The presence of common host sequences in different populations of substituted SV40 DNA

[ 3H]cRNA, synthesized off substituted SV40 DNA by E. coli DNA-RNA polymerase, was cleaved by controlled alkali digestion to small fragments. Fragments containing viral sequences were removed by exhaustive hybridization to plaque-purified SV40 DNA. The remaining nonhybridized population of fragments, which was enriched 12 to 33-fold for host sequences, was used as a hybridization probe to monitor for the occurrence of common host sequences in the substituted variants present in nonplaquepurified SV40 stocks (strains 777, 776, and Rh911) and in nine defective stocks generated by independent high-multiplicity serial passages of plaque-purified virus. A common set of host sequences, derived predominantly from the nonreiterated fraction of the cellular genome, was detected in three populations generated by independent serial passages of plaque-purified virus and in the parental nonplaque-purified stock of strain 777. At least a part of this common set of host sequences was also represented in three other independently derived, serially passaged populations of plaque-purified virus and in nonplaque-purified stocks of strains 776 and Rh911. In contrast, one of the defective stocks generated by serial-passage of plaque-purified virus (strain 777) contained a unique set of host sequences that was not detected in any other SV40 stock. The results suggest that the SV40-host recombination events which generate substituted SV40 variants occur at preferred sites on the cellular genome.