RETROVIRAL RECOMBINATION RATES DO NOT INCREASE LINEARLY WITH MARKER DISTANCE AND ARE LIMITED BY THE SIZE OF THE RECOMBINING SUBPOPULATION

Recombination occurs at high frequencies in all examined retroviruses. The previously determined homologous recombination rate in one retrov iral replication cycle is 4% for markers 1.0 kb apart in spleen necros is virus (SNV), This has often been used to suggest that approximately 30 to 40% of the replication-competent viruses with 7- to 10-kb genom es undergo recombination, These estimates were based on the untested a ssumption that a linear relationship exists between recombination rate s and marker distances. To delineate this relationship, we constructed three sets of murine leukemia virus (MLV)-based vectors containing th e neomycin phosphotransferase gene (neo) and the hygromycin phosphotra nsferase B gene (hygro), Each set contained one vector with a function al neo and an inactivated hygro and one vector with a functional hygro and an inactivated neo. The two inactivating mutations in the three s ets of vectors were separated by 1.0, 1.9, and 7.1 kb. Recombination r ates after one round of replication were 4.7, 7.4, and 8.2% with marke rs 1.0, 1.9, and 7.1 kb apart, respectively, Thus, the rate of homolog ous recombination with 1.0 kb of marker distance is similar in MLV and SNV. The recombination rate increases when the marker distance increa ses from 1.0 to 1.9 kb; however, the recombination rates with marker d istances of 1.9 and 7.1 kb are not significantly different, These data refute the previous assumption that recombination is proportional to marker distance and define the maximum recombining population in retro viruses.