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Currently, the Acquired Immune Deficiency Syndrome (AIDS) epidemic is world-wide and threatens the entire human population. The causative agent of AIDS is Human Immunodeficiency Virus (HIV), a retrovirus. The HIV viral population exhibits tremendous variation, making the development of vaccines difficult and anti-viral drug therapy ineffective due to the emergence of drug-resistant HIV strains. The main goal of this dissertation is to better understand how retroviral variation is generated to ultimately aid the development of effective anti-retroviral therapies and vaccines. The experiments described throughout this dissertation incorporate the use of simple retrovirus model systems to study template switching events during reverse transcription, a process that is critical to the retroviral life cycle. During reverse transcription, the virally-encoded enzyme reverse transcriptase transcribes a DNA copy of the viral RNA genome, the DNA product integrates into the genome of the infected cell where it is expressed using host machinery. Reverse transcription requires two particular template switching events. One of these template switches, plus-strand DNA transfer, is the focus of the first aim of this dissertation, where the efficiency of plus-strand initiation and transfer were explored. Through these experiments, it was determined that retroviruses have evolved a highly efficient mechanism for initiating and transferring plus-strand DNA. Because of the necessity for an enzyme that exhibits low processivity in order to carry out plus-strand DNA transfer, other template switches also occur during reverse transcription, giving rise to frequent mutations. Homologous recombination is one means by which such mutations are distributed; thus, recombination plays a critical role in enabling drug-resistant retroviral strains to arise. Aims 2 and 3 of this dissertation examine the mechanism of homologous recombination. In aim 2, the relative rates of intra-molecular and inter-molecular template switching during one round of retroviral replication were compared. Intra-molecular template switching was found to occur much more frequently than inter-molecular switching between the two viral RNAs copackaged within each virion. In aim 3, the maximum rate of homologous recombination was determined to characterize the size of the retroviral population that can undergo recombination. The size of this population was estimated to be approximately 8%.