NUCLEOTIDE-SEQUENCE AND GENETIC-ANALYSIS OF THE LEADER REGION OF CANADIAN, AMERICAN AND EUROPEAN EQUINE ARTERITIS VIRUS ISOLATES

The extreme 5' end, the entire leader sequence of the Arvac vaccine st rain, and 10 equine arteritis virus (EAV) isolates, including the ATCC Bucyrus reference strain and 5 Canadian field isolates, were determin ed and compared at the primary nucleotide and secondary structure leve ls. The leader sequence of eight EAV isolates, including the Bucyrus r eference strain, and the leader sequence of the Arvac vaccine strain w as determined to be 206 nt in length (not including the putative 5' ca p structure-associated nucleotide) whereas those of the 86AB-A1 and 86 NY-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%. Phylogenetic analysis and estimation of genetic distances, based on t he leader nucleic acid sequences, showed that all EAV isolates/strains are likely to represent a large phylogenetically-related group. An AU G start codon found at position 14 in all EAV isolates/strains could i nitiate an open reading frame (ORF) that could produce a polypeptide o f 37 amino acids, except for the 86NY-A1 isolate where the intraleader polypeptide would contain 54 amino acids. Computer-predicted RNA seco ndary structures were identified in the 11 EAV leader regions analyzed . All EAV isolates/strains showed 3 conserved stem-loops (designated A , B and C). An additional conserved stem-loop (D) was observed in 7 EA V isolates, including the Bucyrus reference strain. The leader region distal to stem-loop D did not contain conserved sequences or stem-loop structures common to the EAV isolates/strains.