UCSF

Viruses impact every form of life on earth, from causing disease in individuals to influencing to applying evolutionary stresses and influencing environmental communities. There are an incredible number of viruses in the biosphere that virological research seeks to characterize in order to understand their health and environmental impacts. Next-generation sequencing (NGS) is a powerful tool for characterizing viral genomes, yet it is imperative to pre-enrich complex samples for viruses of interest in order to optimize coverage. This dissertation describes the development of several new technologies for targeted quantification and enrichment of viruses using droplet microfluidics. These technologies represent a general platform for viral enrichment that can be applied directly or used upstream of other technologies such as NGS. We describe methods for increasingly complex, targeted enrichment, starting with the enrichment of specific DNA molecules and specific viruses. We then describe a viral enrichment strategy capable of identifying microbial viral hosts. Last, we detail a method for enrichment of mammalian cells infected with viruses of interest and describe how this technology can be used to quantify and characterize the latent HIV reservoir. We anticipate that these techniques will enable exploration of numerous virological avenues including viral diversity, viral evolution, host-virus relationships, and viral co-infections.