UCSF

This thesis describes a number of novel techniques designed to assist in the study of various aspects of viral evolution. Chapter one describes a systematic approach to determining the patterns of selective pressure operating on a viral genome during replication and transmission through human hosts. Key regions of the viral capsid in or around antigenic sites are revealed to have been allowed to change rapidly relative to the rest of the human rhinovirus genome. In chapter two, I demonstrate the ability of a novel microarray based resequencing platform to read out the mutational landscape of a viral quasispecies with an unprecedented degree of sensitivity. The utility of this platform is demonstrated by elucidating capsid-wide changes occurring at frequencies below 1% in a poliovirus quasispecies population under selective pressure from the nucleotide analog ribavirin. Chapter three describes a novel sample preparation technique used to dramatically increase the effective read length of short read ultra high throughput sequencing platforms. Taken together, these tools represent a significant addition to the repertoire of molecular biology and computational techniques available to researchers for the study of viral evolution and disease.