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.

The research article focuses on examining the variations and genetic relationships among different laboratory and field strains of Equine Arteritis Virus (EAV) based on their gene sequences. The study specifically evaluates the Open Reading Frame 5 (ORF5) of these strains, identifies distinct groups of EAV strains, and suggests a potential cross-continental virus movement.

Examining the Variations in Different Strains

• The study initially involves a comprehensive analysis of the Open Reading Frame 5 (ORF5) of 3 different laboratory strains originally derived from the prototype Bucyrus strain of EAV and 18 field strains from North America and Europe.
• This investigation brings out substantial differences in the nucleotide and amino acid sequences of the examined viruses compared to a published EAV sequence. These variations range from a minor 0.4% difference to a significant 12.2% deviation in nucleotides, and from a 1.2% to 9.4% deviation in amino acids.
• The comparison among different field isolates also points out variations ranging from 0.3% to 13.1% in nucleotides and from 0.4% to 10.2% in amino acids.

Uniqueness of Each Strain

• The variations, as remarked above, indicate the unique genetic makeup of each virus strain.
• They particularly denote the distinctness of the ORF5 of each EAV strain, which plays an essential role in expressing the neutralization determinants of the virus.

Genotypic and Phenotypic Analysis

• The study continues with a comparative analysis of the deduced amino-acid sequence of the GL protein of these viruses.
• This analysis reveals three variable regions, one putative signal sequence, and four conserved regions.
• It also highlights significant effects of amino acid substitutions in the V1 variable region on the predicted hydrophobicity and secondary structure of the protein. It is an important finding as this region contains a major neutralization site.

Phylogenetic Grouping and Conclusion

• The estimation of genetic distances and the construction of a phylogenetic tree segregates the studied isolates into four distinct groups. These include two North American groups (NA1 and NA2) and two European groups (E1 and E2).
• The analysis of gene sequences from individual isolates across the continents suggests a potential movement of EAV strains between North America and Europe.