Abstract:
Infectious bronchitis virus (IBV) is a Gammacoronavirus that causes a highly contagious respiratory disease
in chickens. A QX-like strain was analysed by high-throughput Illumina sequencing and genetic
variation across the entire viral genome was explored at the sub-consensus level by single nucleotide
polymorphism (SNP) analysis. Thirteen open reading frames (ORFs) in the order 50-UTR-1a-1ab-S-3a-
3b-E-M-4b-4c-5a-5b-N-6b-30UTR were predicted. The relative frequencies of missense: silent SNPs were
calculated to obtain a comparative measure of variability in specific genes. The most variable ORFs in
descending order were E, 3b, 50UTR, N, 1a, S, 1ab, M, 4c, 5a, 6b. The E and 3b protein products play
key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 50UTR did
not alter the predicted secondary structure. The frequency of SNPs in the Spike (S) protein ORF of
0.67% was below the genomic average of 0.76%. Only three SNPS were identified in the S1 subunit, none
of which were located in hypervariable region (HVR) 1 or HVR2. The S2 subunit was considerably more
variable containing 87% of the polymorphisms detected across the entire S protein. The S2 subunit also
contained a previously unreported multi-A insertion site and a stretch of four consecutive mutated amino
acids, which mapped to the stalk region of the spike protein. Template-based protein structure modelling
produced the first theoretical model of the IBV spike monomer. Given the lack of diversity observed at the
sub-consensus level, the tenet that the HVRs in the S1 subunit are very tolerant of amino acid changes
produced by genetic drift is questioned.
