes the GL envelope glycoprotein which expresses the neutralization determinants of the virus. Comparative analysis of the deduced amino acid sequence of the GL protein of the viruses identified three distinct variable regions (V1 [aa 61-121], V2 [141-178], and V3 [aa 202-222]), a putative signal sequence (S [aa 1-18]), and four conserved regions (C1 [aa 19-60], C2 [aa 122-140], C3 [aa 179-201], and C4 [aa 223-255]). Amino acid substitutions in the V1 region of the GL protein of EAV field isolates had significant effects on the predicted hydrophobicity and secondary structure of the protein, which is potentially important because this region contains a major neutralization site. Estimation of genetic distances and phylogenetic tree analysis of these viruses identified four distinct groups of EAV isolates, including two North American (NA1 and NA2) and two European (E1 and E2) groups. The sequence data obtained from individual European and North American isolates suggest movement of viruses between the two continents.