Genetic diversity of porcine circovirus type 2 in China between 1999–2017

Porcine circovirus type 2 (PCV-2), is linked to PCV-2 associated disease, which has caused considerable economic loss in the swine industry. Here, we report the genetic diversity of PCV-2 in China. A total of 74 Chinese PCV-2 strains sequenced between 1999 and 2017 were studied. Based on the ORF2 and complete genomes, we found that apart from the PCV-2a, PCV-2b, and PCV-2d genotypes, two unstable recombination genotypes also exist, referred to as IM1 and IM2 genotypes. We found that the patterns of PCV-2 genetic shift in China are similar to the patterns at the global level. Additionally, for the PCV-2 ORF2 gene of Chinese isolates, we found a similar time to the most recent common ancestor and evolutionary rate to the global values. This indicates that PCV2 genetic diversity in China is driven by genetic drift/recombination of local strains and by the sporadic introduction of foreign genotypes from other countries. Overall, our study illustrates the genetic diversity and evolution dynamics of PCV-2 in China.