Novel Genotypes of Type 2 Porcine Circovirus (PCV2) in PMWS Pigs in China Between 2008 and 2009
The present study analyzed genetic variation and genotypes of 17 strains of type 2 Porcine Circovirus (PCV2) from different epidemic regions in China in 2008 and 2009. All the genomic sequences were 1.767 bp in length. Sequence comparison of complete genomic sequences revealed 95.6-99.9% identity among 17 PCV2 strains and the most variable regions within 1.000-1.700 nt (located in the coding region of ORF2). Comparative analysis of amino acids of the two ORFs revealed that variation extend of ORF2 (93.1-100%) was greater than ORF1 (98.4-100%) and the third codon position showed much more variable than the first and second sites. Mutations in T and B lymphocyte epitopes were also detected by comparative analysis and it was found that T lymphocyte epitopes were more conserved than those of B lymphocytes. Phylogenetic analysis revealed 6 novel genotypes of PCV2 in addition to the 5 known geneotypes (PCV-2a, PCV-2b, PCV-2c, PCV-2d, PCV-2e) reported. Of these genotypes, the PCV-2b, PCV-2d and 3 unidentified genotypes were the most prevailing, within 13, 17 and 16 epidemic provinces, respectively. For the 17 Chinese PCV2 strains examined in this study, 5 strains represented PCV-2b genotype, 6 strains were PCV-2d, 1strain was PCV-2e and other 5 strains were novel genotypes while no strains were PCV-2a and PCV-2c genotype. These findings demonstrated the usefulness and attributes of complete genomic sequences for genetic variation and genotyping of PCV2 and have implications for the studies of population biology, molecular epidemiology and genetic structure of PCV2 and for the effective control of PMWS as well.