North American and European porcine reproductive and respiratory syndrome viruses differ in non-structural protein coding regions

Although North American and European serotypes of porcine reproductive and respiratory syndrome virus (PRRSV) are recognized, only the genome of the E uropean Lelystad strain (LV) has been sequenced completely. Here, the genom e of the pathogenic North American PRRSV isolate 16244B has been sequenced and compared with LV, The genomic organization of 16244B was the same as LV but with only 63.4% nucleotide identity. The 189 nucleotide 5' non-coding region (NCR) of 16244B was distinct from the LV NCR, with good conservation (83%) only over a 43 base region immediately upstream of open reading fram e (ORF) 1 a. Major differences were found in the region encoding the non-st ructural part of the ORF 1 a polyprotein, which shared only 47% amino acid identity over 2503 residues of the six non-structural proteins (Nsps) encod ed. Nsp2, thought to have a species-specific function, showed the greatest divergence, sharing only 32% amino acid identity with LV and containing 120 additional amino acids in the central region. Nsps encoded by the 5'-proxi mal and central regions of ORF1b had from 66 to 75% amino acid identity; ho wever, the carboxy-terminal protein CP4 was distinct (42% identity). The OR F1a-1b frameshift region of 16244B had 98% nucleotide identity with LV, Con sistent with previous reports for North American isolates, the six structur al proteins encoded were 58 to 79% identical to LV proteins. The 3' NCR (15 0 nucleotides) was 76% identical between isolates. These genomic difference s confirm the presence of distinct North American and European PRRSV genoty pes.