| A 1.78 kb sequence, including the E gene, the M gene, the 5a and 5b genes, and the intergenic region between the M gene and the 5a gene, of six U.S. strains of infectious bronchitis virus (IBV) were sequenced and compared to the published data for two additional strains. Pairwise analysis of nucleotide sequences of the entire 1.78 kb region indicated identity ranging from 90% to 99% for the entire region, compared to 87–99% for the E gene, 88–99% for the M gene, 83–98% for the intergenic region between the M and 5a genes, 87–100% for the 5a gene, and 94–99% for the 5b open reading frame. One copy of the intergenic consensus sequence CTTAACAA was found upstream of the start codons of all eight strains for the M gene, the 5a gene, and the N gene. Nucleotide sequencing of a recent field isolate from Alabama (Ala1) revealed distinct shifts in homology in the M gene, indicating two apparent recombination events. The 3′ 475 bases of the M gene of Ala1 were virtually identical to Holland 52, a vaccine strain. A recent field isolate from California (Cal2) was closely related to the Gray strain in the M gene, while another California field isolate (Cal3) contained three apparent recombination events within the M gene.; Two experiments were performed in which cells were infected with Beaudette strain virus, then transfected with one of two non-replicating RNA fragments from another strain: (1) Gray fragment extending from the middle of the E gene through the 3′ end of the genome and (2) Ark DPI fragment extending from the S gene through the 3′ end of the genome. Potential recombinant virus from several passages was analyzed from both supernatant and cells. Several recombinants were detected from each experiment. Two clones showed apparent recombination near the consensus sequence CTTAACAA, which is located at the 3′ end of the leader sequence and upstream of most of the genes of IBV. Two other clones demonstrated putative recombination near a similar sequence, CTTTTG. |
