DISSECTING THE MECHANISMS OF RETROVIRAL RECOMBINATION

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Mutation and recombination are two mechanisms used by retroviruses to increase variation in the viral population. High rate of mutation generates a large pool of variants, and frequent recombination shuffles these mutations to further increase genetic diversity. Variation in the viral population allows a subpopulation of variants to survive and prosper when the environment changes. This is dramatically demonstrated in the study of human deficiency virus (HIV) infection. AZT resistant strains of HIV were generated after the individuals received AZT treatment. Virus can generate variants to evade the host immune system as exemplified by the recently discovered HIV escape mutant that partially escape the immune surveillance by altering the epitopes recognized by cytotoxic T cells. Retroviral recombination occurs during reverse transcription, a step in which a viral DNA copy is generated from virion RNA. Therefore, it is an intrinsic part of viral replication. I propose to study three aspects of retroviral recombination. Recombination between homologous viruses in one population, those between viruses with large lesions and wildtype viruses, and those between genetically distinct viruses will be studied. A Spleen necrosis virus based vector and helper cell line will be used to study recombination during one round of retroviral replication. In aim 1, vectors with extreme homology will be used to study recombination. This is to mimic recombination within a viral quasi- species. These experiments will tell us the efficiency and extent of genetic exchange between different variants in a viral population. In aim 2, experiments are directed to ask whether viruses with large lesions can be easily rescued by recombination. Recombination between two viruses with lesions as well as between a wildtype virus and virus with lesions will be studied. In aim 3, retroviral vectors derived from two genetically distinct viruses will be used to study the possible recombination between two different viruses.