title: Genetic characterisation and phylogenetic analysis of PCV2 isolates from India: indications for emergence of natural inter-genotypic recombinants.
abstract: 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.
authors.affiliation: National CSF Referral Laboratory and Swine Disease Laboratory, Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh 243122, India.
authors.forename: R
authors.initials: R
authors.lastname: Anoopraj
authors.affiliation: Department of Veterinary Pathology, College of Veterinary Science & Animal Husbandry, Central Agricultural University, Selesih, Aizawl 796014, India.
authors.forename: Tridib K
authors.initials: TK
authors.lastname: Rajkhowa
authors.affiliation: National CSF Referral Laboratory and Swine Disease Laboratory, Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh 243122, India.
authors.forename: Susan
authors.initials: S
authors.lastname: Cherian
authors.affiliation: Department of Veterinary Pathology, College of Veterinary Science & Animal Husbandry, Central Agricultural University, Selesih, Aizawl 796014, India.
authors.forename: Rahul S
authors.initials: RS
authors.lastname: Arya
authors.affiliation: National CSF Referral Laboratory and Swine Disease Laboratory, Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh 243122, India.
authors.forename: Neelam
authors.initials: N
authors.lastname: Tomar
authors.affiliation: National CSF Referral Laboratory and Swine Disease Laboratory, Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh 243122, India.
authors.forename: Ashish
authors.initials: A
authors.lastname: Gupta
authors.affiliation: National CSF Referral Laboratory and Swine Disease Laboratory, Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh 243122, India.
authors.forename: Pradeep K
authors.initials: PK
authors.lastname: Ray
authors.affiliation: EBH Laboratory, Division of Pathology, Indian Veterinary Research Institute, Izatnagar, 243122 Uttar Pradesh, India.
authors.forename: R
authors.initials: R
authors.lastname: Somvanshi
authors.affiliation: National CSF Referral Laboratory and Swine Disease Laboratory, Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh 243122, India. Electronic address: saikumarivri@gmail.com.
authors.forename: G
authors.initials: G
authors.lastname: Saikumar
mesh_terms: D000818:Animals; D001483:Base Sequence; D018173:Circoviridae Infections / Q000662:veterinary*; D017925:Circovirus / Q000145:classification* / Q000235:genetics*; D005814:Genes, Viral; D016679:Genome, Viral; D005838:Genotype; D007194:India; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D013552:Swine
keywords: India; Molecular characterisation; PCV2; Recombinant strains