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

Abstract

Background Pigeon circovirus (PiCV) infections in pigeons (Columba livia) have been reported worldwide. Currently, pigeon racing is becoming increasingly popular and considered to be a national sport in China, and even, the greatest competitions of racing pigeons are taking place in China. However, there are still no epidemiologic data regarding PiCV infections among racing pigeons in China. The purpose of our study was to provide information of prevalence, genetic variation and evolution of PiCV from racing pigeons in China. Results To trace the prevalence, genetic variation and evolution of PiCV in sick and healthy racing pigeons, 622 samples were collected from 11 provinces or municipalities in China from 2016 to 2019. The results showed that the positive rate of PiCV was 19.3% (120/622) at the sample level and 59.0% (23/39) at the club level, thus suggesting that the virus was prevalent in Chinese racing pigeons. A sequence analysis revealed that the cap genes of the PiCV strains identified in our study displayed a high genetic diversity and shared nucleotide homologies of 71.9%–100% and amino acid homologies of 71.7%–100%. 28 and 36 unique amino acid substitutions were observed in the Cap and Rep proteins derived from our PiCV strains, respectively. A cladogram representation of PiCV strains phylogeny based on 90 cap gene sequences showed that the strains in this study could be further divided into seven clades (A, B, C, E, G, H, and I) and some of them were closely related to worldwide strains from different types of pigeons. A large number of recombination events (31 events) were also detected in the PiCV genomes from Chinese racing pigeons. Conclusions These findings indicate that PiCV strains circulating in China exhibit a high genetic diversity and also contribute to information of prevalence, genetic variation and evolution of PiCV from racing pigeons in China.

Investigating pigeon circovirus infection in a pigeon farm: molecular detection, phylogenetic analysis and complete genome analysis

“…The full-length genome analysis revealed a variety of PiCV traits, including genetic diversity, insertions, deletions, substitutions, and recombination. The assembled circular whole-genome sequences were detected as seven sizes ranging from 2032 to 2042 nt in length, consistent with the findings of previous studies [ 12 , 22 , 36 , 39 ]. Despite several insertions, deletions, and substitutions detected during the examination of the PiCV genome nucleotide sequence, no mutation was observed in the conserved 9-base sequence of the TAGTATTAC motif situated at the stem ring structure, which may be associated with the beginning of RCR [ 8 , 10 ].…”

“…These sequences exhibit greater similarities with PiCV reference strains from China (72.8–99.5% nucleotide identity, 72.6–100% amino acid identity) than with PiCV reference strains from other countries (70.7–99.2% nucleotide identity, 64.5–100% amino acid identity) (Table 2 ). The start codons encoding 29 isolated PiCV Cap proteins are all "ATG", although other starting codons have been reported [ 22 , 39 ]. The amino acid sequences of 29 identified Cap proteins and the reference strains were aligned to investigate variations in the deduced amino acid sequences.…”

“…The greater diversity of the Cap protein is because the Cap protein, as the protein shell of the virus, is exposed to the host immune cells, and positive selection occurs during this process. Some mutations may affect the structure of the Cap protein, resulting in enhanced virus binding to receptors on target cells, boosting the virus's potential to infect cells..Furthermore, these changes may shield viruses from neutralization by antibodies [ 39 , 44 ]. Previous studies have shown that recombinant Cap protein can induce humoral and cellular immunity in pigeons and can be considered a potential antigen candidate for subunit vaccines against PiCV infections [ 45 , 46 ].…”

“…To analyze the potential recombinant evidence, an integrated software package for the recombination detection program RDP4 [ 43 ] was used to detect potential recombinant strains, parental strains, and possible recombination breakpoints. The complete genome sequences were aligned with those used by Wang et al [ 39 ]. The final dataset comprising 209 sequences was screened.…”

“…In China, the first PiCV infection was detected in meat pigeons in Zhejiang Province in 2009 [ 38 ]. In recent years, several studies have proven that PiCV is prevalent among pigeons in China [ 22 , 33 , 37 , 39 ]. Pigeons are widely employed as food, racing, carrier, and experimental animals.…”