The pigeon circovirus evolution, epidemiology and interaction with the host immune system under One Loft Race rearing conditions

Abstract

This study was aimed to investigate the frequency of PiCV recombination, the kinetics of PiCV viremia and shedding and the correlation between viral replication and host immune response in young pigeons subclinically infected with various PiCV variants and kept under conditions mimicking the OLR system. Fifteen racing pigeons originating from five breeding facilities were housed together for six weeks. Blood and cloacal swab samples were collected from birds every seven days to recover complete PiCV genomes and determine PiCV genetic diversity and recombination dynamics, as well as to assess virus shedding rate, level of viremia, expression of selected genes and level of anti-PiCV antibodies. Three hundred and eighty-eight complete PiCV genomes were obtained and thirteen genotypes were distinguished. Twenty-five recombination events were detected. Recombinants emerged during the first three weeks of the experiment which was consistent with the peak level of viremia and viral shedding. A further decrease in viremia and shedding partially corresponded with IFN-γ and MX1 gene expression and antibody dynamics. Considering the role of OLR pigeon rearing system in spreading infectious agents and allowing their recombination, it would be reasonable to reflect on the relevance of pigeon racing from both an animal welfare and epidemiological perspective.

Keywords: Gene expression; One Loft Race; Pigeon circovirus; Recombination; Viral evolution; ddPCR.

Figure 1

Overview of the experimental schedule.

Figure 2

The results of ddPCR pigeon circovirus quantification during the whole experimental period in blood (a) and cloacal swab (b) samples acquired from the experimental pigeons. The different letters (a,b) indicate a statistically significant difference in PiCV genome copy numbers between the sampling dates (p < 0.05). Whiskers represent the standard deviation values. The results for the individual pigeons are encoded by color according to Fig. 1.

Figure 3

Mean relative expression of the genes encoding IFN-γ (a), and MX1 (b) as well as in-house ELISA detection of anti-PiCV IgY in sera of the experimental pigeons (c) throughout the experiment. The mean relative expression values above 1 (horizontal black line) indicate a higher gene expression compared to the control pigeons. Whiskers represent the standard deviation values. The results for individual pigeons are encoded by color according to Fig. 1.

Figure 3

Mean relative expression of the genes encoding IFN-γ (a), and MX1 (b) as well as in-house ELISA detection of anti-PiCV IgY in sera of the experimental pigeons (c) throughout the experiment. The mean relative expression values above 1 (horizontal black line) indicate a higher gene expression compared to the control pigeons. Whiskers represent the standard deviation values. The results for individual pigeons are encoded by color according to Fig. 1.

Figure 4

(a) The Neighbor-joining tree showing the genetic connections of 388 complete PiCV genome sequences investigated in this study. The sequences were encoded with the following formula: B (blood)/S (swab), loft number (I–V), _pigeon number (1–3), sampling date (a–h), _clone number (C1–10) and the Accession Number. The color marking of individual sequences indicates the loft of origin: green—loft I, blue—loft II, purple—loft III, pink—loft IV and orange—loft V. Sequences belonging to different genotypes are highlighted with different shades of grey. (b) PiCV genotypes recognized in the investigated pigeons during the experiment. Lack of symbols near the pigeon shape indicates an unsuccessful recovery of the complete PiCV genome on the specific sampling date. Digits near the selected shapes indicate the number of PiCV clones belonging to the specific genotype (G I–G XIII) detected in blood samples (red digits) and swab samples (blue digits) taken from the experimental birds. The pigeon lofts are encoded by color according to Fig. 1.

Figure 4

(a) The Neighbor-joining tree showing the genetic connections of 388 complete PiCV genome sequences investigated in this study. The sequences were encoded with the following formula: B (blood)/S (swab), loft number (I–V), _pigeon number (1–3), sampling date (a–h), _clone number (C1–10) and the Accession Number. The color marking of individual sequences indicates the loft of origin: green—loft I, blue—loft II, purple—loft III, pink—loft IV and orange—loft V. Sequences belonging to different genotypes are highlighted with different shades of grey. (b) PiCV genotypes recognized in the investigated pigeons during the experiment. Lack of symbols near the pigeon shape indicates an unsuccessful recovery of the complete PiCV genome on the specific sampling date. Digits near the selected shapes indicate the number of PiCV clones belonging to the specific genotype (G I–G XIII) detected in blood samples (red digits) and swab samples (blue digits) taken from the experimental birds. The pigeon lofts are encoded by color according to Fig. 1.

Figure 5

Schematic illustration of recombination events in complete PiCV genome sequences detected after the start of joint housing of experimental birds. The methods used to detect recombination events are RDP (R), GENCONV (G), BOOTSCAN (B), MAXCHI (M), CHIMERA (C), SISCAN (S) and 3SEQ (T). For each recombination event, the method with the lowest p-value is underlined. The color of the recombinant sequence names indicates the maternal loft of the pigeon from which the recombinant sequence has been obtained, whereas the color of the bars indicates the maternal lofts of the pigeons from which the parental sequences have been obtained: green—loft I, blue—loft II, purple—loft III, pink—loft IV and orange—loft V. The color coding was made according to Fig. 1. All sequence names are encoded with the following formula: B (blood)/S (swab), loft number (I–V), _pigeon number (1–3), sampling date (a–h), _clone number (C1–C10).