Genetic Analysis and Evolutionary Changes of Porcine Circovirus 2

Porcine circovirus 2 (PCV2) has been increasingly isolated worldwide and represents one of the main causes of economic losses in the swine industry. During evolution, PCV2 has diverged into different genotypes and several recombinant strains have been identified. In this study, we performed thorough genetic, evolutionary and codon usage analyses using 1065 non-recombinant open reading frame 2 (ORF2) sequences from NCBI. Based on ML and Bayesian methods of the ORF2 gene, five main genotypes were defined including, PCV2a, PCV2b, PCV2c, PCV2d and PCV2e. The different genotypes displayed a variable degree of codon usage bias, mainly influenced by natural selection. Moreover, the host adaptation of these PCV2 genotypes to different hosts was analyzed for the first time showing that PCV2 is more adapted to swine than bats. Swine was especially relevant in shaping the PCV2b and PCV2d genomes according the Codon adaptation index (CAI) and Similarity index (SiD). When a broader range of circoviruses was considered, a certain incongruence between the phylogenetic history of these viruses and that of their hosts was observed, suggesting that cross-species transmission has played a major role during circoviruses evolution. Our study provides a new perspective of the evolution of Porcine circoviruses and may serve to aid future research on PCV2 origin and evolution patterns.