The entire leader sequence of ten equine arteritis virus (EAV) isolates including the Bucyrus reference strain was determined and analyzed at the primary nucleotide and secondary structure levels. The leader sequence of eight EAV isolates was determined to be 206 nucleotides (nt) in length, whereas those of the 86AB-A1 and 86NY-A1 isolates were found to be 205 and 207 nt in length, respectively. The sequence identity of the leader sequences between the different isolates and the Bucyrus reference strain ranged from 94.2 to 98.5%. An AUG start codon found at position 14 in all EAV isolates could initiate an open reading frame (ORF) that could produce a polypeptide of 37 amino acids, except for the 86NY-A1 isolate where the intraleader polypeptide would contain 54 amino acids. Five patterns of computer-predicted RNA secondary structures were identified in the ten EAV leader regions analyzed. All EAV isolates showed three conserved stem-loops (designated A, B and C). An additional conserved stem-loop (D) was observed in six EAV isolates, including the Bucyrus reference strain. Based on the presence or absence of stem-loop D, all EAV isolates analyzed in this study could be tentatively classified into two genogroups (I and II). The significance of the intraleader ORF and the predicted secondary structures has yet to be determined.
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