Molecular studies of the infectious bronchitis virus genome

Vita.Although SI genes of several Mass and European isolates have been sequenced, this is the first report of the entire SI sequence from recent strains of U.S. originated IBV and of RNA recombination occurring in a naturally infected coronavirus host. Comparisons of the IBV S1 genes further revealed that recombination is common among strains of IBV. Potential "hot spots" have been suggested within 50-150 bases downstream of the S1 gene start codon. The involvement of consensus-like sequences has been identified near and/or at putative sites of "crossover", and sites of the insertions as well as deletions. Such natural recombination is probably common, providing a convenient mechanism for the generation of genetic variants that result in the selection of better adapted or more virulent strains of IBV. The routine use and therefore, exposure of animals to live vaccines may contribute to the evolution of virulent strains of IBV. According to sequence analyses of the S1 genes of 30 strains, IBV could be clustered into 5 groups. However, serotypes do not correlate with this sequence homology classification. Based on the computer analyses, several potential antigenic sites have been suggested. The sequence variations of distinct IBV strains were most often found in these antigenic sites, especially those classified as hypervariable sites (HV1 and HV2) within VI. C4, possessing a high antigenicity index, has been found to be conserved in amino acid sequences and secondary structures among IBV strains. A 16-mer peptide corresponding to the C4 was synthesized and tested against anti-IBV polyclonal and monoclonal antibodies. This peptide reacted with polyclonal anti-IBV antibodies specific for all strains tested and one group specific monoclonal antibody. This conserved region may represent a functionally and/or structurally critical determinant. A conserved region in the 3' end of IBV genome was used as an IBV group specific probe. The infections of various IBV strains were detected by m any hybridization methods including in situ cytohybridization. Satisfactory results were obtained by different labeling methods. A 40-mer oligonucleotide was selected as a Mass41 exclusive probe and used to distinguish IBV infections by non-Mass41 strains