Comparisons of envelope through 5B sequences of infectious bronchitis coronaviruses indicates recombination occurs in the envelope and membrane genes

Abstract

A 1.78 kb sequence, including the E, M, 5a and 5b genes, and the intergenic region between the M and 5a genes, of six US strains of infectious bronchitis (corona)virus (IBV) were sequenced and compared to the published sequences for two additional strains. The overall identities as determined through pairwise analyses of nucleotide sequences of the entire 1.78kb region ranged from 90 to 99%, with the 5b open reading frame (ORF) having the greatest identity (94-99%) while the identities of the E, 5a and M ORFs ranged from 87 to 100%. Nucleotide sequencing of recent field isolates from Alabama (Ala1) and California (Cal3) revealed distinct shifts in homology in the M gene, indicating two apparent recombination events between the Holland 52/Mass41-like strain and an Ark-like strain, both origins of commonly used vaccine strains. Putative sites of recombination could also be identified in both the E and M ORFs of laboratory strains of IBV.

Fig. 1

Phylogenetic trees comparing Ala1, DE072, and eight other strains of infectious bronchitis virus. (A) E gene; (B) M gene; (C) 5a gene; (D) 5b gene.

Fig. 2

Shifts in homology in the M gene of infectious bronchitis virus.

Fig. 3

Nucleotide sequences of the M gene of Ark DPI, Holl52, Alabama 1 (Ala1), and California 3 (Cal3).