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Viral vectors have become crucial to multiple fields as vehicles for gene therapy, vaccines, and reporter genes, among other uses. Two of the most prominent vectors were generated from adenoviruses and adeno-associated viruses (AAVs). Presently, adenoviral vectors have been clinically studied as vaccines for Zika, Ebola, and SARS-CoV-2 viruses. AAVs are now used in FDA approved gene therapy treatments. While vectors have already had an immense impact on the scientific and medical world, there remain many possible new applications as well as areas of improvement for these tools. In chapter two a new virome (SIV infected rhesus macaque) is explored allowing for the discovery of five novel AAV capsids. Structure guided analysis of the RhAAV4282 capsid to the closely related AAV7 capsid enabled the identification of a novel AAV capsid neutralization epitope named the Hypervariable Region IV …