The Sindbis virus RNA genome is divided into two modules-one coding fo
r the nonstructural protein genes and the other coding for the structu
ral protein genes. In our studies of recombination, the two parental R
NAs were defective in different modules. Analysis of the recombinant R
NAs demonstrated that the parental RNAs each contributed its intact mo
dule and that the crossovers occurred within the defective modules. Th
e recombinational events giving rise to infectious virion RNAs could c
reate deletions, rearrangements or insertions as long as they occurred
outside of the functional module. These crossovers produced RNA genom
es that contained two functional subgenomic RNA promoters.