Sequence heterogeneity in satellite tobacco necrosis virus RNA.

Satellite tobacco necrosis virus (STNV) RNAs isolated from early, middle, and late passage virus stocks were found to contain substantial and reproducible sequence variations which increased with passage of the virus. Several instances of clustered or correlated sequence changes were found. This sequence heterogeneity was detected by the use of the DNA oligomer-directed RNase H cleavage method. Terminally labeled RNA molecules were mapped with this method using synthetic DNA oligomers as sequence probes. RNA sequence analysis of RNase H fragments end labeled following DNA oligomer-directed RNase H cleavage also provided a direct way to examine sequence heterogeneity within the viral population.