MOLECULAR EPIDEMIOLOGY & EVOLUTION OF HUMAN SEASONAL CORONAVIRUSES

Abstract

Respiratory viruses are important sources of disease that are perpetually identified in humans. Often, the identity of respiratory viruses is not investigated due to insufficient resources and priority towards severe cases. While seasonal human coronaviruses (hCoVs) are known to be endemic amongst humans since the 1960s, the lack of surveillance has led to a limited understanding about their genetic diversity and evolution. It is critical that we determine the factors and mechanisms leading to the spill over events from their animal hosts. This thesis sought to fill knowledge gaps on evolution of hCoVs by first understanding their epidemiology and genetic diversity amongst the human population before attempting to understand their evolution in the ancestral bat host. We found that hCoVs have different patterns of evolution throughout their endemicity. Also, we investigated the bat origin of hCoV 229E and found that it was able to replicate in bat cells despite deletions that resulted in loss of spike protein. Overall, coronaviruses are likely to have evolved differently throughout their coexistence in the primordial bat hosts before crossing the species barrier into humans.