Cloning and sequencing of 5' terminal sequences from avian infectious bronchitis virus genomic RNA

The subgenomic RNAs of the fowl coronavirus infectious bronchitis virus (IBV) form a 3' co-terminal or 'nested' set. The presence of non-contiguous (leader) sequences fused to the 5' termini of murine hepatitis virus mRNAs has been demonstrated using RNase T1 oligonucleotide mapping and sequencing. The presence of a leader sequence on IBV mRNA A has been demonstrated previously. In this paper the presence of a leader identical to that present on the 5' terminus of IBV mRNA A is demonstrated to be present on the 5' terminus of IBV genomic RNA. This has been achieved by sequencing of primer extension products and cDNA clones containing the genomic leader. Analysis of these clones has revealed the presence of a sequence at the leader/genome-length RNA junction which is closely related to regions of homology identified previously within the genomic RNA sequence at the leader/body junctions of subgenomic RNAs. The implications of this finding for mechanisms of coronavirus RNA synthesis are discussed.