Genetic diversity of avian infectious bronchitis virus California variants isolated between 1988 and 2001 based on the S1 subunit of the spike glycoprotein

Twenty-nine isolates of avian infectious bronchitis virus (IBV) recovered from commercial chicken flocks in California between 1988 and 2001 and identified as California variants by serotype and direct automated cycle sequencing of the IBV spike glycoprotein S1 subunit, were further characterized phylogenetically and by nucleotide sequence comparison. California variants were grouped according to production type of chicken, by comparison with public access sequence databases (NCBI GenBank and EMBL), or based on phylogenetic analysis. Fisher’s Exact test was used to compare mutations per year, purifying and positive selection, predictive antigenicity, and a ≥ 6 bp deletion between California variant groups. A high number of mutations at the nucleotide level (p = 0.013) and a ≥ 6 bp deletion in the nucleotide sequence (p = 0.006) was significantly associated with broiler-type chickens. However, 88% of significant comparisons at the amino acid level such as purifying and positive selection were seen in layer-type chickens. A pronounced predictive antigenicity in the HVR2 region was also associated with layer-type chickens (p = 0.001). The study indicates that IBV in California is in a phase of slow evolution with different evolutionary patterns being associated with the production type of chicken.