Emergence of novel Porcine circovirus 2 genotypes in Southern India

A total of 200 samples from Porcine circovirus 2 suspected (n = 112) and healthy (n = 88) swine populations collected from different districts of Tamil Nadu, south India were used in this study. The samples comprising of serum (n = 124), swabs from natural orifices (n = 52), and postmortem tissues (n = 24). All the samples were processed and subjected to the screening and detection of the PCV2 genome by a specific PCR assay. PCV2 genomes from positive samples were further subjected to genotyping with specifically designed primers for the full-length amplification of the ORF2 gene which codes for capsid protein (Cp) and serves as an epidemiological marker. Randomly, 13 amplified ORF2 genes were sequenced and the aligned sequences were subjected to signature motif analysis and phylogeny in MEGA X. The molecular prevalence of PCV2 infection in Tamil Nadu is 10.5% (n = 21). Signature motif and phylogenetic studies of 13 samples revealed 38.5% (n = 5) presence of each PCV2b intermediate 1(IM1) and PCV2b genotypes, followed by 15.4% (n = 2) PCV2d-2 and 7.7% (n = 1) PCV2d genotypes. The PCV2b-IM1 genotype has a 99.43% sequence homology with Vietnam isolate (JX506730). PCV2b genotypes showed 99.72% sequence identity with Chinese isolate (KX068219). PCV2d-2 genotypes reported in this study have 100% sequence identity with Taiwan isolate (MF169721). PCV2d genotype showed 97.87% sequence identity with Thailand isolate (MF314293). Amino acid analysis of all the 13 full-length ORF2 gene sequences revealed specific mutations in the immune reactive domains of A, B, C, and D. Capsid protein of three PCV2b and five PCV2b IM1 isolates had extra amino acid residue lysine (K) at 234 position of ORF2 similar to PCV2d. For the first time in South India, PCV2b IM1 and PCV2d-2 genotypes are reported. This study evidences the genetic shifts of PCV2 isolates in India and it is analogous to that of global genotypic shift.