A Pilot Study Investigating the Dynamics of Pigeon Circovirus Recombination in Domesticated Pigeons Housed in a Single Loft

Abstract

Pigeon circovirus (PiCV) infects pigeon populations worldwide and has been associated with immunosuppression in younger pigeons. Recombination is a common mechanism of evolution that has previously been shown in various members of the Circoviridae family, including PiCV. In this study, three groups of pigeons acquired from separate lofts were screened for PiCV, and their genome sequence was determined. Following this, they were housed in a single loft for 22 days, during which blood and cloacal swab samples were taken. From these blood and cloacal swabs, PiCV genomes were determined with the aim to study the spread and recombination dynamics of PiCV in the birds. Genome sequences of PiCV were determined from seven pigeons (seven tested PiCV positive) before they were housed together in a loft (n = 58 sequences) and thereafter from the ten pigeons from blood and cloacal swabs (n = 120). These 178 PiCV genome sequences represent seven genotypes (98% pairwise identity genotype demarcation), and they share >88% genome-wide pairwise identity. Recombination analysis revealed 13 recombination events, and a recombination hotspot spanning the 3′ prime region, the replication-associated protein (rep) gene and the intergenic region. A cold spot in the capsid protein-coding region of the genome was also identified. The majority of the recombinant regions were identified in the rep coding region. This study provides insights into the evolutionary dynamics of PiCV in pigeons kept under closed rearing systems.

Epidemiology and Evolution of Emerging Porcine Circovirus-like Viruses in Pigs with Hemorrhagic Dysentery and Diarrhea Symptoms in Central China from 2018 to 2021

“…Rep is considered to be essential for viral replication and plays a crucial role in cellular immunity [6,42]. Recombination events are also widely found in other viruses, such as porcine circovirus, canine circovirus, pigeon circovirus, duck circovirus and goose circovirus [41,[43][44][45][46]. The hotspot of recombination events is Rep, but it is still relatively conserved in ssDNA viruses, indicating that recombination may have little influence on the diversification of Rep.…”

Molecular detection and phylogenetic analysis of pigeon circovirus from racing pigeons in Northern China

“…The high intensity of recombination may suggest that frequent co-infections of different PiCV strains. Moreover, recently, Khalifeh A. et al has demonstrated that recombination plays a role in PiCV evolution through animal experiment [ 58 ]. Thus, the recombination seemed to be a key mechanism for PiCV evolution [ 21 , 23 , 28 , 29 ].…”

Pigeon Circovirus over Three Decades of Research: Bibliometrics, Scoping Review, and Perspectives

“…Within the first decade after the short report of Schmidt [ 1 ], retrieved records showed detection of the virus in several other countries including Northern Ireland [ 16 , 34 , 69 , 70 ], Germany [ 15 , 44 ], Italy [ 31 , 71 ], France [ 72 ], Belgium [ 30 , 33 , 34 ], and Japan [ 21 , 38 ]. Meanwhile, between 2003 and 2012, researchers in Czech Republic [ 29 , 32 ], Poland [ 36 , 58 , 67 , 73 , 74 , 75 , 76 , 77 , 78 , 79 , 80 ], Denmark [ 30 ], Slovenia [ 81 , 82 ], Hungary [ 66 , 83 ], United Arab Emirates [ 84 ], Libya [ 85 ], Nigeria [ 83 , 86 ], and Taiwan [ 59 , 87 , 88 , 89 , 90 , 91 , 92 , 93 ] reported first local detections of PiCV. Lastly, during the most recent decade of PiCV research, new publications and reports were also produced from Brazil [ 40 ], Iran [ 94 , 95 ], Iraq […”

“…More recently, wider interest and more studies focused on the role of recombination as an evolutionary driver of circovirus evolution have been published [ 40 , 66 , 73 , 76 , 102 ]. Besides the observed frequent mutations in the cp gene, this observed high genetic diversity in PiCV sequences is also attributed as a product of constant recombination driving the evolution of this virus [ 75 , 88 ].…”

“…Besides the observed frequent mutations in the cp gene, this observed high genetic diversity in PiCV sequences is also attributed as a product of constant recombination driving the evolution of this virus [ 75 , 88 ]. To understand the genetic recombination in PiCV, in an experimental study, infected and non-infected pigeons were housed in a single loft for a period of 23 days to observe recombination events [ 73 ]. Recombination detection analysis of the 178 whole genome sequences from this study revealed 13 recombination events, with event 2 as most common recombination event present in 109 genomes.…”