Identification of major differences in the nucleocapsid protein genes of a Québec strain and European strains of porcine reproductive and respiratory syndrome virus.

The sequence of the 3'-terminal region of the genome of Québec reference strain IAF-exp91 of porcine reproductive and respiratory syndrome virus (PRRSV) was investigated by analysis of four cDNA clones. The 3'-terminal 530 nucleotides (nt) encompassed a large open reading frame with a coding capacity of 123 amino acids (M(r) 13,649). The predicted protein was extremely basic and hence was considered to correspond to the nucleocapsid (N) protein gene. When compared to the homologous sequences of two reference Netherlands strains (Lelystad and isolate 10) of PRRSV, the IAF-exp91 N protein was found to be five amino acids shorter and displayed a high degree of divergence. Overall, IAF-exp91 strain showed identities of 63% and 59% with both reference European strains at the nucleotide and amino acid level, respectively. Two amino acid stretches, STAPM and SQGAS, present respectively at the N- and C-terminal regions of the N protein of European strains, were missing in the IAF-exp91 N protein sequence. The 3'-terminal non-coding region (151 nt) of the IAF-exp91 strain was 22 nt longer than that of the European strains. The aligned nucleotide sequence of this non-coding region exhibited an overall identity of 59% with that of the European strains. The Québec reference strain of PRRSV appeared to be related more closely to equine arteritis virus and lactate dehydrogenase-elevating virus than are the two European strains of the virus. Preliminary data obtained by reverse transcription-PCR experiments, using specific or common oligonucleotide primers, suggested that this approach could be useful for distinguishing between PRRSV strains from different geographic origins.