Detection, isolation, and complete genome sequencing of pigeon torque teno virus in Indian racing pigeons with pock-like lesions.

This study investigates the potential pathogens associated with joint swelling, yellow exudates, and scab formation near the joints and eyelids in adult white racing pigeons.Pooled samples of scab and swab were collected and subjected to molecular, microbiological, and histopathological analyses. Initial screening focused on the detection of poxvirus using polymerase chain reaction (PCR). Subsequently, next-generation sequencing (metagenomic sequencing) using the Illumina MiSeq platform was performed, followed by virus isolation in embryonated specific pathogen-free chicken eggs and Vero cells, along with histopathological examination.Polymerase chain reaction (PCR) analysis for pigeon pox virus did not produce the expected amplicons, indicating a negative result for this virus. However, metagenomic sequencing identified the complete genome of Pigeon Torque Teno Virus (PTTV), with a genome size of 1574 nucleotides. Comparative sequence analysis revealed a nucleotide sequence similarity of 96.47%-97.7%, with the highest identity to a Canadian PTTV genome previously detected in the Bursa of Fabricius of a dead pigeon. Genome annotation identified two open reading frames (ORFs): encoding replication-associated protein and viral capsid protein. The presence of PTTV was further confirmed through real-time PCR and virus isolation in embryonated SPF chicken eggs and Vero cell cultures.The present study marks the first identification of PTTV in white racing pigeons with joint, ocular, and pock-like lesions. Although pigeon pox virus (PPV) was not detected, the findings suggest that PTTV could be an emerging avian pathogen necessitating further investigation into its pathogenicity, transmission dynamics, and clinical significance in pigeons.