FIG. 4.

Recombination of part of the MHV leader RNA into the 3′ terminus of the M gene. (A) Nucleotide sequence of the M gene-N gene region of revertant 1I aligned with the corresponding regions of the MΔ2 sequence and the leader-N gene region of sgRNA7. The broken line indicates the locus of the apparent crossover between MΔ2 and sgRNA7. Revertants 1H and 3E, which contain mutations in both the MΔ2 stop codon and codon 228 (underlined), and revertants 1A and 1M, which contain just the codon 228 mutation, also appear to result from more-limited crossovers between MΔ2 and sgRNA7. TRS7 denotes the TRS governing synthesis of sgRNA7 (N mRNA). (B) Potential mechanism of formation of the substitution in revertant 1I via a nonhomologous recombination event between sgRNA7 and genomic RNA. (C) Proposed mechanism of formation of the substitution in revertant 1I through an aberrant shift from synthesis of negative-strand sgRNA7 to synthesis of the full-length antigenome, as detailed in Discussion. In panels B and C, note that the leader region is not drawn to scale. UTR, untranslated region.