Evolutionary implications of genetic variations in the S1 gene of infectious bronchitis virus

The large number of phenotypically distinct strains of infectious bronchitis virus (IBV) provide a broad genetic background for examining naturally occurring coronavirus variation. Comparisons of the published nucleotide sequence of S1 genes of strains isolated in Europe, Japan and the USA and four additional American strains described in this report identified 4 genetically distinct groups. The Dutch group was the most divergent sharing only about 60% identity with the American, Mass and European groups which were about 80% homologous with each other. Whereas the strains within the Mass, European and Dutch strains were at least 95% homologous, the strains within the American group were most variable, sharing about 80% identity. The hypervariable region (HVR) which tended to correlate with serotype extended from amino acid residue 53 to 148. In addition to the previously described putative recombination events in the S1 gene of PP14 and SE17, we have now described similar shifts in homology in the corresponding gene of the Gray, Holte, 6/82 (European strain), and Iowa strains. Although minor cross-over sites were identified in the more conserved 3' end at approximately nt 1000 and 1400, a frequently used hot-spot for recombination extended from nt 25 to a region immediately upstream of, but not including, the hypervariable region (HVR). In addition to point mutations, deletions, and insertions, recombination often involving Mass-like and Ark-like sequences, is a commonly used mechanism responsible for the evolution of IBV.