Comparison of the 5 ' leader sequences of North American isolates of reference and field strains of porcine reproductive and respiratory syndrome virus (PRRSV)

The 5' leader is documented to be an important regulatory element in many ( +) ssRNA virus genome. To understand the significance of the 5' leader RNA of PRRSV, we determined the complete leader sequences of fifteen different North American strains of PRRSV and predicted their secondary structures. V iruses analysed included three reference strains and nine field strains ori ginating from different geographic locations. To further examine the leader region, one of the field strains was adapted to grow in tissue culture, an d three clones were isolated. We also predicted the secondary structures of two European strains based on their published sequences. The predicted RNA secondary structures of the leader sequences suggested the existence of th ree conserved domains formed by the 5' region of the leader among the North American strains, two of which were conserved in the European strains. A v ariable structural domain was predicted from the 3' region of the leader se quences of the North American strains, where all tissue culture-adapted iso lates were characterized by a stem-loop while field isolates were character ized by an internal bulge within the stem-loop.