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Retroviral recombination occurs during replication and produces a DNA copy that contains genetic information from two parental RNAs. Recombination increases variation within the viral population by reassortment of mutations. In the presence of selective pressures, such as drug treatments, host immunosurveillance, or anti-viral vaccines, retroviruses are able to evolve rapidly leading to higher viral titers and increased pathogenicity. Two models have been proposed to explain the mechanism of recombination. The first model, minus-strand recombination, proposed that each recombination event generated a recombinant with one template switch. In contrast, the second model, plus-strand recombination, proposed that each recombination event generated a recombinant with two template switches. Previously, the mechanism generating recombinants with multiple template switches could not be determined. We have established that the major mechanism involved is minus-strand recombination. Although all examined retroviruses have been shown to undergo high rates of recombination in multiple rounds of infection, we measured the rates of recombination in a single cycle of replication and established a non-linear relationship between recombination rates and marker distances. In contrast to previous assertions, the rate of recombination was found to not always be proportional to marker distance. In addition, we observed that recombination had a plateau effect. Furthermore, we measured the size of the recombining population, and discovered that only a minority is capable of undergoing recombination. To explore the relationship between distance between the two copackaged RNAs and recombination, we determined the effect of RNA dimerization on recombination. Previous reports showed that the dimer linkage structure (DLS) allowed the copackaged viral RNAs to interact non-covalently, and that it may be a recombination hot spot. We defined the effect of the DLS on the rate and location of recombination events. The rates of recombination were only mildly increased by the presence of the DLS, which indicated that the DLS did not have a global effect on the entire viral genome. Therefore, decreasing the distance between the two copackaged viral RNAs did not have a general effect on recombination events. These observations have led to significant advances in our understanding of recombination during reverse transcription. With this knowledge, a more rational approach to treatment of pathogenic retroviruses and improvements in the usage of retroviruses for gene delivery should be possible.