Two strains of porcine reproductive and respiratory syndrome virus (PRRSV) were isolated, designated GDQJ and GDBY1. Experimental inoculation showed that GDBY1, caused 100% morbidity and 67% mortality, while GDQJ, caused 100% morbidity but no death. Full-length genomes were sequenced. Homologic and phylogenetic analyses indicated that these two strains were closely related to Chinese highly pathogenic PRRSV strains. Surprisingly, identical 30 amino acids (aa) deletion in the NSP2-coding region, a presumed high virulence marker, was present in low virulent strain GDQJ. Further comprehensive analysis of GDQJ genome in comparison with Chinese highly pathogenic PRRSV strains revealed multiple genomic variations, distributing in 5' UTR, NSP1b, NSP2, NSP3, NSP5, NSP7, NSP9, NSP10, GP5, and N regions. Data present in this article confirm that the 30 aa deletion in the NSP2-coding region alone is not a reliable genomic indicator for the high virulence of PRRSV strains emerged in China. The genomic variations of GDQJ strain provided the basis for further studies of virulence determinants for PRRSVs.