Genetic characterisation and phylogenetic analysis of PCV2 isolates from India: Indications for emergence of natural inter-genotypic recombinants

• A first time comprehensive molecular analysis of PCV2 strains in India.
• Circulation of multiple PCV2 genotypes in Indian pigs.
• First ever report of emergence of PCV2 recombinants in Indian pig population.
• Inter-genotypic natural recombination between PCV2a–2C and PCV2b–1C isolates.
• Breakpoint located in cap gene, a less frequently reported site of recombination.

Porcine circovirus type 2 (PCV2), the necessary agent in pathogenesis of porcine circovirus diseases (PCVDs), has a worldwide distribution and is considered as one of the most important emerging viral pathogens of economic importance. PCV2 has been divided into four major genotypes namely PCV2a with five clusters or subtypes (2A–2E), PCV2b with three clusters (1A–1C), PCV2c and PCV2d, based on capsid (cap) gene analysis. PCV2 genome is rapidly evolving through events of recombination and mutation. Though, PCV2a was the predominant genotype initially, PCV2b shared majority of PCV2 sequences submitted to GenBank since 2003. In India, data regarding molecular characterisation of PCV2 is scant or absent. In the present study, we thoroughly analysed genetic heterogeneity of PCV2 strains circulating in Indian pig population. The results revealed that pigs in this region harboured PCV2 viruses of different genotypes including PCV2a–2D, PCV2b–1C and PCV2d. More interestingly, two isolates (PCV2Izn-89-13 and PCV2Izn-218-13) were classified as recombinant strains. Further detailed analysis suggested that these strains evolved from inter-genotypic recombination between PCV2a–2C and PCV2b–1C genotypes within cap gene. This study reports for the first time, the emergence of recombinant PCV2 strains in the Indian pig population.