Infectious bronchitis viruses with naturally occurring genomic rearrangement and gene deletion

Abstract

Infectious bronchitis viruses (IBVs) are group III coronaviruses that infect poultry worldwide. Genetic variations, including whole-gene deletions, are key to IBV evolution. Australian subgroup 2 IBVs contain sequence insertions and multiple gene deletions that have resulted in a substantial genomic divergence from international IBVs. The genomic variations present in Australian IBVs were investigated and compared to those of another group III coronavirus, turkey coronavirus (TCoV). Open reading frames (ORFs) found throughout the genome of Australian IBVs were analogous in sequence and position to TCoV ORFs, except for ORF 4b, which appeared to be translocated to a different position in the subgroup 2 strains. Subgroup 2 strains were previously reported to lack genes 3a, 3b and 5a, with some also lacking 5b. Of these, however, genes 3b and 5b were found to be present but contained various mutations that may affect transcription. In this study, it was found that subgroup 2 IBVs have undergone a more substantial genomic rearrangements than previously thought.

Fig. 1

Schematic representation of the arrangement of the structural genes of IBV and TCoV. S, spike; 3a, 3b and E, gene 3; M, membrane; 4b, 4c ORFs (‘intergenic region’); 5a and 5b, gene 5; N, nucleocapsid; 6b ORF; X2, no identity with any sequence in GenBank. N1/88, Q3/88, V18/91 and V6/92 are Australian subgroup 2 IBV strains. Uncharacterised ORFs are represented by grey boxes, and genes containing mutations that may affect transcription are represented by black boxes

Fig. 2

Comparison of the 4b-like ORFs in Australian IBVs. a) Alignment of the predicted amino acid sequences of the 4b-like ORFs found in Australian IBV strains. A blank line has been introduced to distinguish between subgroup 2 strains (below the line) with Australian reference IBVs (above the line). Gaps are represented by dashes (-), and identical amino acids are indicated with an asterisk (*). The protein motif “CFALSLQE”, which is conserved in all Australian IBV strains, is boxed. Conserved amino acid changes are represented with “:”, while semi-conserved amino acid changes are identified by “.”. b) Hydropathicity plots for Australian IBV vaccine strains VicS and Armidale, subgroup 2 strain N1/88 and TCoV strain ATCC. Hydrophobicity (Kyte-Doolittle scale) is represented by the white line, while hydrophilicity (Hopp-Woods scale) is represented by the grey line. The plots were generated using http://www.vivo.colostate.edu/molkit/hydropathy/

Fig. 3

Alignment of the predicted amino acid sequences of the subgroup 2 3b genes with those of vaccine strains VicS and Armidale. a) Alignment of the predicted amino acid sequences of gene 3b of Australian subgroup 2 strains N1/88, Q3/88 V18/91 and V6/92 with Australian vaccine IBV strains VicS and Armidale. Identical amino acids and bases are indicated by an asterisk (*). Conserved amino acid changes are represented by “:”, while semi-conserved amino acid changes are identified by “.”. b) Nucleotide sequence alignment of the first three codons of gene 3b. The initiation codon is boxed to show the altered initiation codon in the subgroup 2 strains