Molecular cloning and nucleotide sequencing of the 3'-terminal genomic RNA of the porcine reproductive and respiratory syndrome virus.

The genomic RNA of a porcine reproductive and respiratory syndrome virus (PRRSV) isolate from the U.S.A., VR 2385 (ATCC), was copied into cDNA after priming with oligo(dT) and cloned into phage lambda. The cDNA clones representing the 3'-terminal genomic RNA of the virus were isolated and sequenced. The genome is a positive-stranded, polyadenylated RNA with an estimated size of 15 kb. Analysis of the resulting sequence identified three complete open reading frames (ORFs) with the potential to encode polypeptides with predicted M(r)s of 22.2K (ORF 5), 19.1K (ORF 6) and 13.6K (ORF 7). ORF 7, which is closest to the 3' end, is predicted to encode a highly basic nucleocapsid protein displaying 58% amino acid identity to the corresponding protein of the Lelystad virus (LV), a European PRRSV isolate. ORFs 6 and 5, preceding ORF 7, are each predicted to encode proteins containing several hydrophobic domains that are thought to be membrane-associated. The VR 2385 ORF 6 protein is the most conserved structural protein. It has 78% amino acid identity to the equivalent LV protein, and ORF 5 shares only 54% of its amino acid sequence. Northern blot analysis revealed a 3'-coterminal nested set of six subgenomic RNAs in VR 2385 virus-infected CRL 11171 cells. Our results indicate that VR 2385, like LV, is a member of the newly proposed arterivirus group. However, the striking genetic variation and the difference in pathogenicity between LV and VR 2385 suggest that the viruses causing PRRS in the U.S.A. and Europe are highly variable and they may represent different genotypes.