Journal of General Virology (1994), 75, 681~85. Printed in Great Britain 681 Identification of major differences in the nucleocapsid protein genes of a Quebec strain and European strains of porcine reproductive and respiratory syndrome virus Helmi Mardassi, Samir Mounir and Serge Dea* Centre de recherche en virologic, Institut Armand-Frappier, 531 Boulevard des Prairies, Universit~ du Quebec, Laval, Qu(bec, Canada H7N 4Z3 The sequence of the 3'-terminal region of the genome of Qurbec reference strain IAF-expgl of porcine repro- ductive 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 (34,. 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-expgl 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 Qurbec reference strain of PRRSV appeared to be related more closely to equine arteritis virus and lactate dehydrogenase-elevating virus than are the two Euro- pean 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. Porcine reproductive and respiratory syndrome (PRRS) was first described in the United States (Poison et al., 1990) and Canada (Bilodeau et al., 1991) in 1986 to 1987. The disease was initially characterized by severe re- productive failure in sows of any parities (late-term abortions, increased numbers of stillborn, mummified and weakborn pigs, increased preweaning mortality), and respiratory problems affecting pigs of all ages, but mainly unweaned piglets. In 1990, a similar disease was observed in Germany (Lindhaus & Lindhaus, 1991) and rapidly swept through Western European countries in 1991 (Baron et al., 1992; Wensvoort et al., 1992b). The aetiological agent of the syndrome (PPRSV) has been definitively identified as a small spherical enveloped virus, 50 to 65 nm in diameter, with a central isometric nucleocapsid of approximately 25 to 30 nm (Benfield et al., 1992; Wensvoort et al., 1992b). The viral genome is a positive-stranded polyadenylated RNA of about 15 kb, The nucleotidesequence data reportedherewillappear in the EMBL and GenBank nucleotidesequencedatabasesunder accessionnumber U02095 (N-PRRS-IA). which generates in infected cells a 3'-coterminal nested set of six subgenomic mRNAs (Meulenberg et al., 1993 ; Conzelmann et al., 1993). The genomic RNA contains at least eight open reading frames (ORFs) organized similarly to those of equine arteritis virus (EAV) and lactate dehydrogenase-elevating virus (LDV) genomic RNAs. The latter two viruses have been proposed as members of the genus Arterivirus, family Togaviridae (Plagemann & Moennig, 1992; Conzelmann et al., 1993). European isolates of PRRSV appear to belong to the same serotype, whereas antigenic variability has been demonstrated among American isolates, and between American and European isolates (Wensvoort et al., 1992a). Here we report the sequence analysis of the 3'- terminal 530 nucleotides (nt) of the reference Qurbec strain IAF-exp91 of PRRSV (Dea et al., 1992). IAF-exp91 was propagated in primary cultures of porcine alveolar macrophages (PAM) prepared as de- scribed by Wensvoort et al. (1991). After complete degeneration of the monolayers, supernatant fluids were clarified by centrifugation at 5000 g for 20 min, followed by ultracentrifugation through a cushion of 30 % sucrose 0001-1966 © 1994SGM