Determination of the complete nucleotide sequence of a vaccine strain of porcine reproductive and respiratory syndrome virus and identification of the Nsp2 gene with a unique insertion

The complete nucleotide sequence of the genomic RNA of a vaccine strain (SP) of porcine reproductive and respiratory syndrome virus (PRRSV) was determined. It shares approximately 94% identity of nucleotide sequence with two recently reported North American strains, 16244B and VR2332, but only 78% with a European strain, Lelystad virus (LV). Its genome is the longest among the four published complete sequences of PRRSV, due to an insertion in the Nsp2-encoding region. Compared to Nsp2 of the North American strains and the European strain, the predicted Nsp2 of strain SP contains 36 and 155 amino acid insertions, respectively, near the C-terminus, in addition to several highly variable regions. The insertion shows no homology with any equivalent arterivirus proteins. This high sequence disparity of Nsp2 among different PRRSV isolates suggested that it could be used as a marker to differentiate PRRSV genotypes. The 5′ RACE and primer extension analysis of three North American strains demonstrated that the utmost 5′-end nucleotides are conserved among PRRSV strains isolated from two continents. The predicted polyprotein 1a/b contains conserved proteinase, polymerase and helicase domains responsible for polyprotein processing, RNA transcription and replication.