First report on the molecular detection and genetic characterisation of pigeon circovirus in Kerala, India

Pigeon circovirus (PiCV) is a significant immunosuppressive pathogen associated with Young Pigeon Disease Syndrome (YPDS), causing economic losses in pigeon farming. Although PiCV has been widely reported globally, molecular data from southern India are lacking. This study presents the first molecular detection and genetic characterisation of PiCV in pigeons from Kerala. A total of 75 clinical samples including tissues, cloacal swabs and feathers were collected from 27 pigeons showing YPDS-like symptoms. PCR targeting the capsid gene detected PiCV in four samples (5.3%), all from dead birds. Sensitivity analysis revealed that conventional PCR could reliably detect PiCV DNA at concentrations as low as 44 fg/µL, demonstrating diagnostic significance. Histopathological examination of positive tissues revealed lymphoid depletion, basophilic botryoid intracytoplasmic inclusion bodies and inflammatory infiltration, consistent with PiCV's immunosuppressive effects. Sequencing revealed high nucleotide identity among the four field samples (94.63-99.98%), with PiCV samples 2 and 3 nearly identical (99.98%). Comparative analysis with 35 GenBank reference sequences showed that samples 1 to 3 were most similar to a Taiwanese strain (KU593626.1) with 96.33-97.05% identity, while PiCV- 4 was closest to a Polish strain (KC691686.1) at 95.73% identity. Phylogenetic analysis showed all four positive samples from Kerala clustered with global PiCV strains with PiCV- 4 branching earlier, indicating greater genetic divergence among the four field samples. The genetic similarity between local and international strains suggests possible transboundary introduction via pigeon trade, racing or migration. These findings highlight the need for routine molecular surveillance, biosecurity measures and further research into PiCV epidemiology in India to mitigate disease impact in the growing pigeon sector.