Analysis of ORFs 2b, 3, 4, and partial ORF5 of sequential isolates of equine arteritis virus shows genetic variation following experimental infection of horses

Samples from horses experimentally infected with the “large plaque variant (LP3A+)” of equine arteritis virus were analysed. These included 182 nasal swabs collected from day 1 to 14 post-infection (p.i.), and 21 virus isolates obtained from white blood cells of animals that showed a prolonged viraemia between days 30 to 72 p.i. In order to determine the genetic stability of the virus and particularly to characterise the genetic variants found during the prolonged viraemia, partial sequences of open reading frame 5 (ORF5) encoding glycoprotein 5 (GP5) were generated. Viruses with amino acid substitutions in GP5 were used for further amplification and sequencing of a fragment encompassing ORFs 2b, 3, and 4. The ORF5 nucleotide sequences of the virus present in 65 out of 66 nasal swabs were identical to that of the inoculated virus, suggesting that the ORF5 gene of LP3A+ was genetically stable during the first 2 weeks p.i. Contrary to this, a number of mutations were found in the ORF5 of virus isolates obtained from day 30 p.i. The mutations mainly clustered in antigenic neutralization site C within variable region 1 of the GP5 ectodomain. Sequence variability was also identified in ORFs 2b, 3 and 4, with ORF 4 having the highest proportion of non-synonymous changes (4/6).