Evidence for different patterns of natural inter-genotype recombination between two PCV2 parental strains in the field

•We identify 13 recombinants from 32 PCV2 positive clinical samples from the diseased and dead pigs.•13 recombinants are classified into two new clusters in the phylogenetic tree of PCV2.•Two cluster recombinants are derived from different patterns of natural inter-genotype recombination between two PCV2 parental strains with the breakpoint located within ORF2.

Co-infection with different virus strains is a precondition for genome recombination, which give rise to continuous evolution of porcine circovirus type 2 (PCV2). In the present study, 32 PCV2 positive clinical samples from the diseased and dead pigs were identified by classic PCR. 15 of 32 (46.8%) clinical samples were identified as infection with both PCV2a and PCV2b using genotype-specific PCR. 13/15 of PCV2 strains were identified as recombinants using sequencing analysis, phylogenetic analysis, recombination detection program and base-by-base comparison. Further analyses of the full-length sequences of these strains suggest that the natural recombination events occurred between strains DQ104423 (PCV2a) and AY579893 (PCV2b), yield two new recombinant clusters through different recombination patterns with crossover regions located in ORF2. Recombinant cluster 1 included 3 strains, and recombinant cluster 2 included 10 strains. These results demonstrate that recombination between PCV2a and PCV2b strains can occur in cap protein coding region through different patterns and yield different recombinants. Our study not only provided new evidences that PCV2 strains can undergo recombination through a variety of patterns, but also suggests that recombination events easily occur in the co-existence of different strains of PCV2.