Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of beak and feather disease viruses

Abstract

Pigeon circovirus (PiCV) has a~2 kb genome circular ssDNA genome. All but one of the known PiCV isolates have been found infecting pigeons in various parts of the world. In this study, we screened 324 swab and tissue samples from Polish pigeons and recovered 30 complete genomes, 16 of which came from birds displaying no obvious pathology. Together with 17 other publicly available PiCV complete genomes sampled throughout the Northern Hemisphere and Australia, we find that PiCV displays a similar degree of genetic diversity to that of the related psittacine-infecting circovirus species, beak and feather disease virus (BFDV). We show that, as is the case with its pathology and epidemiology, PiCV also displays patterns of recombination, genomic secondary structure and natural selection that are generally very similar to those of BFDV. It is likely that breeding facilities play a significant role in the emergence of new recombinant PiCV variants and given that~50 % of the domestic pigeon population is infected subclinically, all pigeon breeding stocks should be screened routinely for this virus. The GenBank/EMBL/DDBJ accession numbers for the pigeon circovirus genomes determined in this study are KF738843-KF738872. One supplementary table and two supplementary figures are available with the online version of this paper.

Recurrent positive selection and heterogeneous codon usage bias events leading to coexistence of divergent pigeon circoviruses

“…The suspected recombinants were also detected in PiCV capsid gene in Hungary (Cságola et al, 2012). Moreover, recombination and positive selection can further shape the genome diversity of circovirus together (Heath et al, 2004;Stenzel et al, 2014). Our data also suggested both recombination and positive selection driving the evolution of PiCV capsid gene in Taiwan.…”

The epidemiology, molecular characterization and clinical pathology of circovirus infections in pigeons – current knowledge

“…The organization of the PiCV genome is typical for the family Circoviridae and is very similar to the genome of the BFDV (Stenzel et al 2014a Rosario et al 2017). All circoviruses have an ambisense genome organization containing open reading frames (ORFs) on different strands of replicative form dsDNA.…”

“…proteins with unknown functions (Todd et al 2008;Stenzel et al 2014a). All circoviruses contain a conserved intergenic region between the start codons of genes encoding Rep and Cap proteins.…”

“…The pairwise identity between PiCV and BFDV or PCV is estimated at 57% and 35%, respectively, which is why these viruses were classified as different species (Mankertz et al 2000;Todd et al 2001). Research has demonstrated that unlike the gene encoding Rep protein, the cap frequently undergoes mutations (Todd et al 2008;Zhang et al 2011;Cs agola et al 2012;Stenzel et al 2014a;Liao et al 2015;Zhang et al 2015a). The similarity of nucleotide sequences of the cap gene in various PiCV strains is estimated at 87% on average (Figure 3), and the presence of separate clades, which were created based on a comparison of whole genome sequences, results from differences in the nucleotide sequence of capsid protein gene (Zhang et al 2011;Cs agola et al 2012;Stenzel et al 2014a;Yamamoto et al 2015).…”

“…The progress in molecular biology techniques facilitated rapid and accurate detection of infectious diseases. As a result, cases of PiCV infections in pigeons were subsequently reported in various countries and regions, including Northern Ireland (Smyth & Caroll 1995;Todd et al 2001), Germany (Mankertz et al 2000;Raue et al 2005), Italy (Coletti et al 2000;Franciosini et al 2005), France (Abadie et al 2001), Czech Republic (Taras et al 2003), Belgium (Duchatel et al 2005, Poland (Wieliczko et al 2005;Stenzel et al 2012Stenzel et al , 2014a, Slovenia (Krapez et al 2012), Hungary (Cs agola et al 2012), United Arab Emirates (Ledwo n et al 2011), Iran (Mahzounieh et al 2014, Taiwan (Liao et al 2015), China (Zhang et al 2011;Phan et al 2013;Zhang et al 2015a), Japan (Yamamoto et al 2015) and the USA (Roy et al 2003) (Figure 1). In most reports, the virus was detected in the pigeon species of Columba livia domestica, but in several cases, PiCV genetic material was also detected in Senegal doves (Streptopelia senegalensis) and collared doves (Streptopelia decaocto) (Kub ı cek & Taras 2005;Todd et al 2008).…”