A murine coronavirus MHV-S isolate from persistently infected cells has a leader and two consensus sequences between the M and N genes.

A plaque-cloned mouse hepatitis virus mutant, MHV-S No. 8, was isolated from Ki-BALB cells persistently infected with MHV-S. The mRNAs 1 to 6 were larger in the mutant, whereas there was no difference between the two viruses in the size of the smallest mRNA, mRNA 7. Sequence analyses of the genomic RNA, mRNA 6, and mRNA 7 of the two viruses revealed that an additional 111 nt were inserted just upstream of the intergenic consensus sequence preceding the N gene in MHV-S No. 8. The inserted region consisted of two different parts; the 3'-most 30 nt corresponded to nucleotides 28 to 57 of the leader sequence and the 5'-most 81 nt corresponded to nucleotides 58 to 138 of mRNA 7. This structure of No. 8 was most likely generated by RNA-RNA recombination between genomic RNA and subgenomic RNA species. The nucleotide insertion in the intergenic sequence between genes M and N resulted in two consensus sequences separated by 111 nt. Primer extension analysis revealed that the amount of a slightly larger, subgenomic mRNA resulting from initiation of synthesis at the upstream consensus sequence was only 5% of the usual sized mRNA 7 initiated from the downstream consensus sequence.