The evolution and adaptation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, remain incompletely understood. This thesis aims to elucidate the temporal and mechanistic aspects of these viral changes through comprehensive genomic analyses. Specifically, we investigate the evolution of SARS-CoV-2 within immunocompromised individuals with prolonged infections, compare viral adaptations between vaccinated and unvaccinated hosts, and explore interspecies transmission between humans and animals. We found that SARS-CoV-2 evolution rates are increased during prolonged immunocompromised infection, with dominant drug resistant substitutions arising within weeks of treatment. In a population-based analysis, we found evidence of evolution selecting for immune evasive substitutions and preferential transmission of more recent lineages among vaccinated individuals. In a study to examine an animal spillover to we identified the first published Delta variant infection in domestic cats. In a study to examine spillover in wild animals, we identified multiple spillovers and chains of transmission among white-tailed deer in 2021. Later we performed a 1,017 day longitudinal study in Pennsylvania white-tailed deer where we identified seasonal trends of SARS-CoV-2 infection rates, preferential infection for deer in primarily crops/pasture land compared to forest, and persistence of divergent ancestral viral variants in the deer viral reservoir. Together these findings suggest the rise of SARS-CoV-2 variants with increased fitness in humans might most rapidly appear in immunocompromised prolonged infections, but there remains a danger of spill back from highly divergent lineages from animal reservoirs.