Abstract: To study the genetic variation of PRRSV isolates in China, we compared the N and GP5 gene sequences of 53 strains of PRRSV isolates which were isolated from 1996 to 2008 in China, and had been published in GenBank. The cladogram according to the N gene demonstrated that most of the Chinese isolates were belonged to North American type. Among them four highly diverse subgroups were clearly demarcated on the NA-genotype phylogenetic tree. All of the subgroup 1 isolates restricted geographically to regions of the southeast of China were found to be highly variable in the primary neutralizing epitopes. The first PRRSV isolate (CH1a) was of the representation of subgroup 2. Subgroup 3 isolates were shared high identity with MLV vaccine and its parent virus VR2332. The strains in Taiwan were belonged to subgroup 4, which were different from those in mailand China. These results may contribute to the knowledge of PRRSV epidemiology in China, and may help to explain the low efficiency of MLV or inactivated CH-1a vaccine to protect pigs infected the subgroup 1 virus, and the great genetic diversity should be taken into consideration for control and prevention measures. 

Key words: PRRSV; N gene; GP5 gene; genetic variation; molecular epidemiology