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 determ ined. It shares approximately 94% identity of nucleotide sequence with two recently reported North American strains, 16244B and VR2332, but only 78% w ith 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 t he European strain, the predicted Nsp2 of strain SP contains 36 and 155 ami no acid insertions, respectively, near the C-terminus, in addition to sever al highly variable regions. The insertion shows no homology with any equiva lent arterivirus proteins. This high sequence disparity of Nsp2 among diffe rent PRRSV isolates suggested that it could be used as a marker to differen tiate PRRSV genotypes. The 5' RACE and primer extension analysis of three N orth American strains demonstrated that the utmost 5'-end nucleotides are c onserved among PRRSV strains isolated from two continents. The predicted po lyprotein 1 a/b contains conserved proteinase, polymerase and helicase doma ins responsible for polyprotein processing, RNA transcription and replicati on.