Natural recombinants derived from different patterns of recombination between two PCV2b parental strains

Porcine circovirus diseases (PCVD) are globally emerging diseases that have huge economic impacts on swine industry. Porcine circovirus type 2 (PCV2) is considered to be the essential primary causative agent of PCVD. In the present study, recombination analyses of PCV2 identified two possible recombination events with high confidence using recombination detection program, phylogenetic analysis and base-by-base comparison. These recombination events occurred between strains 09CQ (HQ395024) and ZhuJi2003 (AY579893), giving rise to two recombinants 09GS (HQ395028) and HN0907 (GU938303). Phylogenetic analyses of the parental strains at full length level suggest that natural recombination happened between PCV2b strains. Interestingly, recombination of the two parental strains yielded two recombinants through different recombination patterns with crossover regions mainly located in ORF1 and ORF2, respectively. These results demonstrate that recombination between PCV2b strains can occur both in non-structural protein coding region and structural protein coding region. Our study not only indicates that PCV2b strains can undergo recombination through a variety of patterns, but also suggests that recombination contributes to the genetic diversity of PCV2.