The genomic diversity of Chinese porcine reproductive and respiratory syndrome virus isolates from 1996 to 2009

Since it was first reported in 1995, porcine reproductive and respiratory syndrome (PRRS) has become one of the most important swine diseases in China. A large number of field PRRSV strains have been isolated from different regions of China at different times, especially after a highly pathogenic PRRSV emerged in 2006. Previous studies based on ORF5 gene sequences revealed extensive genetic diversity among Chinese PRRSV isolates. To fully understand the extent of genetic diversity of PRRSV in China, we determined the genomic sequence of PRRSV WUH1, a highly pathogenic PRRSV isolated in late 2006. Based on the complete genomic sequences of strain WUH1 and 66 other field Chinese PRRSV strains isolated from 1996 to 2009, we further analyzed their genetic diversity. The results showed that all the tested Chinese PRRSV isolates belong to the North American genotype and can be clearly divided into four highly diverse subgenotypes. Furthermore, the analysis supported the concept that the highly pathogenic PRRSV in China emerged by gradual variation and evolution from the Chinese domestic virus. In addition, different deletions within Nsp2, deletion and potential antigenic drift within GP3, and point mutations within GP5, were extensively observed in Chinese PRRSV isolates. Interestingly, in addition to a unique discontinuous deletion of 30 aa in Nsp2, there was a 1 nucleotide deletion in both the 5′UTR and 3′UTR in nearly all highly pathogenic PRRSV isolates. These results will contribute to the elucidation of the evolutionary mechanisms of PRRSV in China.