Leader switching occurs during the rescue of defective RNAs by heterologous strains of the coronavirus infectious bronchitis virus

A defective RNA (D-RNA), CD-61, derived from the Beaudette strain of the av ian coronavirus infectious bronchitis virus (IBV), was rescued (replicated and packaged) using four heterologous strains of IBV as helper virus. Seque nce analysis of the genomic RNA from the four heterologous IBV strains (M41 , H120, HV10 and D207) identified nucleotide differences of up to 17 % with in the leader sequence and up to 4.3% within the whole of the adjacent 5' u ntranslated region (UTR), Analysis of the 5' ends of the rescued D-RNAs sho wed that the Beaudette leader sequence, present on the initial CD-61, had b een replaced with the corresponding leader sequence from the helper IBV str ain but the adjacent 5' UTR sequence of the rescued D-RNAs corresponded to the original CD-61 Beaudette sequence. These results demonstrated that the phenomenon of leader switching previously identified for the coronaviruses murine hepatitis virus and bovine coronavirus (BCoV) also occurred during t he replication of IBV D-RNAs, Three predicted stem-loop structures were ide ntified within the 5' UTR of IBV, Stem-loop I showed a high degree of covar iance amongst the IBV strains providing phylogenetic evidence that this str ucture exists and is potentially involved in replication, supporting previo us observations that a BCoV stem-loop homologue was essential for replicati on of BCoV defective interfering RNAs.